example of a 1 page biography

What more do you need to know?

Ian doesn't take his bio too seriously but uses every character to highlight everything about him.

He includes his skills as a marketer and podcast host, who he is outside work as a dad, and what he can help you do. His smiles also give the bio a sense of humor and realness.

Don't forget to share this post!

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How to Write a Short Professional Bio (With Examples and Templates)

3 key takeaways

• What a short professional bio is and why you need one
• What to include in a short bio to make it stand out and relevant to your audience
• Examples, templates, and a faster way to write your bio with Teal's Professional Bio Generator

In a world where just about everyone is represented online, your short professional bio often serves as a first introduction.

Often, it's what employers or other professionals will use to form their initial impression. And how you present yourself can help influence whether someone invites you to connect, interview you, or simply move on.

Below, you'll learn what you need to write your bio and how to actually write one. You'll also find templates and some short professional bio examples to use as a guide.

Looking for a quicker way to a polished bio? Sign up for Teal for free and try the Professional Bio Generator.

What is a short professional bio? 

A short professional bio is exactly what it sounds like—a short professional biography that introduces yourself and gives a brief overview of your career and accomplishments. It gives future employees, colleagues, and anyone else you're networking with a more well-rounded picture of who you are.  

While "short" can be subjective, length often depends on the platform and the audience you're sharing your bio with. There's no one-size-fits-all, and you'll tailor the length based on where it's being shared—whether that’s on your personal website, LinkedIn profile, Twitter bio, or your resume.

What’s the difference between a professional bio and short professional bio?

A professional bio and a short professional bio both summarize your career, qualifications, and achievements, but each caters to different contexts and needs. 

A professional bio is a detailed account—that can span several paragraphs—and covers your:

• Career background
• Most noteworthy achievements and impact or results
• Skills you've developed or are developing
• Some personal insights

This version is appropriate for professional websites, long-form pitch documents, or networking platforms (like in your LinkedIn About Me section) where a more thorough introduction is valuable.

On the other hand, a short professional bio is a concise version that filters the most important information from your professional bio into key takeaways. A short bio:

• Communicates your core qualifications
• Briefly touches on your professional persona
• Is ideal for your resume, author bio, or speaking engagements
• Can be used across social media profiles like Twitter and Instagram

What to include in a short bio 

Your short bio should summarize the key takeaways from a longer, more rounded-out professional bio. Think of it as kind of an elevator pitch that highlights what you'd want your target audience (who doesn't know much—if anything—about you) to understand about your career so far.

Here are some things you'll want to address.

• Level of education, if relevant to the audience
• Years of experience in your field, if relevant to the audience
• Your current or former career title
• Major professional accomplishments with impact or goals
• Professional experience, skills, and area(s) of expertise

Now, if you're a student or making a pivot, like transitioning into a new field where you might not have relevant work experience, you'll focus more on your educational achievements (think relevant awards, projects, or volunteer experience) and the skills and knowledge you're developing.

What to include in a short bio if you’re a student

Even if you're still in school, there's plenty of information you can include in your bio, like: 

• Where you're from
• What university, trade school, or boot camp you're attending
• Your area of study or intended major
• Any clubs, teams, volunteering, or other extracurriculars you're a part of 
• Any internships you've completed
• Your career goals 
• Your availability

Generate your professional bio with AI

Want to save time? You can also use the Teal to generate multiple versions of your short professional bio.

How to write a short bio

There's no right or wrong way to write your own bio. Think of this next section as a guide, and remember: short professional bios are unique to each person.

Here are the things you might want to consider if you're ready to write your professional bio:

1. Choose your voice

You have the option to write your short bio from either a first or third-person POV.

In the first person, you'll use  "I, me, and my." In the third person, you'll refer to yourself using your name and preferred pronouns.

As a general rule, using the third person is typically considered more formal, while using the first person is more casual and personal.

 First-person example : "I'm a bestselling author. My work has been published in The New York Times."

Third-person example: "Zane Smith is a bestselling author. His work has been published in The New York Times."

If you want to write and store multiple versions of your short professional bio in different tones or even with different information, use Teal to write and save as many versions as you need for free.

2. Choose your tone

Language can convey different moods. Depending on the context and your personal brand , your bio can sound more buttoned-up or more relaxed and conversational.

These two sentences describe the same person but showcase very different tones and writing styles: 

Example 1: “A recent graduate of the University of Pennsylvania, Sally is currently a consultant at XYZ Consulting based out of their New York office.” 

Example 2: “A recent UPenn grad, Sally swore off econ after years of hard classes only to end up as a consultant at a major firm — but don't worry, she loves it.” 

3. Start with your name and a current or recent role

This isn't a hard and fast rule, but to get your bio started, it's usually easiest to start with your name and current professional title or role. 

Example: “Zane Smith is currently the Demand Generation Manager at ABC Tech Company.”

If you're pivoting careers , you can list your most recent role and use your first sentence to say what you're looking to do next.

Example 1: “Previously the Demand Generation Manager at ABC Tech Company, Zane Smith is actively pursuing new opportunities in marketing management.” 

Example 2 : “Previously the Demand Generation Manager at ABC Tech Company, Zane Smith is now an aspiring 2nd grade teacher.” 

4. Share your accomplishments and achievements

Once you've introduced yourself and your current title, you can flow into your professional background, former job titles, and what you've done or aspire to do. Together, the first two sentences of your bio could read something like this: 

Example:  “Zane Smith is currently the Demand Generation Manager at ABC Tech Company. Previously, he was a Marketing Specialist at FGH Tech Company, where he grew paid traffic to their website by 500% year over year.” 

Pro Tip: Not sure where to start? Try the generative AI in the Teal Resume Builder . With Teal's AI, you can write individual achievements using a job description, keywords, or a custom prompt to articulate your accomplishments effectively and confidently.

5. Share your philosophy or “why” 

Self-promotion can feel incredibly uncomfortable, but it's important to make sure you don't undermine your value. Your “why,” the reason you do what you do every day, can be powerful and meaningful. Adding what gives you the spark to start each workday can set your own professional bio apart from others. 

Example: “Claire was inspired to pursue a career in elder law after volunteering in a nursing home throughout high school and college.” 

6. Add your personal touch

Even though your bio will be used in a professional capacity, it's okay to list a few personal details. We're more than just our jobs, and adding a few personal facts can help illustrate who you are outside of the office. 

Example: “When he's not working, Martin can be found tending to his spice garden and going on nature walks with his golden retriever.” 

Short professional bio examples

Examples of professional bios are invaluable because they provide a clear framework and inspiration for writing your own. They can also help you see how to condense years of experience into a few compelling sentences so you communicate the right details clearly, briefly, and full of impact. 

Short bio example for a personal website

"AUDREE KATE LOPEZ IS A FASHION STYLIST, EDITOR, INDUSTRY EXPERT AND INFLUENCER BASED IN NEW YORK. Audree began her professional career in the fashion departments at Glamour, O, the Oprah Magazine, Editorialist and Redbook magazines. She launched Audree Kate Studios in 2017 and worked on freelance projects at Marc Jacobs, Alice + Olivia, J.Crew and Club Monaco, joined the styling team at Alice + Olivia and became a contributing fashion editor for StyleCaster.com. Over the past few years Audree has styled for various publications, celebrities and retail brands. In 2016, Audree founded a digital course and community for fashion students called Fashion Fundamentals and has hosted workshops and classes around the country, and wrote an ebook titled Fashion Fundamentals."

Why it works: Audrey's bio immediately establishes her as a multifaceted professional within the fashion industry. It outlines her career trajectory and showcases broad experience and evolution, demonstrating growth and adaptability. The mention of initiatives and workshops adds a layer of approachability and commitment to education in her field, improving her appeal as an influencer and mentor.

Professional short bio example on LinkedIn

"Latina creator. Speaker. Tech Mentor. Christen is the Founder of the newly launched app Clara, a community that empowers creators through transparency, brand reviews, and discoverability. An industry vet, Christen has almost a decade of experience working with top content creators at social networking companies such as Instagram, TikTok, and Pinterest. She is a motivational speaker and mentor in the tech space who is passionate about helping people break into the industry through career advice and actionable content."

Why it works: This professional bio online is punchy and concise. It opens by noting Christen's titles and includes years of experience, giving her credibility while underscoring her heritage (which can resonate strongly with a diverse audience on LinkedIn). By focusing on her app, she not only showcases initiative but also aligns herself with trends in tech innovation. Rounding out her short bio are details of working with top content creators, establishing her as a seasoned industry pro.

Short bio example on social media

"Founder of Makelane, a private community for female DTC founders. 70K followers on TikTok where I analyze consumer brands"

Why it works: With only 160 characters to work with, Dulma’s Twitter bio is an example of brevity. It clearly outlines her two main pursuits: managing an online community and producing content for TikTok, making it easy for readers to gauge her interests and activities at a glance.

Company website short bio examples

"Meet our wonderful team We're a tight-knit group of curious creatures, always learning, and constantly seeking out new perspectives and ideas. Get to know our team—they're what makes Teachable, well, Teachable."

Why it works: "Meet our wonderful team" feels like a personal invitation to get to know the group, which can make visitors more inclined to engage. Describing them as "tight-knit" and "curious creatures" adds character and illustrates a vibrant and collaborative work environment. Highlighting that the team is "always learning" and "constantly seeking out new perspectives" positions Teachable as a dynamic and innovative company—committed to growth and evolution.

Tips for writing a short bio

Even though there aren't official rules for writing a bio, there are still some things you should strive for as well as steer clear of if you want to make the best possible impression. 

1. Tailor your professional bio to your audience

Whether it's potential employers, LinkedIn connections, Twitter followers, or visitors to your website, each platform and audience has its own expectations. Keep your information relevant and concise, focusing on what matters most to that intended audience.

2. Be authentic

Your bio is not the place to fudge the truth about who you are. Be honest about what you've done and where you're heading. Not telling the truth could bar you from achieving your goals and land you in hot water. 

3. Prioritize relevant information

We really hate to be the one to tell you this, but unfortunately, most people do not have the time or patience to read a five-paragraph essay about your life story. Sorry to break it to you! 

4. Be relatable

No matter how lofty your accomplishments are, staying grounded may help you establish stronger connections with others. This is where adding personal details and highlighting your personal brand can serve you well. Whether that's with a hobby, interest , or other role outside of work, being relatable can let others understand and get to know you better and determine if you would be a good fit for a company.  

5. Be professional

It's appropriate and expected for you to talk about your professional skills and accomplishments in your short bio. That said, there's a fine line between talking about your achievements and sounding arrogant. These two examples talk about the same accomplishment but come across differently: 

Example 1: “An accomplished pianist, Ryan was selected out of nearly 7,000 applicants to perform at the annual New York State School Music Association festival last spring.” 

Example 2: “An accomplished pianist, Ryan was the obvious choice to perform at the annual New York State School Music Association festival last spring (because he's the best).” 

Also, if you're revising your bio after a lay-off or termination, avoid sounding spiteful. As tempting as it might be, don't make negative statements or accusations in your short bio. Positivity and a good attitude will get you much further.

Short professional bio templates

If you prefer to plug and play or need a short bio in a pinch, don't worry; here are three short bio templates to get you started:

Short professional bio template for working professionals

[First name last name] is [currently/formerly] a [insert most recent job title] at [most recent company name] . A proud graduate of [school or university] , they were inspired to pursue a career in [field] after [explain what led to your decision to work in your industry] . Prior to working at [most recent job title], they were the [previous title] at [previous company], where they were responsible for [insert professional accomplishments here] . In their free time, they can be found [insert your favorite hobbies] . 

Short professional bio template for students

[First name last name] is a current [year] at [institution] majoring in [area(s) of study] . On campus, [First name] is actively involved in [activity name] , for which they [insert details about what you do for the activity you're involved in] . They most recently [interned/worked] at [organization name] , where they had the opportunity to [insert details about what you did on the job] . They intend to work in the [insert field name or industry] after graduation to follow their passion of [insert what you are passionate about] . In their spare time, they can be found [insert your favorite hobbies] . 

Short professional bio template for a gap in employment

[First name last name] is a [position/job title] with [number] years of experience in [specific skills or industry] . Following [briefly mention the reason for the employment gap] , [he/she/they] took some time off to focus on [briefly mention what they did during the gap, e.g., personal development, family obligations, health reasons] . During this time, [he/she/they] also [briefly mention any relevant skills or achievements acquired during the gap] . [Name] is now eager to return to the workforce and is excited to bring [specific skills/accomplishments] to [his/her/their] next role. With a proven track record of [list specific achievements or skills] , [Name] is confident in [his/her/their] ability to contribute to [specific industry/profession] and make an impact in [his/her/their] next position.

If you decide to use any of these templates, tweak it ever-so-slightly. Once you've finished entering your details, try adding a bit of personal flair.

Swap adjectives, remove anything that doesn't quite fit with your vibe or experiences, or append some more personal details as you see fit. Feel free to work off of any one of the bios from these resume examples to get a feel for how different styles can be used across roles.

Create your short professional bio with Teal

In a digital world where your online presence often speaks before you do, writing a good, short professional bio is more important than ever. It's the first glimpse potential employers, clients, or colleagues get of your professional life and persona, and the right presentation can open doors to new opportunities and connections. 

Teal's Professional Bio Generator saves time by speeding up the writing process with AI. Whether you're trying to impress potential employers, clients, or peers, Teal's generator adapts to your needs and experience, allowing you to create a unique short bio for any audience with one click.

Ready to write a professional bio with maximum impact in less time?

Frequently Asked Questions

What is an example of a short professional bio.

An example of a short professional bio is: "Katie is a seasoned marketing professional with over 10 years of experience in digital advertising strategies. She has helped numerous brands achieve their online marketing goals, leading to increased visibility and 3x revenue YoY."

How do you write an impressive short bio?

To write an impressive short bio, focus on your most significant achievements, relevant skills, and experiences that set you apart. Keep it concise and tailored to your audience to engage and leave a memorable impression. You can also use the Teal  AI Resume Builder  Generative AI to craft a bio that highlights your unique professional journey and skills in an engaging way.

What is a short biography about yourself?

A short biography about yourself should concisely summarize your professional background, major accomplishments, and skills. For example, "I'm an innovative software developer with 5 years of experience in creating scalable applications, known for my ability to troubleshoot complex issues and my commitment to delivering high-quality software solutions."

Emily Polner

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How to Write a Biography (Examples & Templates)

A biography is a written account of a person’s life that details their life in chronological order. Another person usually writes this detailed account, and it contains reports of their childhood, career, major life events, relationships, and social impact. It also details their relationships with their family, children, and life accomplishments.

The best way to find out more about a popular figure is through reading their biographies, so you need to make sure you get the correct information. Before writing a biography, you need to do a lot of research and interviews to represent a person’s life accurately.

Types of Biography

A biography is the story of someone’s life as written by another writer. Most biographies of popular figures are written years, or even decades, after their deaths. Authors write biographies of popular figures due to either a lack of information on the subject or personal interest.

A biography aims to share a person’s story or highlight a part of their life.

There are different types of biographies, depending on the story. Some biographies are written true to the story, while some are written as fictional works. Biographies can give you true understanding of a person on an internal as well as external level along with a lot of life lessons.

Autobiography

An autobiography is different from a biography because it is written by the subject of the story, themselves. The author writes in the first-person narrative, and it flows step-by-step like a story of their life. Autobiographies contain personal accounts of the subject’s life, along with their perspectives and opinions on events in their life.

How To Write a Biography

Pick a subject.

Picking a subject is the first step in writing a biography. You can pick an already famous person or a relatively unknown person with a great life story. If you already have a few in mind, you can start by asking yourself some questions such as;

• What has the subject accomplished that makes them a good subject?
• Have they had an impact on society?
• Is the subject a celebrity or a well-known personality?
• Will the biography appeal to a wide audience?

Get Permission

When you pick a subject, the next thing to do is to get permission from them or their family or rights owners. Although, with some historical figures, there may not be any need for permission. Getting permission from your subject makes it easier for you to get stories to put into your book. You can get the chance to obtain additional personal stories and anecdotes that will make your book more interesting by doing so as well.

Do The Research

Research is the most important part of a biography’s process as the entire content of the book is dependent on it. Irrespective of what you know about the subject, you need to carry out as much research as possible to get the story’s facts precisely.

Biography research comes from various sources, depending on the book’s subject. Firsthand reports from family, friends, or personal accounts from the subjects are primary sources. They are usually the most accurate and reliable, and they are crucial for a biography. Secondary sources come from other sources like magazines or documentaries.

Pick a Format

Biographies come in various formats, with each of them having their pros and cons. A typical biography will start at the beginning, usually with the birth and childhood of the subject. Yet, if the biography’s theme involves a different event in their life, the author may want to explore the flashback option or one with concurrent events from different times.

Usually, biographies have a theme or a general life lesson at the center. The author’s role is to tell the subject’s story leading up to the major event.

Which-ever format you choose should place the theme at the center, with the other events detailing the journey.

Create a Timeline Of The Story

Since a biography takes place in chronological order, there needs to be a timeline of the events in the right order. The timeline should contain the key events in the subject’s life, in the order the author plans on revealing them. A great way to declutter the story and keep it interesting is to use flashbacks . This way, the author can introduce past events and explain later events excluding the element of monotony.

Add In Your Thoughts

The good thing about biographies is that you don’t have to stick to the hard facts only. As the author, you can share your opinions and emotions in writing. The author has the freedom to do this by commenting on a significant action by the subject in a manner that describes why they feel the subject may have done what they did.

The author can also include commentary on events depicted in the biography – how it was influenced society or its impact on the lives around them. Recounting these events through a different perspective can make the biography more relatable and interesting to read.

FAQ’s

Why is a biography template important.

A biography template has an outline that makes the writing easier for the author. Biography templates usually contain a sample timeline, format, and questions that provide more information about the subject. With a great biography template, you can cut your writing time in half and spend less time coming up with an outline.

How are biographies better in comparison to autobiographies

Since a different person writes biographies, they tend to be more objective and somewhat accurate than autobiographies. An autobiography tells things from the author’s perspective, so their views and perspective cloud it. Thus, a biography will likely tell a more factual story.

These are the important steps you need to take to help you write a great biography. Now, to make things easier for you, we have a free customizable autobiography and biography template that you can use to start your first book. Get the template and start writing today

What are some of the most important elements to keep in consideration while writing a biography?

Any author looking to write a biography must consider the factors below. They aren’t the only important factors, but a biography isn’t complete without them. • Date and place of their birth • Academic background • Professional expertise • Death, if deceased • Facts and anecdotes about the person • Main accomplishments • Detailed accounts of their child and adult life

Biographies tell the untold stories of some incredibly relevant people in the world. But biographies are not always strictly accurate. So, every biographer needs to follow the necessary steps to provide a biography with all the requirements.

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How to write a professional bio (with examples and templates)

• Rebecca Strehlow
• 11 min read

Get started by: Creating a website →  | Getting a domain →

Which three words would you use to describe yourself? Most of us have been asked this question, and many of us have fumbled through it awkwardly.

Coming up with a personal description can be daunting. But there are times when it’s essential - whether we’re updating our LinkedIn profiles, blogging for Medium or creating a business website of our own.

In this post, we’ll go over how to write a bio, step by step. To help guide you, we’ve also included a handy template, along with some professional bio examples for your inspiration. With these resources, you’ll find that writing a bio, as part of making a website , is much easier than you might think.

What is a bio?

Before you learn how to write a bio, you should have a clear understanding of what it is and why you need it.

In the world of literature, a personal biography can span the length of an entire novel, like Nelson Mandela’s Long Walk to Freedom or Malala Yousafzai’s I Am Malala . In the online world, however, a bio is a short paragraph in which you introduce yourself. Typically, people place bios on the About Us page of their professional website, as well as on their social media pages and other networking platforms.

What to include in a bio

Depending on your audience and goals, your bio can highlight your personal interests, your professional achievements or a mix of both. Here are some of the elements a bio might include:

Job title or workplace

University degree and other qualifications

Hometown or city of residence

Personal or professional goals

Mission statement and values

Skills and expertise

Interests and hobbies

The goal of writing a bio is to provide people with a snapshot of who you are. This is important for a variety of reasons, whether it’s drawing people toward your personal website or promoting your blog, attracting clients and business partners to your brand, or highlighting your achievements for job interviews.

How to write a short bio

The most effective online bios are both professional and concise. Here’s how to write a short professional bio that suits your website or brand:

Introduce yourself

State your company or brand name

Explain your professional role

Include professional achievements

Discuss your passions and values

Mention your personal interests

01. Introduce yourself

Begin your bio by stating your first and last name. If you’re writing in the third person, these should be the first two words of the paragraph. This makes your name easy for your audience to identify and remember. Your bio is a huge part of your personal branding efforts, and should start with a strong intro to make a positive impact.

02. State your company or brand name

Think about whether you want your bio to represent yourself on a personal level, or whether you’d like it to come across as more professional. If you have a personal brand or business - for example, a blog, freelance business or eCommerce site - be sure to mention your brand name at the beginning of your bio. Don’t be afraid if the name sounds simple or redundant. It’s perfectly fine, for instance, to say Mary Smith is the founder and CEO of Smith Digital.

Likewise, feel free to mention the name of another company or brand that you work for if you’d like to associate it with your professional accomplishments - e.g., Mary Smith is a consultant at Google and the founder and CEO of Smith Digital.

03. Explain your professional role

Next, briefly explain your current position. This is relevant whether you’re the founder of a company, a high-level specialist or a beginner in your field, and it can be similar to the description you have on your resume. Your website visitors won’t necessarily know what your job involves, so elaborating on your primary responsibilities helps paint a picture of who you are and what you have to offer. This can also be used, if needed for employment and recruitment opportunities. If you're a freelancer a strong bio can make all the difference in how successful sourcing work can be.

04. Include professional achievements

In addition to explaining what your job entails, highlight milestones that make you stand out. Even if you haven’t won an award or gained external recognition, you can discuss ways in which you’ve contributed to your professional role and touch on new ideas or approaches that you bring to the table.

05. Discuss your passions and values

Once you describe what you do and how you contribute to your role, you’ll need to explain the why . This is one of the most important elements to focus on as you consider how to write a bio.

Think about the values and passions underlying your work, as well as your professional philosophy. What gets you up in the morning? What’s the driving force behind what you do?

You can also think of this part of your professional bio as a kind of mission statement. Perhaps your mission is to serve others, contribute to society, grow your expertise or learn new skills. Whatever your reasons, expanding upon these ideas can help your audience get a better understanding of what truly matters to you. Don't be afraid to deploy storytelling in this part of creating your bio. Explore your narrative and then convey it.

06. Mention your personal interests

The most effective short bios will not only focus on your professional experience, but will also touch on what you like to do in your spare time. Consider mentioning:

Your family

Your hometown

Your hobbies

Side projects you’re working on

Transitioning to a more casual discussion of who you are outside of work is a great way to conclude your bio. This will present you as a more well-rounded person while making you relatable for your audience.

Professional bio template

As you go through the steps on how to write a bio, this handy template will help you get started:

Sentence 1: [Name] is a [job title] who [job description].

E.g., Lisa Green is an English teacher who teaches beginning to advanced literature courses for 10th and 11th grade students at Bloomfield High School.

Sentence 2: [Name] believes that [why you do the work you do].

E.g., Lisa believes that written and analytical skills are not only a fundamental part of academic excellence, but are also the building blocks of critical thinking in high school and beyond.

Sentence 3: [Name/pronoun] has [mention your achievements].

E.g., In addition to managing the English curriculum for the school, she runs an after school program where she works one-on-one with students.

Sentence 4: [Name/pronoun] is a [mention any relevant awards, training or honors].

E.g., She has also been nominated Teacher of the Year for two consecutive years.

Sentence 5: [Name/pronoun] holds a [insert degree] in [field of study] from [university].

E.g., Lisa holds a BA in Creative Writing and a Master’s Degree in Teaching from the University of Michigan.

Once you’ve filled in this template, put it all together into a single paragraph to create an initial framework for your professional biography. Note that you can shorten or expand upon this bio according to your unique needs.

Professional bio examples

Now that you know the basics of writing a professional bio, here are some short bio examples to inspire you. You can use these examples as additional templates for guidance as you craft your own personal biography.

Like the creators of these examples, you can place your bio on your personal or professional website and, later, revise the structure for other online platforms.

01. Bristol Guitar Making School

Of all the professional bio examples, Alex Bishop’s content exudes passion. Strategically placing the bio on the About page of his small business website , he highlights his skills and explains why he finds his work meaningful. In particular, we love his description of why he chose to pursue guitar making:

“​My passion as a guitar maker comes from a life-long obsession with making things. From a young age I have always tried to manipulate objects and materials in order to create something entirely different. I find that working with wood is a way for me to connect with nature. The simple act of shaping wood to make something functional or beautiful brings me endless satisfaction.”

He also lists his accomplishments and awards, adding credibility to his business and building trust among prospective clients.

02. Alexandra Zsigmond

As someone who has served as art director for both The New York Times' opinion section and The New Yorker , it's no surprise that Alexandra Zsigmond's bio is thorough and detailed. Providing statistics or reflections on the things she achieved in her career is a clever way to demonstrate her value without saying so directly. As she explains:

"She has collaborated with a roster of over 1000 artists worldwide and art directed over 4000 editorial illustrations. She is known for greatly expanding the range of visual contributors to the Times, drawing equally from the worlds of contemporary illustration, fine art, animation, and comics."

03. Amanda Shields Interiors

Amanda Shields provides us with another effective bio example on her interior design website. Importantly, she spices up her bio by explaining how home decor aligns with her personal life and why it’s so close to her heart as a mother and entrepreneur:

"After working as a product designer for numerous retailers over the years, and after I had my first child, I decided to take the plunge and start my own home staging business…. Coincidentally, a month later I discovered I was pregnant with my second child. I loved the new challenges I faced as a new entrepreneur and mom and it didn't take long for me to discover that this was my calling…. I felt the need to expand my business and launch Amanda Shields Interiors as its own entity to focus specifically on residential interiors and design."

By placing this content on her website’s About page, she provides potential clients with insights into her expertise and professional experience. She expands upon the choices she made along her career path, strategically making note of her achievements and acquired skills along the way.

Tips for writing a bio

As you write your bio using the professional template above, make sure to keep the following tips in mind:

Keep it concise: Your bio should be sufficiently explanatory, but it should also be short and to the point. A good rule of thumb is to keep each element of your bio - from your job description to your mission statement and hobbies - to about 1-2 sentences. That way, you’ll end up with a brief paragraph that holds your readers’ attention without rambling on.

Consider your audience: The voice and tone you choose for your biography largely depends on your audience and personal goals. If you’re looking for a job and are writing primarily for recruiters, you’ll want to use a serious, professional tone. On the other hand, if you’re creating an Instagram bio , consider using more casual, conversational language that reflects your personality.

Add humor: Relatedly, consider adding humor when appropriate. This is especially valuable if you’ve founded your own business or created your own website , as it can give you a distinct brand identity while helping your audience build a stronger sense of connection with your brand.

Link to your website: When writing a bio for a platform other than your own website - a social media page, another company page, or a guest blog or publication - remember to include a link to your website. This will help you promote your website while highlighting your professionalism and authority.

Adapt for different platforms: You’ll most likely need to adapt the length and writing style of your biography to suit different platforms. For example, you may place a longer bio on your website’s About page and a shorter one on your LinkedIn page. In these cases, use the same main principles for writing a bio while scaling down the most important elements.

By following these tips, you can create a powerful bio that helps you stand out in your field and allows your audience to get to know you better.

How to write a bio in four sentences or less

Really need to create a super short bio? We'd suggest following some of the tips above, just condensing them into less word for a short bio that still makes impact.

But if we really had to choose we'd say focus on - you, your professional role and company. That condenses everything that matters for bio into three sentences. Humor, creativity and uniqueness still all matter - just use fewer words to convey them.

Creating a bio for your website

As we’ve noted in the examples above, one of the most strategic places to put your bio is on your website - so be sure to consider it within your web design plans. Whether the goal of your site is to start and promote your business , showcase your design portfolio or display your resume, including a bio gives your audience a glimpse into the person behind your content. It can also kickstart your professional growth . Show the world what you do, how you do it and why it matters, and people will be drawn to your passion and inspired by your experience.

Pro tip: You can add a bio to many different types of websites, so using templates can help you create yours faster. For example, if you're creating a portfolio website , explore portfolio website templates to help you get started.

Creating a bio for social media

Crafting a professional bio for social media is vital as it introduces you or your brand, and it builds credibility and trust. A well-written bio establishes your expertise, attracts the right audience, and fosters engagement. It helps maintain a consistent brand image, optimizes search and discovery, and opens doors to networking and career opportunities. A compelling bio delivers a concise, informative snapshot of who you are, what you do, and the value you bring, leaving a lasting impression on visitors and potential collaborators alike.

You may need to edit your bio depending on which social media platform you plan to use it on. Some of the most popular ones include Twitter, Facebook, Instagram and TikTok. Focus on getting your bio right on the platforms you plan to focus your personal or brand social media marketing efforts on.

Writing a bio with AI

If you're looking to write your bio fast while creating your website, consider using an AI text generator to build your draft. You'll still need to make sure it goes through. an intensive editing process, so that it really captures the essence of who you are and your professional skills. A bio is about much more than just basic information, so don't forget to include the storytelling too. Build a website with Wix and you can make use of the in-built AI text generator within its Editor .

Why good bios are important for a professional

In a world where first impressions matter, a well-crafted bio can make a significant impact in establishing trust and credibility with potential clients, employers or collaborators. It also offers insight into your personality and values, helping to forge authentic connections with your audience. It acts as a powerful tool for personal branding, allowing you to differentiate yourself in a competitive landscape and leave a memorable impression.

A strong bio also serves as a gateway to opportunities, whether it's securing new clients, landing job interviews or establishing partnerships. It acts as a professional introduction, allowing you to showcase your expertise. A polished and impactful bio is essential for you to effectively communicate your professional identity and stand out in your field.

Writing a bio without experience

Writing a bio when you don't yet have experience can be challenging, but it's an opportunity to showcase your potential and aspirations.

Begin by highlighting your educational background, skills and any relevant coursework or projects you've completed. Focus on your passions, interests and personal qualities that make you unique. Consider including volunteer work, internships or extracurricular activities that demonstrate your commitment and initiative. Emphasize your eagerness to learn and grow in your chosen field and express your future goals and aspirations. Don't be afraid to be honest about your current stage and your willingness to gain experience and develop professionally.

If you don't know what to write in your bio, start by brainstorming your key experiences, achievements, skills and personal attributes. Consider what sets you apart and what you want others to know about you. Look for inspiration from other bios or profiles in your field, and consider seeking feedback from friends, mentors or colleagues. Don't hesitate to highlight your passions, interests and goals, as well as any unique experiences or perspectives you bring to the table. Remember to keep it concise and engaging, and don't be afraid to revise and refine your bio until it accurately represents you.

How to write a bio FAQ

What is a short bio.

A short bio, short for biography, is a concise summary of a your life or professional background. It provides a brief overview of your key achievements, qualifications, experiences, and relevant details. Typically written in the third person, a short bio is often used in various contexts, such as professional profiles, social media accounts, introductions for speaking engagements, author descriptions, and other situations where a brief introduction is required. The length of a short bio can vary, but it's generally kept to a few sentences or a short paragraph to provide a snapshot of the person's background and expertise.

How do I write a bio about myself?

What should i include in a short bio, how do you write a fun bio for work, how do i make my bio stand out, related posts.

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How to write a strong one-line biography (with examples!)

As a blogger or content marketer, you’re spreading your content across the internet to build your name as a thought leader and to drive traffic back to your (or your client’s) website.

One of the best ways to do this is via a strong biography, where sites will often allow you to also link back to somewhere. But you need to get their interest to learn more, so you need a strong one-line biography as most sites will only allow a short biography.

Here’s how you write a strong one-line biography for your blog author page:

Write in 3rd person

Highlight your role/profession.

• Keep it short

Include a call to action

Biographies should be written in third person. Instead of “I am a serial entrepreneur…” you should write “John is a serial entrepreneur…”

Some publications may have different guidelines, in which case you should follow them, but as a general guideline always write your bio in 3rd person.

Your bio should tell readers who you are and what you do, so be sure to highlight your role or profession.

“John is a serial entrepreneur and digital marketing veteran who…”

This gives people more information about you, why you are qualified to be talking about the topic you are bylined on, and helps them decide if they want to click your link to learn more.

Don’t be afraid to brag a little bit! In our world of fake humility, finding someone who is willing to state what they’ve done can be refreshing and encourage them to click to learn more about you.

Don’t overdo it though. A quick interesting fact is usually more than enough to get them interested.

For example:

“John is a serial entrepreneur and digital marketing leader who via his company Credo has generated over a quarter billion dollars in leads for agencies since 2015.”

The lead value number is a brag, but it’s also true and lets people know that John knows what he’s doing.

Have some fun!

In today’s social media world, people want to connect with the person behind the account.

So don’t be afraid to use emojis or a bit of humor.

This advice does not carry over to a professional website like LinkedIn where people are more professional and you should present your best face to the world.

Keep it short, but readable

If you’re required to keep your biography to just one sentence, you have just 15 to 20 words on average to get your point across. You need to be succinct and make every word count.

As such, remove superlatives and flowery language that could make it harder to read. This is not the place to be cute or show off – it’s the place to communicate effectively.

Include a backlink/hyperlink

Most websites where you publish will allow you to link back to a site of your choice from your biography. Don’t be spammy and try to link back to multiple places – link to a place where people can find out more about you or your company easily.

Finally, include a call to action (CTA) if you have enough space and can work it in. At minimum, make sure you follow the above advice and include a hyperlink back to your main website where people can learn more about you or your business.

Some examples

Here are some examples of great bios.

Dan Martell (Instagram)

Dan Martell is a coach to software founders, an entrepreneur with 3 business exits, an award-winning angel investor, and a proud dad and husband.

How do we know this? Because he says so in his Instagram bio. Short and effective.

Kimberly Bryant

Kimberly Bryant is the founder of Black Girls Code , a company that “build[s] pathways for young women of color to embrace the current tech marketplace as builders and creators by introducing them to skills in computer programming and technology.” Here is her Twitter biography, which clearly states what she does and gives insight into who she is.

Chris Ducker

Chris Ducker is a UK-based entrepreneur who “helps midlife leaders and entrepreneurs build future proof businesses around their expertise” with his Youpreneur coaching program.

Pat Flynn is a serial entrepreneur, dad, and husband who also has a physical product and a Pokemon card side hustle with over 100,000 YouTube subscribers. Here’s his Instagram profile:

Rand Fishkin

Rand is also a serial entrepreneur and currently the CEO of Sparktoro, an audience insight software tool. He’s formerly the cofounder and CEO of Moz, an SEO software suite. His LinkedIn bio says succinctly what he does, and also adds a bit of personality to let you know what he believes.

John Doherty

John is the founder and CEO of Credo and EditorNinja. (Hi, I’m John writing this!). His bio tells you what he cares about (his family and Colorado), what he does and the various projects he works on as well as his accomplishments.

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Posted on Jun 30, 2023

How to Write a Biography: A 7-Step Guide [+Template]

From time to time, nonfiction authors become so captivated by a particular figure from either the present or the past, that they feel compelled to write an entire book about their life. Whether casting them as heroes or villains, there is an interesting quality in their humanity that compels these authors to revisit their life paths and write their story.

However, portraying someone’s life on paper in a comprehensive and engaging way requires solid preparation. If you’re looking to write a biography yourself, in this post we’ll share a step-by-step blueprint that you can follow. 

How to write a biography: 

1. Seek permission when possible 

2. research your subject thoroughly, 3. do interviews and visit locations, 4. organize your findings, 5. identify a central thesis, 6. write it using narrative elements, 7. get feedback and polish the text.

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While you technically don’t need permission to write about public figures (or deceased ones), that doesn't guarantee their legal team won't pursue legal action against you. Author Kitty Kelley was sued by Frank Sinatra before she even started to write His Way , a biography that paints Ol Blue Eyes in a controversial light. (Kelley ended up winning the lawsuit, however).  

Whenever feasible, advise the subject’s representatives of your intentions. If all goes according to plan, you’ll get a green light to proceed, or potentially an offer to collaborate. It's a matter of common sense; if someone were to write a book about you, you would likely want to know about it well prior to publication. So, make a sincere effort to reach out to their PR staff to negotiate an agreement or at least a mutual understanding of the scope of your project. 

At the same time, make sure that you still retain editorial control over the project, and not end up writing a puff piece that treats its protagonist like a saint or hero. No biography can ever be entirely objective, but you should always strive for a portrayal that closely aligns with facts and reality.

If you can’t get an answer from your subject, or you’re asked not to proceed forward, you can still accept the potential repercussions and write an unauthorized biography . The “rebellious act” of publishing without consent indeed makes for great marketing, though it’ll likely bring more headaches with it too. 

✋ Please note that, like other nonfiction books, if you intend to release your biography with a publishing house , you can put together a book proposal to send to them before you even write the book. If they like it enough, they might pay you an advance to write it.  

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Craft a professional pitch for your nonfiction book with our handy template.

Once you’ve settled (or not) the permission part, it’s time to dive deep into your character’s story.  

Deep and thorough research skills are the cornerstone of every biographer worth their salt. To paint a vivid and accurate portrait of someone's life, you’ll have to gather qualitative information from a wide range of reliable sources. 

Start with the information already available, from books on your subject to archival documents, then collect new ones firsthand by interviewing people or traveling to locations. 

Browse the web and library archives

Put your researcher hat on and start consuming any piece on your subject you can find, from their Wikipedia page to news articles, interviews, TV and radio appearances, YouTube videos, podcasts, books, magazines, and any other media outlets they may have been featured in. 

Establish a system to orderly collect the information you find 一 even seemingly insignificant details can prove valuable during the writing process, so be sure to save them. 

Depending on their era, you may find most of the information readily available online, or you may need to search through university libraries for older references. 

For his landmark biography of Alexander Hamilton, Ron Chernow spent untold hours at Columbia University’s library , reading through the Hamilton family papers, visiting the New York Historical Society, as well as interviewing the archivist of the New York Stock Exchange, and so on. The research process took years, but it certainly paid off. Chernow discovered that Hamilton created the first five securities originally traded on Wall Street. This finding, among others, revealed his significant contributions to shaping the current American financial and political systems, a legacy previously often overshadowed by other founding fathers. Today Alexander Hamilton is one of the best-selling biographies of all time, and it has become a cultural phenomenon with its own dedicated musical. 

Besides reading documents about your subject, research can help you understand the world that your subject lived in. 

Try to understand their time and social environment

Many biographies show how their protagonists have had a profound impact on society through their philosophical, artistic, or scientific contributions. But at the same time, it’s worth it as a biographer to make an effort to understand how their societal and historical context influenced their life’s path and work.

An interesting example is Stephen Greenblatt’s Will in the World . Finding himself limited by a lack of verified detail surrounding William Shakespeare's personal life, Greenblatt, instead, employs literary interpretation and imaginative reenactments to transport readers back to the Elizabethan era. The result is a vivid (though speculative) depiction of the playwright's life, enriching our understanding of his world.

Many readers enjoy biographies that transport them to a time and place, so exploring a historical period through the lens of a character can be entertaining in its own right. The Diary of Samuel Pepys became a classic not because people were enthralled by his life as an administrator, but rather from his meticulous and vivid documentation of everyday existence during the Restoration period.

Once you’ve gotten your hands on as many secondary sources as you can find, you’ll want to go hunting for stories first-hand from people who are (or were) close to your subject.

With all the material you’ve been through, by now you should already have a pretty good picture of your protagonist. But you’ll surely have some curiosities and missing dots in their character arc to figure out, which you can only get by interviewing primary sources.

Interview friends and associates

This part is more relevant if your subject is contemporary, and you can actually meet up or call with relatives, friends, colleagues, business partners, neighbors, or any other person related to them. 

In writing the popular biography of Steve Jobs, Walter Isaacson interviewed more than one hundred people, including Jobs’s family, colleagues, former college mates, business rivals, and the man himself.

🔍 Read other biographies to get a sense of what makes a great one. Check out our list of the 30 best biographies of all time , or take our 30-second quiz below for tips on which one you should read next. 

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When you conduct your interviews, make sure to record them with high quality audio you can revisit later. Then use tools like Otter.ai or Descript to transcribe them 一 it’ll save you countless hours. 

You can approach the interview with a specific set of questions, or follow your curiosity blindly, trying to uncover revealing stories and anecdotes about your subject. Whatever your method, author and biography editor Tom Bromley suggests that every interviewer arrives prepared, "Show that you’ve done your work. This will help to put the interviewee at ease, and get their best answers.” 

Bromley also places emphasis on the order in which you conduct interviews. “You may want to interview different members of the family or friends first, to get their perspective on something, and then go directly to the main interviewee. You'll be able to use that knowledge to ask sharper, more specific questions.” 

Finally, consider how much time you have with each interviewee. If you only have a 30-minute phone call with an important person, make it count by asking directly the most pressing questions you have. And, if you find a reliable source who is also particularly willing to help, conduct several interviews and ask them, if appropriate, to write a foreword as part of the book’s front matter .

Sometimes an important part of the process is packing your bags, getting on a plane, and personally visiting significant places in your character’s journey.

Visit significant places in their life

A place, whether that’s a city, a rural house, or a bodhi tree, can carry a particular energy that you can only truly experience by being there. In putting the pieces together about someone’s life, it may be useful to go visit where they grew up, or where other significant events of their lives happened. It will be easier to imagine what they experienced, and better tell their story. 

In researching The Lost City of Z , author David Grann embarked on a trek through the Amazon, retracing the steps of British explorer Percy Fawcett. This led Grann to develop new theories about the circumstances surrounding the explorer's disappearance.

Hopefully, you won’t have to deal with jaguars and anacondas to better understand your subject’s environment, but try to walk into their shoes as much as possible. 

Once you’ve researched your character enough, it’s time to put together all the puzzle pieces you collected so far. 

Take the bulk of notes, media, and other documents you’ve collected, and start to give them some order and structure. A simple way to do this is by creating a timeline. 

Create a chronological timeline

It helps to organize your notes chronologically 一 from childhood to the senior years, line up the most significant events of your subject’s life, including dates, places, names and other relevant bits. 

You should be able to divide their life into distinct periods, each with their unique events and significance. Based on that, you can start drafting an outline of the narrative you want to create.  

Draft a story outline 

Since a biography entails writing about a person’s entire life, it will have a beginning, a middle, and an end. You can pick where you want to end the story, depending on how consequential the last years of your subject were. But the nature of the work will give you a starting character arc to work with. 

To outline the story then, you could turn to the popular Three-Act Structure , which divides the narrative in three main parts. In a nutshell, you’ll want to make sure to have the following:

• Act 1. Setup : Introduce the protagonist's background and the turning points that set them on a path to achieve a goal. 
• Act 2. Confrontation : Describe the challenges they encounter, both internal and external, and how they rise to them. Then..
• Act 3. Resolution : Reach a climactic point in their story in which they succeed (or fail), showing how they (and the world around them) have changed as a result. 

Only one question remains before you begin writing: what will be the main focus of your biography?

Think about why you’re so drawn to your subject to dedicate years of your life to recounting their own. What aspect of their life do you want to highlight? Is it their evil nature, artistic genius, or visionary mindset? And what evidence have you got to back that up? Find a central thesis or focus to weave as the main thread throughout your narrative. 

Or find a unique angle

If you don’t have a particular theme to explore, finding a distinct angle on your subject’s story can also help you distinguish your work from other biographies or existing works on the same subject.

Plenty of biographies have been published about The Beatles 一 many of which have different focuses and approaches: 

• Philip Norman's Shout is sometimes regarded as leaning more towards a pro-Lennon and anti-McCartney stance, offering insights into the band's inner dynamics. 
• Ian McDonald's Revolution in the Head closely examines their music track by track, shifting the focus back to McCartney as a primary creative force. 
• Craig Brown's One Two Three Four aims to capture their story through anecdotes, fan letters, diary entries, and interviews. 
• Mark Lewisohn's monumental three-volume biography, Tune In , stands as a testament to over a decade of meticulous research, chronicling every intricate detail of the Beatles' journey.

Finally, consider that biographies are often more than recounting the life of a person. Similar to how Dickens’ Great Expectations is not solely about a boy named Pip (but an examination and critique of Britain’s fickle, unforgiving class system), a biography should strive to illuminate a broader truth — be it social, political, or human — beyond the immediate subject of the book. 

Once you’ve identified your main focus or angle, it’s time to write a great story. 

While biographies are often highly informative, they do not have to be dry and purely expository in nature . You can play with storytelling elements to make it an engaging read. 

You could do that by thoroughly detailing the setting of the story , depicting the people involved in the story as fully-fledged characters , or using rising action and building to a climax when describing a particularly significant milestone of the subject’s life. 

One common way to make a biography interesting to read is starting on a strong foot…

Hook the reader from the start

Just because you're honoring your character's whole life doesn't mean you have to begin when they said their first word. Starting from the middle or end of their life can be more captivating as it introduces conflicts and stakes that shaped their journey.

When he wrote about Christopher McCandless in Into the Wild , author Jon Krakauer didn’t open his subject’s childhood and abusive family environment. Instead, the book begins with McCandless hitchhiking his way into the wilderness, and subsequently being discovered dead in an abandoned bus. By starting in medias res , Krakauer hooks the reader’s interest, before tracing back the causes and motivations that led McCandless to die alone in that bus in the first place.

You can bend the timeline to improve the reader’s reading experience throughout the rest of the story too…

Play with flashback 

While biographies tend to follow a chronological narrative, you can use flashbacks to tell brief stories or anecdotes when appropriate. For example, if you were telling the story of footballer Lionel Messi, before the climax of winning the World Cup with Argentina, you could recall when he was just 13 years old, giving an interview to a local newspaper, expressing his lifelong dream of playing for the national team. 

Used sparsely and intentionally, flashbacks can add more context to the story and keep the narrative interesting. Just like including dialogue does…

Reimagine conversations

Recreating conversations that your subject had with people around them is another effective way to color the story. Dialogue helps the reader imagine the story like a movie, providing a deeper sensory experience. 

One thing is trying to articulate the root of Steve Jobs’ obsession with product design, another would be to quote his father , teaching him how to build a fence when he was young: “You've got to make the back of the fence just as good looking as the front of the fence. Even though nobody will see it, you will know. And that will show that you're dedicated to making something perfect.”

Unlike memoirs and autobiographies, in which the author tells the story from their personal viewpoint and enjoys greater freedom to recall conversations, biographies require a commitment to facts. So, when recreating dialogue, try to quote directly from reliable sources like personal diaries, emails, and text messages. You could also use your interview scripts as an alternative to dialogue. As Tom Bromley suggests, “If you talk with a good amount of people, you can try to tell the story from their perspective, interweaving different segments and quoting the interviewees directly.”

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These are just some of the story elements you can use to make your biography more compelling. Once you’ve finished your manuscript, it’s a good idea to ask for feedback. 

If you’re going to self-publish your biography, you’ll have to polish it to professional standards. After leaving your work to rest for a while, look at it with fresh eyes and self-edit your manuscript eliminating passive voice, filler words, and redundant adverbs. 

Then, have a professional editor give you a general assessment. They’ll look at the structure and shape of your manuscript and tell you which parts need to be expanded on or cut. As someone who edited and commissioned several biographies, Tom Bromley points out that a professional “will look at the sources used and assess whether they back up the points made, or if more are needed. They would also look for context, and whether or not more background information is needed for the reader to understand the story fully. And they might check your facts, too.”  

In addition to structural editing, you may want to have someone copy-edit and proofread your work.

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Importantly, make sure to include a bibliography with a list of all the interviews, documents, and sources used in the writing process. You’ll have to compile it according to a manual of style, but you can easily create one by using tools like EasyBib . Once the text is nicely polished and typeset in your writing software , you can prepare for the publication process.  

In conclusion, by mixing storytelling elements with diligent research, you’ll be able to breathe life into a powerful biography that immerses readers in another individual’s life experience. Whether that’ll spark inspiration or controversy, remember you could have an important role in shaping their legacy 一 and that’s something not to take lightly. 

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How to Write a Biography

Biographies are big business. Whether in book form or Hollywood biopics, the lives of the famous and sometimes not-so-famous fascinate us.

While it’s true that most biographies are about people who are in the public eye, sometimes the subject is less well-known. Primarily, though, famous or not, the person who is written about has led an incredible life.

In this article, we will explain biography writing in detail for teachers and students so they can create their own.

While your students will most likely have a basic understanding of a biography, it’s worth taking a little time before they put pen to paper to tease out a crystal-clear definition of one.

What Is a Biography?

A biography is an account of someone’s life written by someone else . While there is a genre known as a fictional biography, for the most part, biographies are, by definition, nonfiction.

Generally speaking, biographies provide an account of the subject’s life from the earliest days of childhood to the present day or, if the subject is deceased, their death.

The job of a biography is more than just to outline the bare facts of a person’s life.

Rather than just listing the basic details of their upbringing, hobbies, education, work, relationships, and death, a well-written biography should also paint a picture of the subject’s personality and experience of life.

Full Biographies

Teaching unit.

Teach your students everything they need to know about writing an AUTOBIOGRAPHY and a BIOGRAPHY.

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Features of a Biography

Before students begin writing a biography, they’ll need to have a firm grasp of the main features of a Biography. An excellent way to determine how well they understand these essential elements is to ask them to compile a checklist like the one-blow

Their checklists should contain the items below at a minimum. Be sure to help them fill in any gaps before moving on to the writing process.

The purpose of a biography is to provide an account of someone’s life.

Biography structure.

ORIENTATION (BEGINNING) Open your biography with a strong hook to grab the reader’s attention

SEQUENCING: In most cases, biographies are written in chronological order unless you are a very competent writer consciously trying to break from this trend.

COVER: childhood, upbringing, education, influences, accomplishments, relationships, etc. – everything that helps the reader to understand the person.

CONCLUSION: Wrap your biography up with some details about what the subject is doing now if they are still alive. If they have passed away, make mention of what impact they have made and what their legacy is or will be.

BIOGRAPHY FEATURES

LANGUAGE Use descriptive and figurative language that will paint images inside your audience’s minds as they read. Use time connectives to link events.

PERSPECTIVE Biographies are written from the third person’s perspective.

DETAILS: Give specific details about people, places, events, times, dates, etc. Reflect on how events shaped the subject. You might want to include some relevant photographs with captions. A timeline may also be of use depending upon your subject and what you are trying to convey to your audience.

TENSE Written in the past tense (though ending may shift to the present/future tense)

THE PROCESS OF WRITING A BIOGRAPHY

Like any form of writing, you will find it simple if you have a plan and follow it through. These steps will ensure you cover the essential bases of writing a biography essay.

Firstly, select a subject that inspires you. Someone whose life story resonates with you and whose contribution to society intrigues you. The next step is to conduct thorough research. Engage in extensive reading, explore various sources, watch documentaries, and glean all available information to provide a comprehensive account of the person’s life.

Creating an outline is essential to organize your thoughts and information. The outline should include the person’s early life, education, career, achievements, and any other significant events or contributions. It serves as a map for the writing process, ensuring that all vital information is included.

Your biography should have an engaging introduction that captivates the reader’s attention and provides background information on the person you’re writing about. It should include a thesis statement summarising the biography’s main points.

Writing a biography in chronological order is crucial . You should begin with the person’s early life and move through their career and achievements. This approach clarifies how the person’s life unfolded and how they accomplished their goals.

A biography should be written in a narrative style , capturing the essence of the person’s life through vivid descriptions, anecdotes, and quotes. Avoid dry, factual writing and focus on creating a compelling narrative that engages the reader.

Adding personal insights and opinions can enhance the biography’s overall impact, providing a unique perspective on the person’s achievements, legacy, and impact on society.

Editing and proofreading are vital elements of the writing process. Thoroughly reviewing your biography ensures that the writing is clear, concise, and error-free. You can even request feedback from someone else to ensure that it is engaging and well-written.

Finally, including a bibliography at the end of your biography is essential. It gives credit to the sources that were used during research, such as books, articles, interviews, and websites.

Tips for Writing a Brilliant Biography

Biography writing tip #1: choose your subject wisely.

There are several points for students to reflect on when deciding on a subject for their biography. Let’s take a look at the most essential points to consider when deciding on the subject for a biography:

Interest: To produce a biography will require sustained writing from the student. That’s why students must choose their subject well. After all, a biography is an account of someone’s entire life to date. Students must ensure they choose a subject that will sustain their interest throughout the research, writing, and editing processes.

Merit: Closely related to the previous point, students must consider whether the subject merits the reader’s interest. Aside from pure labors of love, writing should be undertaken with the reader in mind. While producing a biography demands sustained writing from the author, it also demands sustained reading from the reader.

Therefore, students should ask themselves if their chosen subject has had a life worthy of the reader’s interest and the time they’d need to invest in reading their biography.

Information: Is there enough information available on the subject to fuel the writing of an entire biography? While it might be a tempting idea to write about a great-great-grandfather’s experience in the war. There would be enough interest there to sustain the author’s and the reader’s interest, but do you have enough access to information about their early childhood to do the subject justice in the form of a biography?

Biography Writing Tip #2: R esearch ! Research! Research!

While the chances are good that the student already knows quite a bit about the subject they’ve chosen. Chances are 100% that they’ll still need to undertake considerable research to write their biography.

As with many types of writing , research is an essential part of the planning process that shouldn’t be overlooked. If students wish to give as complete an account of their subject’s life as possible, they’ll need to put in the time at the research stage.

An effective way to approach the research process is to:

1. Compile a chronological timeline of the central facts, dates, and events of the subject’s life

2. Compile detailed descriptions of the following personal traits:

•      Physical looks
•      Character traits
•      Values and beliefs

3. Compile some research questions based on different topics to provide a focus for the research:

• Childhood : Where and when were they born? Who were their parents? Who were the other family members? What education did they receive?
• Obstacles: What challenges did they have to overcome? How did these challenges shape them as individuals?
• Legacy: What impact did this person have on the world and/or the people around them?
• Dialogue & Quotes: Dialogue and quotations by and about the subject are a great way to bring color and life to a biography. Students should keep an eagle eye out for the gems that hide amid their sources.

As the student gets deeper into their research, new questions will arise that can further fuel the research process and help to shape the direction the biography will ultimately go in.

Likewise, during the research, themes will often begin to suggest themselves. Exploring these themes is essential to bring depth to biography, but we’ll discuss this later in this article.

Research Skills:

Researching for biography writing is an excellent way for students to hone their research skills in general. Developing good research skills is essential for future academic success. Students will have opportunities to learn how to:

• Gather relevant information
• Evaluate different information sources
• Select suitable information
• Organize information into a text.

Students will have access to print and online information sources, and, in some cases, they may also have access to people who knew or know the subject (e.g. biography of a family member).

These days, much of the research will likely take place online. It’s crucial, therefore, to provide your students with guidance on how to use the internet safely and evaluate online sources for reliability. This is the era of ‘ fake news ’ and misinformation after all!

COMPLETE TEACHING UNIT ON INTERNET RESEARCH SKILLS USING GOOGLE SEARCH

Teach your students ESSENTIAL SKILLS OF THE INFORMATION ERA to become expert DIGITAL RESEARCHERS.

⭐How to correctly ask questions to search engines on all devices.

⭐ How to filter and refine your results to find exactly what you want every time.

⭐ Essential Research and critical thinking skills for students.

⭐ Plagiarism, Citing and acknowledging other people’s work.

⭐ How to query, synthesize and record your findings logically.

BIOGRAPHY WRITING Tip #3: Find Your Themes In Biography Writing

Though predominantly a nonfiction genre, the story still plays a significant role in good biography writing. The skills of characterization and plot structuring are transferable here. And, just like in fiction, exploring themes in a biographical work helps connect the personal to the universal. Of course, these shouldn’t be forced; this will make the work seem contrived, and the reader may lose faith in the truthfulness of the account. A biographer needs to gain and maintain the trust of the reader.

Fortunately, themes shouldn’t need to be forced. A life well-lived is full of meaning, and the themes the student writer is looking for will emerge effortlessly from the actions and events of the subject’s life. It’s just a case of learning how to spot them.

One way to identify the themes in a life is to look for recurring events or situations in a person’s life. These should be apparent from the research completed previously. The students should seek to identify these patterns that emerge in the subject’s life. For example, perhaps they’ve had to overcome various obstacles throughout different periods of their life. In that case, the theme of overcoming adversity is present and has been identified.

Usually, a biography has several themes running throughout, so be sure your students work to identify more than one theme in their subject’s life.

BIOGRAPHY WRITING Tip: #4 Put Something of Yourself into the Writing

While the defining feature of a biography is that it gives an account of a person’s life, students must understand that this is not all a biography does. Relating the facts and details of a subject’s life is not enough. The student biographer should not be afraid to share their thoughts and feelings with the reader throughout their account of their subject’s life.

The student can weave some of their personality into the fabric of the text by providing commentary and opinion as they relate the events of the person’s life and the wider social context at the time. Unlike the detached and objective approach we’d expect to find in a history textbook, in a biography, student-writers should communicate their enthusiasm for their subject in their writing.

This makes for a more intimate experience for the reader, as they get a sense of getting to know the author and the subject they are writing about.

Biography Examples For Students

• Year 5 Example
• Year 7 Example
• Year 9 Example

“The Rock ‘n’ Roll King: Elvis Presley”

Elvis Aaron Presley, born on January 8, 1935, was an amazing singer and actor known as the “King of Rock ‘n’ Roll.” Even though he’s been dead for nearly 50 years, I can’t help but be fascinated by his incredible life!

Elvis grew up in Tupelo, Mississippi, in a tiny house with his parents and twin brother. His family didn’t have much money, but they shared a love for music. Little did they know Elvis would become a music legend!

When he was only 11 years old, Elvis got his first guitar. He taught himself to play and loved singing gospel songs. As he got older, he started combining different music styles like country, blues, and gospel to create a whole new sound – that’s Rock ‘n’ Roll!

In 1954, at the age of 19, Elvis recorded his first song, “That’s All Right.” People couldn’t believe how unique and exciting his music was. His famous hip-swinging dance moves also made him a sensation!

Elvis didn’t just rock the music scene; he also starred in movies like “Love Me Tender” and “Jailhouse Rock.” But fame came with challenges. Despite facing ups and downs, Elvis kept spreading happiness through his music.

Tragically, Elvis passed away in 1977, but his music and charisma live on. Even today, people worldwide still enjoy his songs like “Hound Dog” and “Can’t Help Falling in Love.” Elvis Presley’s legacy as the King of Rock ‘n’ Roll will live forever.

Long Live the King: I wish I’d seen him.

Elvis Presley, the Rock ‘n’ Roll legend born on January 8, 1935, is a captivating figure that even a modern-day teen like me can’t help but admire. As I delve into his life, I wish I could have experienced the magic of his live performances.

Growing up in Tupelo, Mississippi, Elvis faced challenges but found solace in music. At 11, he got his first guitar, a symbol of his journey into the world of sound. His fusion of gospel, country, and blues into Rock ‘n’ Roll became a cultural phenomenon.

The thought of being in the audience during his early performances, especially when he recorded “That’s All Right” at 19, sends shivers down my spine. Imagining the crowd’s uproar and feeling the revolutionary energy of that moment is a dream I wish I could have lived.

Elvis wasn’t just a musical prodigy; he was a dynamic performer. His dance moves, the embodiment of rebellion, and his roles in films like “Love Me Tender” and “Jailhouse Rock” made him a true icon.

After watching him on YouTube, I can’t help but feel a little sad that I’ll never witness the King’s live performances. The idea of swaying to “Hound Dog” or being enchanted by “Can’t Help Falling in Love” in person is a missed opportunity. Elvis may have left us in 1977, but he was the king of rock n’ roll. Long live the King!

Elvis Presley: A Teen’s Take on the Rock ‘n’ Roll Icon”

Elvis Presley, born January 8, 1935, was a revolutionary force in the music world, earning his title as the “King of Rock ‘n’ Roll.” Exploring his life, even as a 16-year-old today, I’m captivated by the impact he made.

Hailing from Tupelo, Mississippi, Elvis grew up in humble beginnings, surrounded by the love of his parents and twin brother. It’s inspiring to think that, despite financial challenges, this young man would redefine the music scene.

At 11, Elvis got his first guitar, sparking a self-taught journey into music. His early gospel influences evolved into a unique fusion of country, blues, and gospel, creating the electrifying genre of Rock ‘n’ Roll. In 1954, at only 19, he recorded “That’s All Right,” marking the birth of a musical legend.

Elvis wasn’t just a musical innovator; he was a cultural phenomenon. His rebellious dance moves and magnetic stage presence challenged the norms. He transitioned seamlessly into acting, starring in iconic films like “Love Me Tender” and “Jailhouse Rock.”

However, fame came at a cost, and Elvis faced personal struggles. Despite the challenges, his music continued to resonate. Even now, classics like “Hound Dog” and “Can’t Help Falling in Love” transcend generations.

Elvis Presley’s impact on music and culture is undeniable. He was known for his unique voice, charismatic persona, and electrifying performances. He sold over one billion records worldwide, making him one of the best-selling solo artists in history. He received numerous awards throughout his career, including three Grammy Awards and the Grammy Lifetime Achievement Award.

Elvis’s influence can still be seen in today’s music. Many contemporary artists, such as Bruno Mars, Lady Gaga, and Justin Timberlake, have cited Elvis as an inspiration. His music continues to be featured in movies, TV shows, and commercials.

Elvis left us in 1977, but his legacy lives on. I appreciate his breaking barriers and fearlessly embracing his artistic vision. Elvis Presley’s impact on music and culture is timeless, a testament to the enduring power of his artistry. His music has inspired generations and will continue to do so for many years to come.

Teaching Resources

Use our resources and tools to improve your student’s writing skills through proven teaching strategies.

BIOGRAPHY WRITING TEACHING IDEAS AND LESSONS

We have compiled a sequence of biography-related lessons or teaching ideas that you can follow as you please. They are straightforward enough for most students to follow without further instruction.

BIOGRAPHY LESSON IDEA # 1:

This session aims to give students a broader understanding of what makes a good biography.

Once your students have compiled a comprehensive checklist of the main features of a biography, allow them to use it to assess some biographies from your school library or on the internet using the feature checklist.

When students have assessed a selection of biographies, take some time as a class to discuss them. You can base the discussion around the following prompts:

• Which biographies covered all the criteria from their checklist?
• Which biographies didn’t?
• Which biography was the most readable in terms of structure?
• Which biography do you think was the least well-structured? How would you improve this?

Looking at how other writers have interpreted the form will help students internalize the necessary criteria before attempting to produce a biography. Once students have a clear understanding of the main features of the biography, they’re ready to begin work on writing a biography.

When the time does come to put pen to paper, be sure they’re armed with the following top tips to help ensure they’re as well prepared as possible.

BIOGRAPHY LESSON IDEA # 2:

This session aims to guide students through the process of selecting the perfect biography subject.

Instruct students to draw up a shortlist of three potential subjects for the biography they’ll write.

Using the three criteria mentioned in the writing guide (Interest, Merit, and Information), students award each potential subject a mark out of 5 for each of the criteria. In this manner, students can select the most suitable subject for their biography.

BIOGRAPHY LESSON IDEA # 3:

This session aims to get students into the researching phase, then prioritise and organise events chronologically.

Students begin by making a timeline of their subject’s life, starting with their birth and ending with their death or the present day. If the student has yet to make a final decision on the subject of their biography, a family member will often serve well for this exercise as a practice exercise.

Students should research and gather the key events of the person’s life, covering each period of their life from when they were a baby, through childhood and adolescence, right up to adulthood and old age. They should then organize these onto a timeline. Students can include photographs with captions if they have them.

They can present these to the class when they have finished their timelines.

BIOGRAPHY LESSON IDEA # 4:

Instruct students to look over their timeline, notes, and other research. Challenge them to identify three patterns that repeat throughout the subject’s life and sort all the related events and incidents into specific categories.

Students should then label each category with a single word. This is the thematic concept or the broad general underlying idea. After that, students should write a sentence or two expressing what the subject’s life ‘says’ about that concept.

This is known as the thematic statement . With the thematic concepts and thematic statements identified, the student now has some substantial ideas to explore that will help bring more profound meaning and wider resonance to their biography.

BIOGRAPHY LESSON IDEA # 5:

Instruct students to write a short objective account of an event in their own life. They can write about anyone from their past. It needn’t be more than a couple of paragraphs, but the writing should be strictly factual, focusing only on the objective details of what happened.

Once they have completed this, it’s time to rewrite the paragraph, but they should include some opinion and personal commentary this time.

The student here aims to inject some color and personality into their writing, to transform a detached, factual account into a warm, engaging story.

A COMPLETE UNIT ON TEACHING BIOGRAPHIES

Teach your students to write AMAZING BIOGRAPHIES & AUTOBIOGRAPHIES using proven RESEARCH SKILLS and WRITING STRATEGIES .

• Understand the purpose of both forms of biography.
• Explore the language and perspective of both.
• Prompts and Challenges to engage students in writing a biography.
• Dedicated lessons for both forms of biography.
• Biographical Projects can expand students’ understanding of reading and writing a biography.
• A COMPLETE 82-PAGE UNIT – NO PREPARATION REQUIRED.

FREE Biography Writing Graphic Organizer

Use this valuable tool in the research and writing phases to keep your students on track and engaged.

WRITING CHECKLIST & RUBRIC BUNDLE

⭐⭐⭐⭐⭐ (92 Reviews)

To Conclude

By this stage, your students should have an excellent technical overview of a biography’s essential elements.

They should be able to choose their subject in light of how interesting and worthy they are, as well as give consideration to the availability of information out there. They should be able to research effectively and identify emerging themes in their research notes. And finally, they should be able to bring some of their personality and uniqueness into their retelling of the life of another.

Remember that writing a biography is not only a great way to develop a student’s writing skills; it can be used in almost all curriculum areas. For example, to find out more about a historical figure in History, to investigate scientific contributions to Science, or to celebrate a hero from everyday life.

Biography is an excellent genre for students to develop their writing skills and to find inspiration in the lives of others in the world around them.

HOW TO WRITE A BIOGRAPHY TUTORIAL VIDEO

OTHER GREAT ARTICLES RELATED TO BIOGRAPHY WRITING

How to write an Autobiography

How to Write a Historical Recount Text

15 Awesome Recount & Personal Narrative Topics

Personal Narrative Writing Guide

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How to Write a Biography

Last Updated: May 28, 2024 Fact Checked

This article was co-authored by Stephanie Wong Ken, MFA . Stephanie Wong Ken is a writer based in Canada. Stephanie's writing has appeared in Joyland, Catapult, Pithead Chapel, Cosmonaut's Avenue, and other publications. She holds an MFA in Fiction and Creative Writing from Portland State University. This article has been fact-checked, ensuring the accuracy of any cited facts and confirming the authority of its sources. This article has been viewed 1,864,098 times.

Writing a biography can be a fun challenge, where you are sharing the story of someone’s life with readers. You may need to write a biography for a class or decide to write one as a personal project. Once you have identified the subject of the biography, do your research so you know as much about them as possible. Then, dive into the writing of the biography and revising it until it is at its finest.

Researching Your Subject

• If the subject does not give you permission to write the biography, you may want to choose a different subject. If you decide to publish the biography without the subject’s permission, you may be susceptible to legal action by the subject.
• If the subject is no longer alive, you obviously do not need to ask permission to write about them.

• You may create research questions to help focus your research of the subject, such as, What do I find interesting about the subject? Why is this subject important to readers? What can I say that is new about the subject? What would I like to learn more about?

• For in person interviews, record them with a tape recorder or a voice recorder on your computer or phone.
• You may need to interview the subject and others several times to get the material you need.

• You may also want to visit areas where the subject made a major decision or breakthrough in their life. Being physically in the area can give you a sense of how the subject might have felt and help you write their experiences more effectively.

• When researching the time period ask yourself: What were the social norms of that time? What was going on economically and politically? How did the social and political climate affect the subject?

• You may also include historical events or moments that affected the subject on the timeline. For example, maybe there was a conflict or civil war that happened during the person’s life that affected their life.

Writing the Biography

• You may end up focusing on particular areas of the person’s life. If you do this, work through a particular period in the person’s life chronologically.

• For example, you may have a thesis statement about focusing on how the person impacted the civil rights movement in America in the 1970s. You can then make sure all your content relates back to this thesis.

• Flashbacks should feel as detailed and real as present day scenes. Use your research notes and interviews with the subject to get a good sense of their past for the flashbacks.
• For example, you may jump from the person’s death in the present to a flashback to their favorite childhood memory.

• For example, you may focus on the person’s accomplishments in the civil rights movement. You may write a whole section about their contributions and participation in major civil rights marches in their hometown.

• For example, you may notice that the person’s life is patterned with moments of adversity, where the person worked hard and fought against larger forces. You can then use the theme of overcoming adversity in the biography.

• For example, you may note how you see parallels in the person’s life during the civil rights movement with your own interests in social justice. You may also commend the person for their hard work and positive impact on society.

Polishing the Biography

• Revise the biography based on feedback from others. Do not be afraid to cut or edit down the biography to suit the needs of your readers.

• Having a biography riddled with spelling, grammar, and punctuation errors can turn off your readers and result in a poor grade if you are handing in the text for a class.

• If the biography is for a class, use MLA , APA , or Chicago Style citations based on the preferences of your instructor.

Biography Help

Community Q&A

• Be careful when publishing private or embarrassing information, especially if the person is not a celebrity. You may violate their "Right of Privacy" or equivalent. Thanks Helpful 31 Not Helpful 5
• Have the sources to back up your statements about the subject's life. Untruthful written statements can lead to litigation. If it is your opinion, be clear that it is such and not fact (although you can support your opinion with facts). Thanks Helpful 16 Not Helpful 15

You Might Also Like

• ↑ https://grammar.yourdictionary.com/writing/how-to-write-a-biography.html
• ↑ https://au.indeed.com/career-advice/career-development/how-to-write-a-bio
• ↑ https://www.writersdigest.com/writing-articles/3-tips-for-writing-successful-flashbacks
• ↑ https://www.grammarly.com/blog/how-to-write-bio/
• ↑ https://writingcenter.unc.edu/tips-and-tools/editing-and-proofreading/
• ↑ https://www.plagiarism.org/article/how-do-i-cite-sources

About This Article

Before you write a biography, gather as much information about the subject that you can from sources like newspaper articles, interviews, photos, existing biographies, and anything else you can find. Write the story of that person’s life, including as much supporting detail as you can, including information about the place and time where the person lived. Focus on major events and milestones in their life, including historical events, marriage, children, and events which would shape their path later in life. For tips from our reviewer on proofreading the biography and citing your sources, keep reading! Did this summary help you? Yes No

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So you’d like to know how to write a biography. We can help with that! Learning how to write a biography doesn't have to be intimidating. In fact, it can be a lot of fun!

In this guide, we show you how to write a biography from the initial book idea all the way through to publishing your book , and we throw in a free template to help you on your way. 

Ready to learn how to start a biography? Let’s jump right in. 

Get Our 6″ x 9″ Pre-Formatted Book Template for Word or Mac

We will send you a Book Template for US Trade (standard paperback size).

How to Write a Biography in 11 Simple Steps

Here are the steps you need to take to learn how to write a biography:

1. Read other biographies 

Austin Kleon, Author of Steal Like an Artist , says “the writer tries to master words. All of these pursuits involve the study of those who have come before and the effort to build upon their work in some way.”

In other words, if you want to learn how to write a biography, you need to read the best biographies written by other excellent authors!

In this case, it would behoove you to read several biographies – whether historical or celebrity biographies is up to you and your sub-genre. 

A good author to start with? Walter Isaacson . He’s written highly acclaimed biographies on everyone from Abraham Lincoln and Steve Jobs to Leonardo Da Vinci and Elon Musk. 

Once you've read some well-crafted biographies, you'll have a better idea of how to start a biography of your own.

2. Identify your subject

In order to learn how to start a biography, you need to choose who you’d like to write about – if you don’t already have someone in mind.  

The most important factor will be, of course, your interest in the person you’re planning to write about. You’ll spend months (or even years) deep-diving into this person’s history, so you want to choose someone who you’re unlikely to tire of. 

When learning how to write a biography, here are few factors to consider: 

• How impactful has your potential subject’s life been? In other words, will people care to learn more about this person? 
• How readily available is information about your potential subject? Biographies require extensive research, so it’s critical to choose someone who has enough information out there to dig into! Consider whether your subject has done interviews, written journals, has family or a partner willing to speak with you, and more. 
• Are there already books written about your potential subject? Just because there’s an existing biography about the person you’re interested in doesn’t (necessarily) mean you can’t write another one. But if there are two or three biographies, you may want to reconsider. If you do choose to write about someone who has already been well-documented, be mindful about approaching the topic with a new angle or perspective. For instance, there are several biographies about George Washington, but author Alexis Coe wrote one about how Washington isn’t “quite the man we remember.” This brilliant iteration has over 12,000 ratings on Goodreads .
• Is there a market demand for a book about your potential subject? If you’re learning how to write a biography, you need to be mindful of whether folks will want to read it. Do some research to determine if readers will be receptive to a book about the person you’re interested in. 

Related: Is a Biography a Primary Source?

3. Get permission to write about your subject

We’ll start by stating the obvious. It’s a good idea to get permission to write about your subject, even if you’re not legally required to. For one thing, it’s just good manners. Plus, you’re much more likely to get unfettered access to the information and sources you need to write your book. 

But do you have to get permission? It depends.

In some cases, if your subject is considered a “public figure,” permission may not be required. The definition of a public figure varies depending on your jurisdiction, so you should always consult a lawyer before writing a biography. 

If you do decide to proceed without permission, be mindful of how your book will be received and any legal issues that may arise. That's why we always recommend asking permission from your subject when learning how to write a biography.

Related : Difference Between A Memoir and Biography

4. Create an outline

The next step of learning how to write a biography is to outline your story. It’s critical to outline your biography before you begin writing it. Among other things, it helps ensure you cover every topic you’d like to and get the book in the correct chronological order. It also helps you identify themes that emerge as you organize your ideas. 

Need help creating your outline? Learn how to do it (and take advantage of free templates!) in our guide to outlining a book . 

5. Select a working title (using a title generator) 

Now is the fun part of learning how to write a biography! It’s time to create a working title for your book. A working title is just what it sounds like: it’s a title that works – for now. 

Of course, it’s helpful to have something to call the book as you’re working on it. And it encourages you to think about the message you’d like your book to convey. When your biography is complete, you can always do a little more research on how to write book titles for your specific sub-genre and update your working title accordingly.

Or, you can decide you still love your initial title and publish your book with that one! 

We’ve made it easy for you to develop a working title – or multiple – using our book title generator . 

Don't like it?

6. Write a rough draft 

Okay, now it’s time to start writing your rough draft. Don’t be intimidated; just focus on getting something down on the page. As experts on all things writing and self-publishing, we’ve got a rough draft writing guide to help you get through this phase of writing a biography.

Remember to be as balanced and objective as possible when learning how to write a biography.

Make good use of your primary and secondary sources, and double-check all of your facts. You’ve got this!  

7. Self-edit

There are several different types of editing that we recommend each manuscript undergo. But before you give your rough draft to anyone else to review, you should edit it yourself. 

The first step to self-editing?

Take a break! It’s essential to give your mind some time to recuperate before you go over your work. And never self-edit as you go!

After you’ve completed your break, here are a few things to consider as you edit: 

• Grammar. This one is self-explanatory and usually the easiest. You can use an AI editor to make a first pass and quickly catch obvious spelling errors. Depending on prompts and your experience with the tool, you can also use AI to catch some grammar and syntax issues as well.
• Content and structure . This is the time to make sure the bones of your piece are good. Make sure your content flows logically (and in chronological order), no important pieces of information are missing, and there isn’t redundant or unhelpful information. 
• Clarity and consistency. Keep an eye out for any confusing copy and ensure your tone is uniform throughout the book.
• Try reading your draft aloud. You’d be surprised at how many errors, shifts in tone, or other things you’d like to change that you don’t notice while reading in your head. Go ahead and do a read-through of your draft out loud. 

8. Work with an editor

Once you’ve created the best draft you can, it’s time to hire an editor. As we mentioned, there are multiple types of book editing, so you’ll need to choose the one(s) that are best for you and your project when learning how to write a biography. 

For instance, you can work with a developmental editor who helps with big-picture stuff. Think book structure, organization, and overall storytelling. Or you might work with a line editor who focuses on grammar, spelling, punctuation, and the like. 

There are also specialized copy editors, content editors, fact-checkers, and more.

It’s in your best interest to do a substantial amount of research before choosing an editor since they’ll have a large impact on your book. Many editors are open to doing a paid trial so you can see their work before you sign them on for the entire book. 

9. Hire a book cover designer

Once you’ve worked with your editor(s) to finalize your book, it’s time to get your book ready to go out into the world. So the nest step in learning how to write a biography is to hire a book cover designer to create a cover that grabs readers’ attention (pssst: did you know that all SelfPublishing authors get done-for-you professional book design? Ask us about it !).

10. Get an ISBN 

The next step in learning how to write a biography is getting an ISBN number for your book – or an International Standard Book Number. It’s a unique way to identify your book and is critical for ordering, inventory tracking, and more. 

Bear in mind that each rendition of your book – regardless of when you publish them – will need their own ISBN numbers. So if you initially publish as a softcover and hardcover book and then decide to publish an ebook with the same exact content, you'll need 3 total ISBN numbers.

To get an ISBN, head to ISBN.org and follow the steps they provide.  Or reference our guide right here for step-by-step instructions (complete with photos) on how to get an ISBN number for self-published books.

11. Create a launch plan 

Now is the most exciting part of learning how to write a biography. It’s time to get your book out into the world! You’ll need to map out your plan, schedule events , finalize your pricing strategy, and more. 

And you can't just launch your book in a single day. When you go through all the work of learning how to write a biography, you want your book to succeed – and that requires a strategic marketing plan. Luckily, we have an entire guide to launching a book to help you figure it out. 

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• Open access
• Published: 03 June 2024

Evaluating competency-based medical education: a systematized review of current practices

• Nouf Sulaiman Alharbi 1 , 2 , 3  

BMC Medical Education volume  24 , Article number:  612 ( 2024 ) Cite this article

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Few published articles provide a comprehensive overview of the available evidence on the topic of evaluating competency-based medical education (CBME) curricula. The purpose of this review is therefore to synthesize the available evidence on the evaluation practices for competency-based curricula employed in schools and programs for undergraduate and postgraduate health professionals.

This systematized review was conducted following the systematic reviews approach with minor modifications to synthesize the findings of published studies that examined the evaluation of CBME undergraduate and postgraduate programs for health professionals.

Thirty-eight articles met the inclusion criteria and reported evaluation practices in CBME curricula from various countries and regions worldwide, such as Canada, China, Turkey, and West Africa. 57% of the evaluated programs were at the postgraduate level, and 71% were in the field of medicine. The results revealed variation in reporting evaluation practices, with numerous studies failing to clarify evaluations’ objectives, approaches, tools, and standards as well as how evaluations were reported and communicated. It was noted that questionnaires were the primary tool employed for evaluating programs, often combined with interviews or focus groups. Furthermore, the utilized evaluation standards considered the well-known competencies framework, specialized association guidelines, and accreditation criteria.

This review calls attention to the importance of ensuring that reports of evaluation experiences include certain essential elements of evaluation to better inform theory and practice.

Peer Review reports

Medical education worldwide is embracing the move toward outcome-based education (OBME) [ 1 , 2 ]. One of the most popular outcome-based approaches being widely adopted by medical schools worldwide is competency-based medical education (CBME) [ 3 ]. CBME considers competencies as the ultimate outcomes that should guide curriculum development at all steps or stages—that is, implementation, assessment, and evaluation [ 3 , 4 , 5 ]. To embrace CBME and prepare medical students for practice, medical educators usually utilize an organized national or international competency framework that describes the abilities that physicians must possess to meet the needs of patients and society. There are numerous global competency frameworks that reflect the characteristics of a competent doctor, for example, CanMEDS, Scottish Doctor, Medical School Projects, ACGME Outcome Project, the Netherlands National Framework, and Saudi Meds [ 1 , 6 , 7 , 8 ].

With the worldwide implementation of CBME and availability of different competency frameworks, educators are expected to evaluate various modifications made to existing medical curricula [ 9 , 10 ]. Such evaluation is intended to explore whether the program is operating as planned and its outcomes are achieved as intended in comparison to predetermined standards as well as to ensure improvement [ 11 , 12 , 13 ]. Furthermore, program evaluation revolves around two main concepts, that is, merit and worth [ 12 , 14 ]. In 1981, Guba and Lincoln explained that the merits of a program are intrinsic, implicit, and independent and do not refer to a specific context or application, while evaluating a program’s worth entails judging the value of any aspect of it in reference to a certain context or precise application [ 12 , 14 ].

To enable educators to determine the merits and worth of an educational program or curriculum, evaluation experts have proposed several models [ 14 , 15 ]. Evaluation models are guiding frameworks that demonstrate what appropriate evaluation looks like and detail how it should be designed and implemented [ 16 ]. Although almost all evaluation models focus on exploring whether a program attains its objectives, they vary in numerous aspects, including their evaluation philosophy, approaches, and the specific areas that they encompass [ 17 ].

It is essential that educators choose a suitable evaluation model when they implement CBME, as the right model will enable them to pinpoint [ 15 , 18 , 19 ]. In other words, a program helps identify areas of success, challenges, and opportunities for improvement in CBME implementation, leading to a deeper comprehension of CBME strategies and their effectiveness. Moreover, implementing CBME demands significant efforts and a wide range of financial, human, time, and infrastructure resources [ 20 ]. Thus, ensuring that these efforts and resources are well utilized to enhance educational and healthcare outcomes is crucial. In addition, evaluation provides valuable evidence for accreditation, quality assurance, policies, and guidelines. Otherwise put, it supports informed decision-making on many levels [ 21 ]. On another front, sharing evaluation results and being transparent about evaluation processes can enhance public trust in available programs, colleges, and universities [ 19 ]. However, deciding which evaluation model to adopt can be challenging [ 9 ].

Not only can it be difficult to select an appropriate model to evaluate a CBME program, but CBME evaluation itself has numerous challenges, particularly given the lack of a common definition or standardized description of what constitutes a CBME program [ 9 , 22 , 23 ]. The complexity of CBME further tangles evaluation efforts, given the multilayered nature of CBME’s activities and outcomes and the need to engage a wide variety of stakeholders [ 11 ]. Moreover, the scarcity and variable quality of reporting in studies focusing on the evaluation of CBME curricula exacerbate these challenges [ 24 ]. Furthermore, few published articles provide a comprehensive overview of available evidence on the topic.

This review is therefore designed to synthesize the findings of published studies that have reported CBME evaluation practices in undergraduate and postgraduate medical schools and programs. Its objective is to explore which CBME program evaluation practices have been reported in the literature by inspecting which evaluation objectives, models, tools, and standards were described in the included studies. In addition, the review inspects the results of evaluations and how they were shared. Thus, the review will serve in supporting educators to make evidence-based decisions when designing a CBME program. In addition, it will provide a useful resource for educators to embrace what was done right, learn from what was done wrong, improve many current evaluation practices, and compare different CBME interventions across various contexts.

Following a preliminary search within relevant journals for publications addressing evaluation practices utilized to assess competency-based curricula in medical education, the researcher used the PEO (participant, educational aspect, and outcomes) model to set and formulate the search question [ 24 ] as follows: participants : healthcare professionals and healthcare profession students; educational aspect : CBME curricula; outcome : program evaluation practices.

Next, the researcher created a clear plan for the review protocol. This review is classified as a systematized review rather than a systematic review [ 25 ]. While it does not meet the criteria for a systematic review because it relies on a single researcher and does not evaluate the quality of the studies included, it adheres to most of the steps outlined in the “Systematic Reviews in Medical Education: A Practical Approach: AMEE guide 94” [ 26 ]. Moreover, the researcher met with a medical educator with a strong background in CBME, an expert in review methods, and a librarian who is an expert in available databases and provided guidance and support for navigating such databases. Feedback was obtained from all three and used to finalize the review protocol. The protocol was followed to ensure that the research progressed in a consistent and systematized manner.

For this review, full-text articles published in peer-reviewed journals in English from 1 January 2000 to 31 December 2022 were searched within the following electronic data bases: PubMed, ERIC, Education Source, and CINHAL. The following terms were utilized to conduct the search: (Competency Based Medical Education OR Outcome Based Medical Education) AND (Evaluation OR assessment) AND (Undergraduate OR Postgraduate) AND (Implementing OR Performance OR Framework OR Program* OR Project OR Curriculum OR Outcome) (Additional file 1 ).

The researcher included articles that were published in English and reported evaluation practices for CBME or OBME curricula whether for undergraduate or postgraduate healthcare professionals. The researcher did not consider research reviews, commentaries, perspective articles, conference proceedings, and graduate theses in this review. In addition, articles that addressed students’ assessments rather than program evaluation were not included. Furthermore, articles that focused on teaching a particular skill (e.g., communication skills) or specific educational strategies (e.g., the effectiveness of Problem Based Learning) were excluded from this review.

To facilitate the screening of articles and ensure the process was properly documented, an online review software that streamlines the production of reviews (Covidence) was utilized, and all the lists of articles retrieved from the specified databases were uploaded to the tool website (available at www.covidence.org ). The tool set the screening to start with the titles and abstracts then to proceed to full texts. During these stages, the reasons for excluding an article were precisely noted. Moreover, the PRISMA diagram (available at http://www.prisma-statement.org/ ) was produced by Covidence to illustrate the process of screening and including articles in this review.

After the decision was made to include an article, a data extraction tool created for the purpose of this review was used (Additional file 2 ). Since the term “program evaluation practices” is general and does not clearly define the method or focus of the analysis involved in critiquing evaluation efforts, the analysis of available evaluation practices in this review was based on the Embedded Evaluation Model (EEM) provided by Giancola (2020) for educators to consider when embedding evaluations into educational program designs and development [ 27 ]. The EEM outlines several steps. In the first step, “Define,” educators are expected to build an understanding of the evaluated program, including its logic and context. In the second step, “Plan,” educators must establish the evaluation-specific objectives and questions and select the model or approach along with the methods or tools that will be utilized to achieve those objectives. The next step, “Implement and Analyze,” requires educators to determine how the data will be collected, analyzed, and managed. In the fourth step, “Interpret the Results,” educators are expected to derive insights from the results in terms of how the evaluation can help with resolving issues and improving the program as well as how the results should be communicated and employed. Finally, in the “Inform and Refine” step, educators should focus on applying the results to realize improvements to the program and promote accountability [ 27 ].

In addition to supporting the aim of the current review, the theoretical insights from Giancola (2020) help to ensure alignment with best practices in curriculum evaluation. Thus, for each article, the extraction tool collected the following information: the author, the publication year, the country and name of the institution that implemented the CBME curriculum, the aim and method of the article, the type of curriculum based on the health profession specialty (e.g., medicine, nursing), the level of the curriculum (postgraduate or undergraduate), the evaluation objective, the approach/model or tool, the evaluation standard, the evaluation results, and the sharing of the evaluation results. The extracted information points are essential to contextualize the evaluation and allow educators to make sense of it and adapt or adjust it to their own situations. Understanding the context of an evaluation is important considering the wide variety of available educational environments, the diversity of evaluators, and the differences in goals, modes, and benchmarks for evaluation, all of which influence how an evaluation is framed and conducted [ 27 ].

The author, publication year , and name and country of the institution that implemented the CBME curriculum provide identifiers for the original article and enable educators to seek further information about a study. The aim and method of the article were highlighted because they clarify the general context in which the evaluation was conducted. For example, this information can help educators understand whether an evaluation was carried out as a single action in response to a certain problem or was a phase or part of a larger project. The type of curriculum based on the health profession specialty (e.g., medicine, nursing) along with the level of the curriculum (postgraduate or undergraduate) have specific implications related to the nature of each specialty and the level of the competencies associated with the advancement of the program. All of the previously mentioned information is vital for educators to define and understand the program they are aiming to evaluate, which is the first step in the EEM. The evaluation objective , approach/model or tool , evaluation standard , evaluation results , and sharing of the evaluation results help to answer the research question of the current review by dissecting various aspects of the evaluation activities. In addition, the reporting of these aspects provides valuable insight into evaluation directives, plans, and execution. For educators, the evaluation objective usually clarifies the focus of the evaluation (e.g., how the program was implemented, the action done to execute education or outcomes of the program, and its effectiveness). The approach/model or tool of an evaluation is a core element of the design and implementation of the evaluation, as it determines the theoretical guidelines that underlie the evaluation and the practical steps for its execution. Based on the evaluation standard, which refers to the target used to compare the evidence or results of the evaluation, educators can judge the relevance of the evaluation to their own practices or activities. This information aligns with steps two and three of the EEM. The evaluation results are the results of the evaluation, which form the cornerstone for emerging solutions or future improvements. Finally, sharing the evaluation results , or communicating the evaluation, is a key part of handling the results and working toward their application. This information is aligned with steps four and five of the EEM.

Search results

Searching the identified databases revealed a total of 640 articles, and 183 total duplicates were removed. A total of 457 articles was considered for screening (371 PubMed, 13 ERIC, 23 Education Source, 50 CINHAL) (Fig.  1 ). Of those articles, 87 were retrieved for full-text screening. Ultimately, 38 studies met the inclusion criteria and were considered eligible to be included in the current review.

Flowchart illustrating the process of including articles in the review

Findings of the included studies

The 38 studies that met the inclusion criteria were published between 2010 and 2021, and the majority (15%; n  = 6) were published in 2019. The studies represented the following countries: Canada (37%, n  = 14) [ 10 , 11 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ], USA (27.5%, n  = 11) [ 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 ], Australia (5%, n  = 2) [ 51 , 52 ], China (5%, n  = 2) [ 53 , 54 ], Dutch Caribbean islands (2.5%, n  = 1) [ 55 ], Germany (2.5%, n  = 1) [ 56 ], Guatemala (2.5%, n  = 1) [ 57 ], Korea (2.5%, n  = 1) [ 58 ], the Netherlands (2.5%, n  = 1) [ 59 ], New Zealand (2.5%, n  = 1) [ 60 ], The Republic of Haiti (2.5%, n  = 1) [ 61 ], Turkey (2.5%, n  = 1) [ 62 ], and the region of West Africa (2.5%, n  = 1) [ 63 ].

According to the evidence synthesized from the included studies, most of the evaluation practices were reported in competency-based curricula that targeted the level of postgraduate professionals (57%, n  = 22) and were medical in nature (71%, n  = 27) (Fig.  2 ).

Curricula specialties in included articles

The findings showed that 37% ( n  = 14) of the articles did not report the precise objective of evaluating the curriculum. Moreover, 84% ( n  = 32) did not report the evaluation approach or model used to assess the described curricula. The approaches or models reported include Pawson’s model of realist program evaluation [ 37 ], theory-based evaluation approaches [ 10 ], Stufflebeam’s context, inputs, processes, and products (CIPP) model [ 62 ], the concerns-based adoption model, sensemaking and outcome harvesting [ 33 ]the CIPP model [ 48 ], and quality improvement (QI) for program and process improvement [ 50 ]. On the other hand, a wide variety of evaluation tools was reported including observations (3%, n  = 1) [ 28 ] surveys or questionnaires (58%, n  = 22) [ 10 , 28 , 29 , 31 , 34 , 35 , 36 , 38 , 39 , 41 , 42 , 45 , 49 , 50 , 51 , 52 , 53 , 55 , 56 , 58 , 59 , 63 ] interviews (16%, n  = 6) [ 10 , 28 , 37 , 41 , 47 , 62 ], focus groups (13%, n  = 5) [ 35 , 37 , 41 , 50 , 59 ], historical document review or analysis (8%, n  = 3) [ 10 , 29 , 33 ], educational activity assessment or analysis of the activity by separate reviewers (5%, n  = 2) [ 55 , 61 ], stakeholder discussions or reports about their inputs (5%, n  = 2) [ 43 , 44 ], curriculum mapping (3%, n  = 1) [ 32 ], feedback from external reviews from accrediting bodies (3%, n  = 1) [ 32 ], the Dundee Ready Education Environment Measure (DREEM) (3%, n  = 1) [ 56 ], and students’ or participants’ assessments (5%, n  = 2) [ 38 , 46 ].

Of the studies, 37% ( n  = 14) utilized multi methods [ 10 , 28 , 29 , 30 , 32 , 34 , 35 , 37 , 38 , 41 , 48 , 52 , 56 , 59 ]. Furthermore, 7.8% ( n  = 3) of the studies reported the nature of the tool, for example, quantitative or qualitative, without specifying the exact tool utilized [ 57 , 60 ]. Moreover, 63% ( n  = 24) of the studies included in this review did not report the evaluation standards applied while assessing the competency-based curricula addressed. Yet, those studies that reported their standards were stated in various ways as follows: some publications referred to the standards of specific specialized associations or societies, such as the American Academy of Family Physicians and College of Family Physicians Canada [ 61 ], Royal Australian and New Zealand College of Psychiatrists [ 60 ], and The American Association of Occupational Health Nurses [ 45 ]. Other publications utilized known competency frameworks as their standards, such as CanMED [ 36 , 37 , 59 ], or the competencies of the American Board of Surgery [ 43 ] Association of Canadian Faculties of Dentistry [ 31 ], Royal College of Ophthalmologists [ 52 ], The Florida Consortium for Geriatric Medical Education [ 50 ], or the Dutch Advisory Board for Postgraduate Curriculum Development for Medical Specialists [ 59 ]. Furthermore, many of the publications referred to accreditation standards, such as the Accreditation Standards of the Australian Medical Council [ 51 ], Competencies of Accreditation Council for Graduate Medical Education [ 43 ], Accreditation Body in the Competency-based Curriculum [ 32 ], and the Commission on Dental Accreditation of Canada [ 31 ]. All the publications included in the review reported the results of their evaluations.

Finally, the results revealed that almost half (52.6%, n  = 20) of the authors of the articles mentioned that they were publishing their experience with the intent of sharing lessons learned, yet they did not refer to any other means of sharing the results of their evaluations. In contrast, the other half did not mention any measures taken to communicate and share the evaluation results. Additional file 3 includes the characteristics and details of the data extracted from the studies included addressing evaluation practices in healthcare professionals’ education.

Evaluating a curriculum appropriately is important to ensure that the program is operating as intended [ 13 ]. The present study aimed to review the available literature on the evaluation practices of competency-based undergraduate and postgraduate health professionals’ schools and programs. This review inspected which evaluation objectives, models, tools, and standards were described as well as the results of evaluations and how the results were shared. The synthesized evidence indicates that most of the programs reporting evaluation practices were postgraduate-level medical programs. This focus on CMBE among postgraduate programs can be related to the fact that competency-based education is organized around the most critical competencies useful for health professionals after graduation. Thus, they are better judged at practice [ 64 , 65 , 66 ]. Moreover, although competency-based curricula were introduced to many health professions over 60 years ago, such as pharmacology and chiropractic therapy, within the medical field they have only evolved in the last decade [ 67 ].

Furthermore, the data revealed that there is a discrepancy in how evaluation practices were reported in the literature in terms of evaluation objectives, approaches/models, tools, standards, documenting of results, and communication plans. Each area will be further discussed in the following paragraphs considering the ten-task approach and embedded evaluation model [ 27 , 68 ]. Both guide evaluation as an important step in curriculum development in medical education, detail the evaluation process, and outline many important considerations from design to execution [ 27 , 68 ].

Evaluation is a crucial part of curriculum development, and it can serve many purposes, such as ensuring attaining educational objectives, identifying areas of improvement, improving decision-making, and assuring quality [ 13 , 27 ]. Consequently, when addressing evaluation, it is important for educators to start by explaining the logic of the curriculum by asking, for example, what the program’s outcomes are and whether it is designed for postgraduates or undergraduates [ 27 ]. Moreover, educators must be precise in setting evaluation objectives, which entails answering certain questions: who will use the evaluation data; how will the data be used at both the individual and program level; will the evaluation be summative or formative; and what evaluation questions must be answered [ 27 , 68 , 69 ] However, many of the studies included in this review did not clearly explain the context of the curricula or report the objectives of their evaluation endeavors; rather, they settled for clarifying the objectives of the study or of the publication itself. One reason for this is that evaluation and educational research have many similarities [ 13 ] Nevertheless, the distinction between the two should be clarified, as doing so will enable other medical educators to better understand and benefit from the evaluation experience shared. Moreover, since CBME outcomes are complicated and should be considered on many levels, evaluation plans should include a focus, level, and timeline. The focus of an evaluation can be educational, with outcomes relevant to learners, or clinical, with health outcomes relevant to patients. The level of an evaluation can be micro, meso, or macro, targeting an individual, a program, or a system, respectively. The timeline of an evaluation can investigate outcomes during the program, after the program (i.e., how well learners have put what they learned in a CBME program into practice), and in the long term (i.e., how well learners are doing as practicing physicians) [ 70 ].

Once the evaluation objectives are clearly identified and prioritized, it is logical to start considering the evaluation approach or model that is most appropriate to attain these objectives considering the available resources. In other words, evaluation design should be outlined [ 27 , 68 ]. The choice of an evaluation approach or model affects the accuracy of assessing certain tasks carried out by or to specific subjects in a particular setting [ 68 , 71 , 72 , 73 , 74 , 75 ] This accuracy is referred to as an evaluation’s internal validity. Yet, the external validity of an evaluation entails that the evaluation results are generalizable to other subjects and other settings [ 68 ]. Each model has its own strengths and weaknesses, which require careful examination when planning an evaluation [ 14 , 73 , 74 , 75 ]. Explaining and justifying why a particular evaluation approach was chosen for a specific curriculum can enrich the lessons learned from the evaluation and aid other educators. Furthermore, some of the available models were more utilized within various educational contexts than others [ 17 ] that calls for a continuous documentation of the evaluation approaches or models used to inform theory and practice. Considering the importance of reporting the approaches and models used, it is unfortunate that most of the publications did not indicate the approach/model they used for evaluation, which limits educators’ abilities to utilize the plans and build on their evidence.

Another critical task in the evaluation process is deciding on the measurement tool or instrument to be used. The tool choice will determine what data will be gathered and how they will be collected and analyzed [ 27 , 68 ]. Thus, the choice should consider the evaluation objective as well as the uses, strengths, and limitations of each tool. The evidence in this review indicates that questionnaires or surveys were the most utilized tools in evaluating competency-based curricula. This result can be attributed to the advantages of this method (for example, it is a convenient and economical tool that is easy to administer and analyze and can be utilized with many individuals) [ 27 , 68 ]. Nevertheless, it is important to highlight that questionnaires and surveys usually target attitudes and perceptions, which usually entails only a surface-level evaluation, according to the Kirkpatrick model [ 76 ]. The results also showed that in around 50% of the mixed-methods evaluations, the questionnaires were combined with another tool, such as interviews or focus groups. Understandably, utilizing an additional tool aims to deepen the level of the evaluation focus to include learning, behaviors, or results [ 76 ].

The evaluation evidence must be compared with a standard or target for educators to judge the program and make decisions [ 12 ]. Standards can be implicit or explicit, but they usually provide an understanding of what is ideal [ 12 ]. Worryingly, the results of this review revealed that many of the included studies did not clarify the standards they used to judge different CBME curricula. However, the studies that reported their standards used accreditation criteria or broad competencies frameworks, such as CanMeds, which consider the guides of specialized associations, such as family physicians or nursing. Although deciding what standard to use can be challenging to those designing and evaluating programs, evaluating without an understanding of the level of quality desired can lead to many complications and a waste of resources.

Communicating and reporting evaluation results are crucial to attaining the evaluation objectives [ 27 , 68 , 75 ]. Moreover, effective communication strategies have many important functions, such as providing decision makers with the necessary data to make an informed decision. Informing other stakeholders about the results is also important to achieve their support in implementing program changes and nourish a culture of quality [ 77 , 78 ]. Around half of the authors of studies included in this review indicated that they were publishing to share their own evaluation experiences, while the other half did not. Regardless, none of the studies shared or indicated how their results were reported and communicated, which is an important part of the evaluation cycle that should not be overlooked when sharing evaluation lessons within the scientific community. Reporting the results also ensures quality transformation by closing the evaluation cycle and encourages future engagement in evaluation among different stakeholders [ 78 , 79 , 80 ]. Moreover, the results of the evaluation should be shared publicly to contribute to increasing public trust in educational programs and their outcomes [ 19 , 69 ].

In summary, this review of evaluation practices within competency-based curricula for undergraduate and postgraduate health professional programs provides valuable insight into the current landscape. The results of the review show that most evaluation practices published pertain to postgraduate medical programs. In addition, by examining the objectives, models, tools, standards, and communication of evaluation results, this study exposes a discrepancy between the reported evaluation practices and identified evaluation elements. This discrepancy extends to the data that are reported, which makes it even more difficult to synthesize a holistic picture and definitively fulfill the aim of the review. Moreover, the issue of missing information poses serious challenges for educators who try to leverage existing knowledge to inform their curriculum development and improvement efforts, and it highlights the need for a more systematic and transparent approach to evaluation within CBME.

This review illustrates the importance of agreeing on the main evaluation elements to be reported when publishing a CBME evaluation. Establishing a shared understanding of these fundamental elements will give educators a framework for enhancing the practical utility of evaluation methodologies. In addition, educators and practitioners can ensure that the evaluation process yields more insightful outcomes and is better tailored to meet the needs of the educational context.

Data availability

The datasets used during the current study are available from the corresponding author on reasonable request.

Abbreviations

Outcome-Based Medical Education

Competency-Based Medical Education

Embedded Evaluation Model

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The author would like to acknowledge the support that Prof. Ahmad Alrumayyan and Dr. Emad Masuadi gave this research by reviewing its protocol and providing general feedback. In addition, the author would like to acknowledge Dr. Noof Albaz for the discussions about educational program evaluation, which contributed to improving the final version of this manuscript. Thanks, are also due to Mr. Mohammad Alsawadi for reviewing the utilized search terminologies and participating in the selection of appropriate databases and searching them to obtain the needed lists of articles.

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RNA-clique: a method for computing genetic distances from RNA-seq data

• Andrew C. Tapia 1 ,
• Jerzy W. Jaromczyk 1 ,
• Neil Moore 1 &
• Christopher L. Schardl 2  

BMC Bioinformatics volume  25 , Article number:  205 ( 2024 ) Cite this article

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Although RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated approach to compute genetic distances as well. Challenges to using mRNA sequences for computing genetic distances include the relatively high conservation of coding sequences and the presence of paralogous and, in some species, homeologous genes.

We developed a new computational method, RNA-clique, for calculating genetic distances using assembled RNA-seq data and assessed the efficacy of the method using biological and simulated data. The method employs reciprocal BLASTn followed by graph-based filtering to ensure that only orthologous genes are compared. Each vertex in the graph constructed for filtering represents a gene in a specific sample under comparison, and an edge connects a pair of vertices if the genes they represent are best matches for each other in their respective samples. The distance computation is a function of the BLAST alignment statistics and the constructed graph and incorporates only those genes that are present in some complete connected component of this graph. As a biological testbed we used RNA-seq data of tall fescue ( Lolium arundinaceum ), an allohexaploid plant ( \(2n = 14\text { Gb}\) ), and bluehead wrasse ( Thalassoma bifasciatum ), a teleost fish. RNA-clique reliably distinguished individual tall fescue plants by genotype and distinguished bluehead wrasse RNA-seq samples by individual. In tests with simulated RNA-seq data, the ground truth phylogeny was accurately recovered from the computed distances. Moreover, tests of the algorithm parameters indicated that, even with stringent filtering for orthologs, sufficient sequence data were retained for the distance computations. Although comparisons with an alternative method revealed that RNA-clique has relatively high time and memory requirements, the comparisons also showed that RNA-clique’s results were at least as reliable as the alternative’s for tall fescue data and were much more reliable for the bluehead wrasse data.

Results of this work indicate that RNA-clique works well as a way of deriving genetic distances from RNA-seq data, thus providing a methodological integration of functional and genetic diversity studies.

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In this paper, we describe and evaluate RNA-clique, a new approach for computing genetic distance matrices using only RNA-seq data. The method employs rigorous filtering for alignments of orthologous transcripts and uses as its input sets of RNA-seq samples from individuals being compared. The computed distance is a function of alignment statistics and a graph representing inferred orthologies between genes in the set of samples.

This work is key to an NSF-funded project in the Dimensions of Biodiversity program by providing a novel approach to integrate studies of functional diversity (in this case, RNA-seq) and genetic diversity. The technique is to be applied to plant population surveys to assess the interaction of plant genetic diversity to response to environmental variables and diverse symbiotic microbes. Typically, genetic distances are computed using whole, or, more often, partial genomic DNA sequences. Genomic DNA sequences are well-suited for such calculations—they allow us to detect precisely the differences in the genome sequences of two or more individuals. Unfortunately, obtaining genomic DNA sequences can also be costly, especially for organisms with large genomes such as vertebrates or vascular plants.

RNA-seq data are typically used for identifying and measuring expression levels of genes, and RNA-seq studies compare gene expression among multiple individuals or the same individual under different conditions. Since transcripts mostly reflect genomic DNA (aside from splicing and, rarely, RNA-editing), there is potential for using RNA-seq for computing genetic distances as well. A way of computing genetic distances using RNA-seq data would be convenient and economical for projects that need RNA-seq data for other purposes but do not need genomic DNA sequences for any other applications.

The method we propose takes a cautious approach by stringently filtering the sequences used for estimating distances. Thus, the way we use RNA-seq data is analogous to a reduced-representation genome sequencing [ 1 ]. Because we filter so much data and because most transcribed sequence is coding sequence, which is more highly conserved than other regions of the genome, a potential problem is retaining sufficient variation to discriminate between individuals. Hence, we test RNA-clique with multiple RNA-seq samples from each of four plants derived from one ecotype. The results indicated the feasibility of the approach described (Fig.  1 ).

PCoA plot for the distance matrix computed for a set of 16 RNA-seq samples. Each sample represents a clone of one of four genotypes of the grass tall fescue ( Lolium arundinaceum ). Genotypes are designated CTE27, CTE46, FATG4, and NTE. Presence ( \(+\) ) or absence (−) of endophyte (the symbiotic fungus Epichloë coenophiala ) was relevant to the original gene expression studies [ 2 ]

Existing tools for computing genetic distances using RNA-seq data alone are scarce. One possible option is the approach implemented in the Cnidaria software of Aflitos et al. [ 3 ]. Cnidaria can operate on either raw RNA-seq reads or assembled transcriptomes. The software uses a “ k -mer counting” approach. The simplest variation of the approach implemented in Cnidaria computes the distance between two samples as the Jaccard distance between the intersections of the sets of k -mers that appear in the sequences of the two samples with those that appear in at least two samples. (The Jaccard distance is taken to be 1 minus the Jaccard similarity. The Jaccard similarity is the number of elements in the sets’ intersection divided by the number of elements in the sets’ union. Since the similarity is a ratio of counts of elements,  k -mers, in this case, both the similarity and distance are dimensionless.)

Cnidaria computes distances without alignment—the input sequences are neither aligned to a reference genome nor to each other. The k -mer counting approach instead works on the principle that similar sequences share more k -mers. This means that orthologous sequences are not directly identified and compared, and we are concerned that results might be influenced by paralogous genes or, in the case of polyploid organisms, sets of homeologs. In this paper, we propose an approach in which orthologous sequences from RNA-seq data are identified and compared directly. We also compare RNA-clique with Cnidaria in terms of accuracy of results and resource usage (“ Distance tests and Resource usage tests ” sections).

RNA-clique utilizes a graph to represent orthology relationships among genes in the samples considered. The graph produced as part of our method bears some resemblance to those built for finding the Clusters of Orthologous Groups (COGs) of Tatusov et al. [ 4 ]. The graph of RNA-clique differs from that of COG in that the edges represent a bidirectional best match between genes (or a non-empty intersection between the top N best matches in both directions if the parameter \(N > 1\) ), whereas the edges in the COG graph may represent a unidirectional best match between proteins. Additionally, the eponymous subgraphs identified by the COG method consist of proteins inferred to be related as either orthologs or paralogs. In contrast, the “ideal” components of our method (described in “ Computing distances for multiple samples ” section) contain genes inferred to be related only as orthologs. COG does also identify some subgraphs presumed to be related as orthologs only—triangles (cliques with exactly three vertices) are “minimal COGs” in which each pair of proteins is orthologous. The ideal components of our method may be viewed as an of extension of this idea, since every ideal component is a clique. Furthermore, every ideal component is a COG (ignoring the distinction between genes and proteins), but not vice versa.

Although graphical representations of homology relationships are not new, their application to genetic distance computation with RNA-seq data is a contribution of the method described here. RNA-clique is designed to offer robustness in the presence of similar non-orthologous sequences. Unlike Cnidaria, RNA-clique explicitly identifies and compares orthologous transcripts using graph-based filtering. The graphs constructed by RNA-clique are also distinct from those of COG, which does not differentiate between orthologous and paralogous sequences. Identifying only orthologs allows RNA-clique to avoid overestimation of distances that could result from comparing paralogs or homeologs.

The purpose of the algorithm developed is to compute values that quantify the similarity or distance among two or more individuals using sequences of RNA transcripts from those individuals captured with RNA-seq. The output of the algorithm is a matrix of values between 0 and 1 for each pair of individuals under consideration; we refer to these values as “genetic distances.” The genetic distance for a pair of individuals is interpreted as the degree of dissimilarity between the individuals’ genomes. The output distance matrix is then useful for downstream analyses such as genotyping and phylogenetics—the distances may be used to distinguish individuals by genotype or infer evolutionary relationships. Requirements of the method were that it be applicable to RNA-seq data from organisms with large and complex genomes and that pairwise comparisons for genetic distance calculations be between orthologs only, and not involve comparisons of paralogs or homeologs (which occur in allopolyploid species).

We first describe in general terms how RNA-clique uses RNA-seq data to compute pairwise genetic distances in “ Distance computation algorithm ” section. Descriptions of the data with which we tested our method and the tests performed are presented in the following “ Data and Tests performed ” sections, respectively.

Distance computation algorithm

Assembling transcriptomes and selecting top genes.

Each “sample” is an RNA-seq dataset from an individual, and different samples may be from the same individual (biological replicates) or different individuals. As in gene expression studies, it is important to include biological replicates for each individual. The dataset from each sample is first assembled into a “transcriptome,” which consists of many assembled transcripts or isotigs and is partitioned into “isotig sets” (i.e., genes). Each isotig in an isotig set is assumed to represent a splice variant or an allelic variant from the same gene, and every isotig in a transcriptome is assumed to have an associated “ k -mer coverage”, which quantifies the amount of sequence from the input sequence reads that contributes to the assembled isotig. The k -mer coverage of a gene is defined as the maximum k -mer coverage among the isotigs of that gene, and, after assembly, the top n genes are identified based on k -mer coverage.

Computing distance for a pair of samples

Distance computation for a pair of samples is described below. The next subsection (“ Computing distances for multiple samples ” section) describes modifications to this basic approach for computing pairwise distances among more than two samples.

The top n genes (see “ Assembling transcriptomes and selecting top genes ” section) from both samples are used as the query and subject sequences in two BLASTn searches [ 5 , 6 ]. In the first search, the top n genes from the first sample are BLASTed against the top n genes from the second sample, and in the second search, the top n genes from the second sample are BLASTed against the top n genes from the first sample. The result of either BLAST search is a table (dataframe) representing high-scoring segment pairs (HSPs). Partial example results for forward and reverse HSPs are shown in Tables 1 and 2 . Note that although what we refer to as HSPs are commonly known as “hits,” in the terminology used by NCBI BLAST+, a hit may consist of one or more HSPs. Each HSP (i.e., each row in the table) specifies a query gene ID, query isotig ID, subject gene ID, subject isotig ID, bitscore, number of identical nucleotides, length, and gaps for the alignment. The bitscore measures the quality of an alignment in a way that does not depend on the size of the database (in this case, the subject transcriptome) and thus can be used to compare HSPs from different BLAST searches.

For both tables of HSPs, we select the top N HSPs for each query gene ID, where N is a positive integer and a configurable parameter of the algorithm. For this paper, we always use \(N = 1\) , though future work may explore other settings for this parameter. Results of selecting the top HSP of each query gene ID in the example are shown in Tables 3 and 4 .

Note that each row in both tables contains one gene ID from the first sample and one gene ID from the second sample. We rename the columns in both tables to reflect this. In the table for the first search, the query gene ID and subject gene ID become the sample 1 gene ID and sample 2 gene ID, respectively. In the table for the second search, the query gene ID and subject gene ID become the sample 2 gene ID and sample 1 gene ID, respectively. The example tables become Tables 5 and 6 after renaming.

Then, we filter both lists of HSPs to include only HSPs for which there is an HSP in both lists with the same sample 1 gene ID and sample 2 gene ID. The rows of the two tables are then merged into a single table. Note that the resulting table has at least two rows with the same sample 1 and sample 2 gene ID (Table 7 ).

We then select the row with highest bitscore for each pair of sample 1 and sample 2 IDs present in the concatenated table. The result is a table that maps each pair of sample 1 and sample 2 IDs to a single best bitscore for that pair of genes (Table 8 ). Note that we may keep multiple rows in the case of ties, but in such cases there will still be a unique best bitscore for each gene pair.

Finally, we select the row with highest bitscore for each sample 1 gene (Table 9 ). In the resulting dataframe, we interpret each row as the most likely ortholog in sample 2 of the gene in sample 1. Again, we may keep multiple rows in the case of ties. We refer to the resulting table as the gene matches table for the two samples.

The similarity between the two samples is then the sum of the number of identical nucleotides for all rows in the table divided by the sum of the difference between the alignment lengths and gaps for all rows in the table. Equivalently, in symbols, let \(\iota _i\) , \(\lambda _i\) , and \(\gamma _i\) represent the number of identical nucleotides, alignment length, and total gap length, respectively, for the i th row in the table. Then, the similarity S between the two samples is

The distance (or dissimilarity) D between the two samples is then defined as \(D = 1 - S\) . Since \(\iota _i\) , \(\lambda _i\) , and \(\gamma _i\) are counts of base pairs, the resulting similarity is a dimensionless ratio of base pairs.

Computing distances for multiple samples

Of course, one straightforward way to find pairwise distances for more than two samples would be to apply the above procedure for finding the distance between two samples for each possible pair of samples. Although such an approach would be simple, we anticipate that this approach would give “unfair” comparisons because the homologous genes used for the comparison differ among pairs of samples. To address potential fairness problems, we employ a graph-based algorithm to find a subset of orthologous genes shared by all samples.

We construct a graph, that is, a collection of vertices connected by edges, in which each vertex represents a gene in a particular sample; we can uniquely identify any vertex by its sample ID and gene ID. We draw an edge between two vertices if and only if the gene pair represented by the two vertices appears in the gene match table for the samples represented by the vertices. Intuitively, we can interpret an edge as indicating that the genes represented by its incident vertices are likely orthologs. We will refer to the resulting graph as the gene matches graph for the set of samples being considered. Figure  2 shows an example of a single connected component (a maximal set of vertices in which each pair of vertices is connected via a path of edges) from a gene matches graph.

Example component of a gene matches graph. Vertex labels show sample ID and gene ID, and vertex colors indicate sample ID

We can classify the components of the gene matches graph according to number of vertices. We define a small component as one with fewer vertices than there are samples, and, likewise, we define a large component as one with at least as many vertices as there are samples. Examples of small and large components for the case in which we have five samples are shown in Figs.  3 and 4 , respectively.

Examples of small components in the case of five samples

Examples of large components in the case of five samples

Additionally, we classify some components as ideal components . We define an ideal component as a component that is a complete subgraph (that is, a clique, a subgraph with an edge between every pair of vertices) with exactly one gene from each sample. Note that this definition implies that an ideal component must also be a large component because an ideal component has exactly as many vertices as there are samples. An example ideal component (for the case of five samples) is shown in Fig.  5 .

An example ideal component for five samples

Since no two genes from the same sample may be connected by an edge, any complete component with exactly as many vertices as there are samples must have exactly one gene from each sample. Hence, we can equivalently consider an ideal component to be any component that is a complete subgraph and has as many vertices as there are samples.

The intent is that the vertices of an ideal component should represent genes for which exactly one ortholog is identified in every sample. Thus, in computing distances for multiple samples, we use only those rows of gene match tables whose sample 1 and sample 2 genes appear in some ideal component of the gene matches graph. The result of filtering the example data from Table 9 in this way is shown in Table 10 .

Four sets of data were used for testing—one set of simulated transcriptomes and three sets of real data from past RNA-seq studies. Two of the datasets are from studies of the grass tall fescue ( Lolium arundinaceum ), and one is from a study of bluehead wrasse ( Thalassoma bifasciatum ), a teleost fish [ 7 ].

Tall fescue transcriptomes

Tall fescue, like many grasses (e.g., bread wheat) is “polyploid” due to an ancestry of hybridization between related species with intervening doubling of chromosome numbers. Having three diploid ancestors, tall fescue is hexaploid with a genome size estimated at \(6x = 2C = 14.4 \text { Gb}\) , over twice as large as the human genome [ 8 ]. The grass has a total of 42 chromosomes consisting of three homeologous sets, each with seven pairs of homologous chromosomes. For this reason, many genes—perhaps most—are represented by two or three homeologous sets, each having one or two (or at the population level, potentially more than two) homologous alleles [ 9 ]. Such polyploids are very common in certain plant families, and also in parthenogenic (or otherwise unisexual) animals and represent a special challenge to distinguish homologous versus homeologous gene relationships from mRNA or even genomic DNA sequence data. The tall fescue plant sources of the RNA-seq samples all derive from a single cultivar (‘Kentucky 31’), which in turn derives from a single ecotype—that is, all samples are descended from plants collected at the same location [ 2 , 10 ]. The species is an obligate outcrosser, so each original plant represents a unique genotype. In the prior studies, the plants were divided and propagated as multiple clones, and the 16-sample dataset derives from multiple clones of each of four genotypes (plants). In some cases, clones were treated to eliminate the symbiotic fungus (endophyte) Epichloë coenophiala , and endophyte status ( \(+\) or −) is tracked in our analysis.

The RNA-seq reads were publicly available on NCBI’s Sequence Read Archive (SRA) and were assembled using the rnaSPAdes mode of version 3.15.5 of the SPAdes assembler [ 11 ]. We expected distances between samples from the same set of clones to be much smaller (ideally, zero) than distances between samples in different sets. The information for the samples used is summarized in Table 11 .

rnaSPAdes may identify some transcripts as isoforms (or “isotigs”) of the same gene. Table 11 shows that the number of transcripts was much larger than the number of genes for each sample, but analyzing the frequency with which genes had one or more transcripts revealed that overwhelmingly most genes had very few isoforms (see Fig.  6 ).

A histogram showing the frequency of isoform counts for genes in the 16 tall fescue samples. Note that the y-axis uses a logarithmic scale

RNA-seq data of four other samples available on the SRA (Table 12 ) were also used only in a test of the effect of the parameter n on the number of large components and ideal components in the gene matches graph (“ Parameter tests ” section). These reads were likewise assembled into transcriptomes with rnaSPAdes 3.15.5.

Bluehead wrasse transcriptomes

RNA-seq data for the bluehead wrasse originated from a study of gene expression in two tissue types involved in functional sex change [ 7 ]. In bluehead wrasse, individuals can undergo sex change in response to social cues. Specifically, loss of the terminal phase (TP) male from a bluehead social group can cause females and smaller initial phase males to become TP males. The original study of Liu et al. utilized the sequences of RNA extracted from the gonads and brain (midbrain/forebrain) of 12 individuals captured from patch reefs near Key Largo, Florida. The latter tissue type was used because of its role in social decision making.

Like the tall fescue RNA-seq reads, the bluehead wrasse reads were available from the SRA. Each tissue sample from each individual has been assigned an accession in the NCBI BioSample database and a sample ID incorporating the a numeric identifier for the individual and a letter, “G” or “F”, denoting tissue type “gonad” or “midbrain/forebrain”, respectively (Table 13 ). Each sample was associated with two SRA experiments, and, in turn, each experiment was associated with a single SRA run [ 7 ]. Each SRA run was associated with paired-end RNA-seq reads. Using the rnaSPAdes mode of SPAdes 3.15.5, we assembled all RNA-seq reads associated with each sample into a single transcriptome for that sample. Reads from different SRA experiments were provided as separate libraries to SPAdes. One SRA experiment, SRX1176335, belonging to BioSample SAMN04009766, was associated with some additional reads that were treated as unpaired reads from the same library as the others belonging to the experiment.

Simulated transcriptomes

We used the birth-death model implemented in the DendroPy Python library to generate a random phylogenetic tree with 16 extant taxa [ 12 ]. For the birth-death model, we used a birth rate of 1 and a death rate of 0.5; the simulation was allowed to continue until there were exactly 16 extant taxa. The taxa were labeled using the default scheme in DendroPy—i.e., a taxon’s label is simply “T” followed by the index of the taxon. The tree resulting from this simulation is shown in Fig.  7 .

Using the same library, we generated random root state sequences for 50000 simulated transcripts. Transcript lengths were drawn randomly from the frequency distribution of transcript lengths for the 16 tall fescue transcriptomes—that is, the probability of choosing a transcript length was proportional to the number of transcripts with that length among the 16 tall fescue transcriptomes. For each position in a transcript, the base at that position was selected uniformly at random from the set of four DNA bases. (This is the default behavior in DendroPy’s nucleotide character evolution model.) The count of transcripts, 50000, was selected based on the results of the tests determining the effects of the parameter n on the number of ideal components, described in “ Parameter tests ” section.

We used the HKY85 model with an evolution rate of 0.01 to simulate evolution of these base transcripts over the previously generated phylogenetic tree. The value 0.01 was selected after it was determined that the initially selected value 0.1 was too high for BLAST to be able to identify orthologs. We obtained 50000 sets of orthologous transcripts, each containing one transcript per extant taxon.

A tree showing the “ground-truth” phylogeny for the 16 simulated transcriptomes

Tests performed

For all tests described in the following sections, the parameter N (the number of top HSPs to select for each query gene ID after the initial BLASTn searches in both directions) and the BLASTn e -value cutoff were fixed. The settings for these parameters were selected at the outset of testing. N was set to 1 to avoid matching non-orthologous genes, and the e -value cutoff was fixed at \(10^{-99}\) to ensure only homologous sequences were reported by BLASTn.

Parameter tests

A number of tests were performed to determine the effects of certain parameters on the gene matches graph. Specifically, we tested the effects of the parameter n (the number of genes selected) and the number of samples s on the number of large components and the number of ideal components. To accomplish this, we ran RNA-clique for various values of these parameters. For n , this was accomplished by directly setting this value of this parameter at the beginning of each run of RNA-clique. For s , we ran RNA-clique with various sized subsets of samples. In all tests, after each run of RNA-clique, the number of ideal components and large components in the gene matches graph was recorded.

For both the four-sample set and the 16-sample set, we tested the effect of varying parameter n , whereby we select the top n genes based on k -mer coverage (“ Assembling transcriptomes and selecting top genes ” section). We reasoned that genes with lower k -mer coverage are less likely to form ideal components, so that the number of ideal components should plateau at higher values of n . Greatly exceeding the number of genes required to reach that plateau would contribute to computation time with little or no gain of usable data for the subsequent distance comparisons. For the set of four tall fescue samples (Table 12 ), we ran RNA-clique with settings of the parameter n varying from 1000 to 306329 (the maximum number of genes among the four samples) in steps of 1000. For the set of 16 tall fescue samples (denoted \({\mathcal {F}}_{16}\) in this section; Table 11 ), we ran RNA-clique with a different sequence of parameter settings for n ; this sequence of settings are the x -axis coordinates of the points in Fig. 9 . We used this sequence for the set of 16 tall fescue samples because the sequence increases exponentially, has easily readable values, and has many fewer elements than the sequence used for the set of four tall fescue samples. The second of these properties was important to capture the relationship between n and the number of components of each type for small values of n , and the last property was important for saving time since running RNA-clique requires more time for larger sets of samples. For both sets of samples, and for each setting of n , the number of ideal components and large components in the gene matches graph resulting from running RNA-clique with that setting was recorded, and these pairs of values were plotted to illustrate the relationships between the variables.

For the set of 16 tall fescue samples, we also tested the effect of the number of samples (i.e., the parameter s ) on the counts of each type of component in the resulting gene matches graph by running RNA-clique with subsets of various size. Of course, for \(0< s < 16\) , we have more than one subset \({\mathcal {S}} \subset {\mathcal {F}}_{16}\) such that \(|{\mathcal {S}}| = s\) (that is, the number of elements in S is s ), and, moreover, for \(0< s < 15\) , there exist \({\mathcal {S}} \subset {\mathcal {F}}_{16}\) and \({\mathcal {T}} \subset {\mathcal {F}}_{16}\) such that \(|{\mathcal {S}}| = |{\mathcal {T}}| - 1 = s\) and \({\mathcal {S}} \not \subset {\mathcal {T}}\) . Hence, testing the effect of s on the component counts by independently selecting a random subset of size s from \({\mathcal {F}}_{16}\) for each value of s tested could be a flawed approach.

Instead of independently selecting random subsets of size s for each value of s , we first selected a permutation of the elements of \({\mathcal {F}}_{16}\) . We then used size s prefixes of the permutation—that is, the first s elements of the permutation—as our subsets of size s . Using such prefixes ensured that each subset tested was a superset of the last—that is, the subset used for \(s + 1\) was always a superset of the subset used for s . We used this prefix approach for our first set of sample count tests. Specifically, we applied the prefix approach for a permutation in which samples were sorted by genotype and a permutation in which samples were interleaved by genotype. For each of these tests, we used \(n = 50000\) ; the selection of this value for n was informed by the results of our tests with \({\mathcal {F}}_{16}\) observing the effect of n on component counts. For each prefix of both permutations, we ran RNA-clique, and, again, the number of large and ideal component counts were recorded. The purpose of the genotype-interleaved and genotype-ordered tests was to allow us to see whether the ideal component count drops more dramatically when a sample with a new genotype is added.

Prefix tests cannot address the problem that there are many possible subsets of s from \({\mathcal {F}}_{16}\) , and, hence, they cannot fully capture the relationship between number of samples and component counts. To address this shortcoming, subsets of \({\mathcal {F}}_{16}\) were sampled using a “fair” strategy that tries subsets selected uniformly at random from subsets of a specific size and tries to spend the same amount of time on each size (i.e., each value of s ). Since computing the gene matches graph generally takes more time for larger values of s , the fair strategy can initially try more subsets for smaller values of s . Since the number of combinations \({16 \atopwithdelims ()s}\) is increasing up to \(s = 8\) , this trend would not continue indefinitely; we would eventually exhaust all subsets for smaller values of s . For each subset \({\mathcal {S}}\) tried, we also varied values of n , but only the data for the case where \(n = 50000\) are reported and discussed here. For each subset of size s and each value of n , we ran RNA-clique and recorded the number of large and ideal components. For each subset of size s , we plotted the number of large components and ideal components to observe the relationship between s and the number of each kind of component. Using this fair sample count approach, we tested a total of 606 subsets of varying sizes.

Distance tests

For the set of 16 tall fescue samples, the set of 24 bluehead wrasse samples, and the set of 16 simulated transcriptomes, pairwise distance matrices were estimated. In all tests, we set the parameter \(n = 50000\) . We visualized the distance matrices as heatmaps and principal coordinates analysis (PCoA) plots, and phylogenetic analysis employed the neighbor-joining algorithm implemented in Biopython’s Phylo module [ 13 ].

Distance tests with Cnidaria

The distance tests for the set of 16 tall fescue samples and the set of 24 bluehead wrasse samples were repeated using the existing method Cnidaria instead of RNA-clique. Although Cnidaria can use either raw RNA-seq data or assembled transcriptomes, the distance tests were only performed using the assembled transcriptome mode. The distance test for the set of bluehead wrasse samples was also repeated using a hybrid approach in which the graph-based filtering of RNA-clique was first used to select those genes with orthologs in all samples, and the resulting orthologs were provided as input to Cnidaria.

Resource usage tests

We measured the time and memory usage of both RNA-clique and Cnidaria for varying values of n , s , and j , the number of parallel jobs, using the set of 16 tall fescue samples. Because Cnidaria may be executed on either raw RNA-seq reads or assembled transcriptomes, we tested both configurations. We also calculated the resource usage for assembling the 16 tall fescue sample transcriptomes; a fair comparison between Cnidaria in RNA-seq read mode with either method in transcriptome mode should account for time needed to assemble reads into transcriptomes. Since resource usage depends on the quantity of input data, the top n genes were selected at the beginning of both the RNA-clique and transcriptome-based Cnidaria tests. Although selection of the top n genes is not part of the original Cnidaria method, it was necessary to perform this step for Cnidaria to ensure a fair comparison. Since selection of the top n transcripts was necessary for both RNA-clique and one of the Cnidaria modes, we measured the selection step separately.

Time usage of a program was measured as the total wall-clock time elapsed during execution of the program. Memory usage was measured as the maximum sum resident set size (RSS) of the program’s process tree during execution. The RSS measures only virtual memory of the process that occupies space in RAM. The sum RSS for the process tree was polled every 0.1 s using the procpath utility.

Tests of resource usage for varying values of n used the full set of 16 tall fescue samples and set n to the same set of values used for the parameter n tests of the 16 tall fescue samples described in “ Parameter tests ” section. Since the top n genes cannot be computed for the unassembled RNA-seq reads, we did not run Cnidaria in RNA-seq mode for the parameter n resource usage tests. Tests of resource usage for varying values of s set \(n = 50000\) and used prefixes of size 4 to 16 of a random permutation of the set of 16 tall fescue samples—this strategy was borrowed from the prefix tests in the parameter tests described in “ Parameter tests ” section.

Both RNA-clique and Cnidaria can benefit from parallelism by performing computation in multiple threads or processes. RNA-clique can select top genes, build BLAST databases and execute BLASTn searches in parallel. Cnidaria can build its Jellyfish k -mer databases using multiple threads and can also split its data into multiple “pieces” which may be analyzed in parallel [ 14 ]. For the tests of resource usage as n and s varied, no parallelism was utilized. We separately tested the effect of the number of parallel jobs j (i.e., threads or processes) on resource usage for both methods. In these parallelism tests, the full set of 16 tall fescue samples was used with the fixed parameter setting \(n = 50000\) . The number of parallel jobs was varied from 1 to 16.

Resource usage tests for assembly were performed with SPAdes (version 3.15.5). SPAdes was allowed to allocate up to 120 GB of memory (though no assembly required that amount of memory). Although assembly can benefit from paralellism by running multiple assemblies in parallel or increasing the number of threads to use with SPAdes, neither option was utilized—only a single assembly was run at a time with one thread.

All tests assessing resource usage were performed on a computer with an AMD Ryzen 9 3950X CPU @ 2.2 GHz. The CPU had 16 physical cores, and frequency boosting up to 4.761 GHz was enabled. The computer had 117 GiB of RAM, and all data were read from and written to a PCIe 4.0 NVMe drive.

Large component and ideal component counts in the gene matches graph as the parameter n changes for the set of four tall fescue samples

Large component and ideal component counts in the gene matches graph as the parameter n changes for the set of 16 tall fescue samples

Plots displaying gene matches graph component counts for varying values of n in the set of four tall fescue samples and the set of 16 tall fescue samples are shown in Figs.  8 and 9 , respectively. Counts for both component types almost always increased with n . The rate of increase in ideal components increased for small values of n but decreased for large values of n until the counts of ideal components leveled off.

Large components and ideal components for prefixes of varying size s from a permutation of the 16 tall fescue samples in which samples are interleaved by genotype. Marker shapes denote the kind of component counted. Colors indicate the genotype of the last sample in the prefix

Large components and ideal components for prefixes of varying size s from a permutation of the 16 tall fescue samples in which samples are ordered by genotype. Marker shapes denote the kind of component counted. Colors indicate the genotype of the last sample in the prefix

For our genotype-ordered permutation, we found that adding a sample of a genotype not already present resulted in slightly greater decrease in ideal components than adding a sample with a genotype already present (Figs.  10 and 11 ).

Large component and ideal component counts for randomly selected subsets of size s . The opacity of each point shown for s samples is inversely proportional to the number of subsets of size s tested

Figure  12 shows component counts for many randomly selected subsets of each size s from the set of 16 tall fescue samples. The variances in both component types decreased as s increased. (Note that there were fewer results for larger values of s , both because \(\left( {\begin{array}{c}16\\ s\end{array}}\right)\) , 16 choose s, is decreasing for \(s > 8\) and because tests become more time consuming as s increases, requiring the “fair” strategy to attempt fewer tests for large s .)

Heatmap showing distance between samples in the set of 16 tall fescue samples. A scale mapping colors to distance values is shown on the right, and each cell of the heatmap is annotated with its distance expressed in ten thousandths. Note that no diagonal is shown for this matrix

The heatmap in Fig.  13 visualizes the distance matrix obtained for the set of 16 fescue samples. The samples are ordered by genotype and endophyte status on both axes. Distances measured ranged from \(0.0063\) to \(0.0092\) between samples.

Figure  1 visualizes the distance matrix for the 16 tall fescue samples using PCoA, in which samples of the same genotype formed clusters. Generally, the distance between two samples of the same genotype was less than the distance between two samples of different genotypes. Although three samples each from two of the genotypes either possessed or lacked endophyte, little or no effect of endophyte was observed in the PCoA plot. (No additional separation was evident in a 3-dimensional PCoA, not shown.)

Heatmap showing distance between samples in the set of 24 bluehead wrasse samples. A scale mapping colors to distance values is shown on the right, and each cell of the heatmap is annotated with its distance expressed in ten thousandths. Note that no diagonal is shown for this matrix

Figure 14 is a heatmap visualizing the distance matrix for the set of 24 bluehead wrasse samples. The samples are ordered first by individual and then by genotype. Distances among the bluehead wrasse samples ranged from 0.0026 to 0.0056. For most samples, the closest sample was the other sample from the same individual. The exceptions were the individual 52 and individual 114 samples. The individual 52 forebrain was closest to the individual 114 gonad, and vice versa. Likewise, the individual 52 gonad was closest to the individual 114 forebrain, and vice versa. This stark result suggested that our method detected sample labeling errors.

PCoA plot for the distance matrix of the 24 bluehead wrasse samples. Each point represents a sample, and color indicates the individual to which a sample was assigned in the SRA

The PCoA plot in Fig. 15 also visualizes the bluehead wrasse distance matrix. Although most samples were much closer to the other sample from the same individual than they were to any other sample, both individual 52 samples were closest to individual 114 samples, and both individual 114 samples were closest to individual 52 samples.

In the simulation study with 16 sets of sequences, the phylogenetic tree inferred from the calculated genetic distance matrix was topologically identical to the ground-truth tree in Fig.  7 .

Heatmap showing distances computed by Cnidaria for the set of 16 tall fescue samples. A scale mapping colors to distance values is shown on the right, and each cell of the heatmap is annotated with its distance expressed in hundredths

Figure 16 visualizes the distance matrix computed with Cnidaria for the set of 16 tall fescue samples. Distances ranged from 0.32 to 0.56. Although the range differed from that for the distances computed using RNA-clique (Fig. 13 ), the two distance matrices showed a similar pattern. The distances between samples of the same genotype were lower than those between samples of different genotype in both matrices.

PCoA plot for the distance matrix computed with Cnidaria for the 16 tall fescue samples. Color and shape indicate genotype, and fill indicates endophyte status

Figure 17 is a PCoA plot created from the matrix in Fig. 16 . As in the PCoA plot for the distance matrix computed using RNA-clique (Fig. 1 ), the samples clustered according to genotype, but the CTE27 and CTE46 clusters showed greater spread in the PCoA plot for the Cnidaria distance matrix.

Heatmap showing distances computed with Cnidaria for the set of bluehead wrasse samples. A scale is shown to the right, and cells are annotated with distance values expressed in hundredths

The heatmap in Fig. 18 visualizes the distance matrix calculated by Cnidaria for the set of 24 bluehead wrasse samples. Unlike the samples in Fig. 14 , those in Fig. 18 are ordered first by tissue and second by individual. Distances ranged from 0.32 to 0.62. Distances between samples of the same tissue type were generally estimated to be smaller than those between samples of different tiissue type. Although the lowest distances were not between samples from the same individual (as they were in Fig. 14 ), the values on the diagonal of the upper-right quadrant of the matrix (the submatrix consisting of distances between samples of different tissue type) showed that distances between samples from the same individual tended to be lower than distances between other pairs of samples from different tissue types.

PCoA plot for the distance matrix computed with Cnidaria for the 24 bluehead wrasse samples. Color and shape denote tissue type

Figure 19 is a PCoA plot for the Cnidaria bluehead wrasse distance matrix. All forebrain/midbrain samples formed a cluster, but the gonad samples were apparently spread out into multiple small clusters along the second principal component axis. Nevertheless, the gonad samples were near each other on the first axis, and all gonad samples were distant from the forebrain/midbrain cluster.

Heatmap showing distances computed with Cnidaria for the set of bluehead wrasse samples, after using RNA-clique to filter transcripts so that only genes in ideal components are included. A scale is shown to the right, and cells are annotated with distance values expressed in hundredths

PCoA plot for the distance matrix computed with Cnidaria for the 24 bluehead wrasse samples, after using RNA-clique to filter transcripts so that only genes in ideal components are included. Color denotes tissue type

The heatmap in Fig. 20 visualizes the distance matrix obtained with the combined RNA-clique and Cnidaria approach (using RNA-clique to select genes with orthologs in all samples) for the set of 24 bluehead wrasse samples. As in Fig. 18 , samples were sorted by tissue type and individual. Samples of the same tissue type were typically less distant than samples of different tissue types, but the difference between tissue types was less extreme than that observed in Fig. 18 . Moreover, for any given sample, the best match was often the other sample from the same individual. Figure 21 is a PCoA plot for the distance matrix computed for the 24 bluehead wrasse samples using the hybrid approach. Although clusters were denser in Fig. 19 than in Fig. 21 , there nevertheless remained a clear separation between forebrain/midbrain and gonad samples in the latter plot.

Execution times for running parts of various RNA-seq to distance matrix pipelines with varying numbers of samples and one parallel job. “Selection” is the script that selects the top \(n = 50000\) genes from each of the transcriptomes, which was executed before RNA-clique or Cnidaria in its assembled mode

Tests of the effect of sample count ( s ; Fig. 22 ) showed that, when only one parallel job was used, transcriptome assembly with SPAdes was the most time-consuming process in any of the pipelines for obtaining genetic distance matrices from RNA-seq data. The “Selection” process represented the selection of top n genes by k -mer coverage (“ Assembling transcriptomes and selecting top genes ” section), which was used in both the RNA-clique and assembled-mode Cnidaria pipelines. Times shown for RNA-clique and assembled-mode Cnidaria did not include the selection time. RNA-clique was the second or third most time-consuming process, depending on s . RNA-clique’s running time was approximately quadratic in s for the values of s tested; all other programs were roughly linear in s . Applying quadratic least-squares regression to the running times for RNA-clique produced a model ( \(r^2 = 0.9984\) ) of RNA-clique’s running time in seconds as a function of s , \(t_{\text {R}}(s) = 3263.683s^2 + 10541.403s + 8169.31\) . Likewise, applying linear least-squares regression to the running times for Cnidaria in assembled mode produced a model ( \(r^2 = 0.9995\) ) of Cnidaria’s running time in seconds as a function of s , \(t_{\text {C}}(s) = 414.866s + 672.287\) .

Maximum RSS for running parts of various pipelines with varying numbers of samples and one parallel job

Maximum RSS (memory usage) for varying values of s is shown in Fig. 23 . Although maximum RSS values for SPAdes assembly were recorded, the values were not included in the plot because they were much higher (as large as 14.66 GiB) than those for the other programs. Both modes of Cnidaria had a maximum RSS of 3.46 GiB, independent of the value of s . The selection process maximum RSS increased in steps due to differences in transcriptome size among the samples but never exceeded 135.75 MiB. Although memory usage for RNA-clique was lower than that for Cnidaria for \(s < 16\) , the maximum RSS of RNA-clique scaled roughly quadratically with s . Applying quadratic least-squares regression to the maximum RSS of RNA-clique produced a model ( \(r^2 = 0.9999\) ) of RNA-clique’s memory usage in MiB as a function of s , \(m_{\text {R}}(s) = 477.319s^2 + 1647.475s + 1480.589\) .

Execution times for running parts of the RNA-clique and assembled-mode Cnidaria pipelines with varying values for n , the number of top genes to select

Figure 24 shows the execution times of the selection process, RNA-clique, and Cnidaria for various settings of the parameter controlling the number of top genes to select by k -mer coverage, n . Selection required very little time—always less than 150 s. The rate of change in running times in Fig. 24 decreased with n , causing the running times to level off.

Maximum RSS for parts of the RNA-clique and assembled-mode Cnidaria pipelines with varying values for n , the number of top genes to select

Figure 25 shows the maximum RSS for the selection process, RNA-clique, and Cnidaria for varying values of n . As in the results measuring the effect of the number of samples s on maximum RSS, Cnidaria used no more than 3.46 GiB, regardless of parameter setting. The selection process maximum RSS increased slightly with n . The difference in memory usage for \(n = 226633\) (the maximum setting of n ) and for \(n = 1000\) was only 9.5 MiB, a \(7\%\) increase. The maximum RSS for RNA-clique likewise increases with n (and is generally much higher than the memory usage for selection), but the rate of change in maximum RSS for RNA-clique also decreases with n .

Execution times for parts of various RNA-seq to distance matrix pipelines with varying numbers of parallel jobs

Figure 26 shows results of the tests of the effect of parallelism (number of parallel jobs) on running times of the selection process, Cnidaria (both raw and assembled mode), and RNA-clique. All steps saw much improvement in running time with additional parallel jobs, especially RNA-clique, for which the duration decreased by 5.49 hours, \(88.3\%\) .

Maximum RSS for selection of top 50,000 genes with varying numbers of parallel jobs

For RNA-clique and Cnidaria, the maximum RSS increased very little (less than \(0.3 \%\) ) as the number of parallel jobs increased. The memory needed by the selection process increased much more (around \(1054 \%\) ) and increased roughly linearly with the number of parallel jobs. Only maximum RSS values for the selection process were included in Fig. 27 .

Results of the distance tests on plant, animal, and simulated testbeds suggest that the method proposed, RNA-clique, gives sufficiently accurate pairwise distances to distinguish RNA-seq samples according to genotype or individual. Moreover, results of the parameter tests suggest that, for sufficiently similar individuals, enough genes were retained in ideal components on which to base the genetic comparisons. In the tall fescue 16-sample testbed, selecting the top \(50000\) isotig sets by k -mer coverage gave more than \(5000\) ideal components on which to base the distance calculations, and even with a very narrow range of inferred distances from approximately 0.9– \(0.65\%\) , samples from each genotype clearly clustered in a 2D PCoA plot. Likewise, for the bluehead wrasse 24-sample testbed, the samples clustered by individual. Comparisons with an alternative method, Cnidaria, favor RNA-clique. Although Cnidaria may be more scalable than RNA-clique, results from RNA-clique appear more reliable.

The PCoA plot for the 16 tall fescue samples (shown in Fig.  1 ) shows four distant and non-overlapping clusters of individuals—one for each genotype—and the heatmap confirms that the distances between individuals of the same genotype are always relatively low compared to distances between individuals of different genotypes (Figure S1 ). Nevertheless, RNA-clique detects noise in the form of small differences for each pair of individuals with the same genotype. Although plants with the same genotype should be clones, there are no two individuals for which the similarity is computed to be exactly 1. Of course, it is possible some detected differences between clones reflect actual mutations, but differences may also stem from various sources of error. One class of error that could affect the accuracy of the distances are sequencing errors. To understand the effect of a sequencing error on the calculated distance, suppose we have a pair of transcripts, \(t_1\) and \(t_2\) , in one of the filtered gene matches tables, and, due to a sequencing error, \(t_1\) has an erroneous base \(b'\) where it should have b in the aligned region. Also, let c represent the corresponding base in \(t_2\) . (We assume there is no sequencing error at that position in \(t_2\) .) If \(b = c\) , then the erroneous base will appear as a spurious mismatch (a “false positive” difference). If instead \(b \ne c\) and \(b' = c\) , the erroneous base will appear as a spurious identity (a “false negative” difference). Finally, if \(b \ne c\) and \(b' \ne c\) , the erroneous base has no effect for that pair of transcripts—RNA-clique correctly counts it as a mismatch (a “true positive” difference).

Since the tall fescue samples are not haploid, homeologous transcripts may be a source of false differences. Specifically, if a genotype is heterozygous for some gene, but different alleles are captured in the transcriptomes of different clones, there is a risk that a transcript in one clone may erroneously be compared with a transcript that is not its true closest match in another clone. This kind of error would inflate the computed distances. Furthermore, even if all alleles are captured in the RNA-seq reads for all clones, there is a risk that the assembler may assemble reads belonging to different homeologs into a single isotig. If this happens inconsistently across different samples, the assembled transcripts for one clone may differ from those of another, and these differences could contribute to the computed distance between the clones. Such an assembly error could result in either overestimation or underestimation of distances.

The extent to which each of these factors contributes to the differences observed between samples of the same genotype may be explored in future research, and future refinements to RNA-clique may incorporate strategies for mitigating some factors. For example, sequencing and assembly errors may be detectable by consulting the original reads. Sequencing errors may appear as low-quality bases, and assembly errors could be detected by determining whether a detected difference between isotigs can be accounted for by an alternative assembly for one or both of the isotigs. In either case, differences identified as potentially spurious may be excluded from the distance calculation. Such refinements may be especially useful for very small or especially complex datasets. Although certain factors may lead to overestimation of distance in some circumstances, the results indicate that RNA-clique is effective at unambiguously grouping samples by genotype. The results of the tests with the set of 16 tall fescue samples also show that analyzing multiple samples per genotype is especially helpful for genotyping despite non-zero distances among clones since such distances are smaller than those between samples with different genotypes.

The results for the distance tests with the set of 24 bluehead wrasse samples show that RNA-clique can determine pairs of samples that belong to the same individual for at least 10 of the 12 individuals (20 of 24 samples). The method ostensibly gives some incorrect distances for individuals 52 and 114, but since RNA-clique identifies two pairs of closely related samples, both with one sample from each of the two individuals, we believe the error is likely caused by incorrect labeling of the samples. The labels for two samples of the same tissue type from individuals 52 and 114 may have been swapped in the SRA. That the swap is also evident in the results from Cnidaria (the upper-right quadrants of Figs. 18 and 20 ) suggest that the apparent mismatch is not a problem with RNA-clique. Furthermore, the results suggest that RNA-clique is a useful tool for verifying that RNA samples are correctly attributed to source individuals.

A comparison between the results obtained from RNA-clique and those obtained from Cnidaria shows that RNA-clique is as reliable or more reliable than Cnidaria, depending on the dataset. Results obtained by the two methods for the set of 16 tall fescue samples are very similar (though the scales of the distances are different). Nevertheless, the CTE27 and CTE46 clusters in the PCoA plot of the Cnidaria results (Fig. 17 ) are less dense than those in the corresponding plot of the RNA-clique results. Since we expect that samples of the same genotype should be identical, and, thus, should have no distance, this difference in the two plots may indicate that RNA-clique gives more accurate distances for these genotypes than does Cnidaria. In contrast, results obtained with the two methods for the set of 24 bluehead wrasse samples are markedly different. Almost all samples in the PCoA plot for RNA-clique (Fig. 15 ) form two-sample clusters according to individual as expected, but for Cnidaria, samples instead cluster according to tissue type (Fig. 19 ).

The Cnidaria method fails to identify the same genotypes in the bluehead wrasse dataset but succeeds with the tall fescue dataset. We considered as a possibility that the different tissues in the fish expressed sufficiently different sets of genes that most k -mers were specific to one or the other tissue. However, applying our ideal components strategy, which is meant to filter for true orthologs, does not qualitatively change the outcome. Another possibility is that, despite filtering for orthologs, the mRNA structures are sufficiently different due to, for example, alternative splicing [ 15 , 16 ]. An alternatively spliced intron would lead to a number of unique k -mers comparable to the k -mer length, and those may dominate the distance calculation. In contrast, the distance used in RNA-clique is designed to avoid any effect of such differences in mRNA structure, and, perhaps for this reason, succeeds with the fish RNA-seq testbed.

Tests assessing the effect of parameter n , the number of top genes selected at the beginning of our method, on the number of ideal components in the gene matches graph reveal that there are diminishing returns for selecting more genes past a certain point (for the set of four tall fescue samples, we judge around \(n = 20000\) ). For the set of 16 tall fescue samples, the difference between the count of ideal components at \(n = 50000\) and at the maximum value for n , \(n = 226633\) , was only \(216\) ; the increase in ideal components was only approximately \(3.5 \%\) . Therefore, for that study we judge \(50000\) genes to be adequate for the analysis, and this represents much savings in time compared to exhaustive analysis.

Still, it is apparent that the extent to which we benefit (in terms of ideal component count) from selecting more genes depends on the number and kinds of samples we have, among other factors. The ideal component count increases little past \(n = 50000\) for the set of 16 tall fescue samples, but there is still much that can be gained from selecting more than \(50000\) genes in the set of four tall fescue samples. Future work may focus on modeling relationships between the ideal component count and the parameters n and s . Such a model might be useful for selecting appropriate values of n for new data if we can extrapolate predicted ideal component counts for large values of n from counts for smaller values of n for which the gene matches graph is faster to build.

Tests assessing the effect of the parameter s on the component counts show that although we obtain fewer ideal components on average as we increase s for a given value of n , we typically lose fewer components with each successive sample. Of course, some individuals in the set of 16 tall fescue samples are expected to be much more closely related than others, and the genotype-interleaved tests suggest that the similarity of a newly added sample to those previously considered can affect the decrease in ideal components. As we might expect, sufficiently dissimilar samples can cause the component count to drop to zero; we observed this with simulated data when we used a mutation rate of \(0.1\) (data not shown) instead of the rate of \(0.01\) we used for the tests described here. For very distantly related pairs of samples, there may be no BLAST hits at all; if such a pair is present among the set of samples, the gene matches graph will have no ideal components. For other sets of samples, there may be BLAST hits for every pair, but there may still be insufficient hits to form an ideal component. The effect of the samples’ similarity on the number of ideal components we obtain is a possible topic of future research that could be explored with additional simulated data. Specifically, observing how the number of ideal components we obtain varies as we change mutation rate may provide some insight into the relationship between similarity and ideal component count.

Results from the resource usage tests show that Cnidaria scales better than RNA-clique in terms of memory and time requirements, but RNA-clique’s resource usage is nevertheless sufficiently small to make it a practical method for handling moderately large sets of samples. Extrapolation with the regression models of running time and memory usage for RNA-clique ( \(t_{\text {R}}\) and \(m_{\text {R}}\) , respectively; “ Resource usage tests ” section) predicts that the computer used for the resource usage tests should be able to run RNA-clique with sets containing as many as 94 samples ( \(m_{\text {R}}(94) \le 117 \times 2^{10} < m_{\text {R}}(95)\) ), which would take 9.21 days with a single parallel job, or 25.85 hours with 16 parallel jobs. Provided enough memory, RNA-clique should be able to handle in one week sets of up to 82 samples with one parallel job ( \(t_{\text {R}}(82) \le 60^2 \times 24 \times 7 < t_{\text {R}}(83)\) ) or up to 239 samples with 16 parallel jobs ( \((1 - 0.883) \times t_{\text {R}}(239) \le 60^2 \times 24 \times 7 < (1 - 0.883) \times t_{\text {R}}(240)\) ). To run RNA-clique with 82 samples would require 87.88 GiB, and to run RNA-clique with 239 samples would require 741.862 GiB. In contrast, Cnidaria should be able to handle very large sets of samples. The model for Cnidaria’s time usage ( \(t_{\text {C}}\) ; “ Resource usage tests ” section) suggests that Cnidaria should be able to handle in one week sets of up to 8747 samples with one parallel job ( \(t_{\text {C}}(8747) \le 60^2 \times 24 \times 7 < t_{\text {C}}(8748)\) ) or up to 15884 samples with 16 parallel jobs ( \((1 - 0.449) \times t_{\text {C}}(15884) \le 60^2 \times 24 \times 7 < (1 - 0.449) \times t_{\text {C}}(15885)\) ).

Since RNA-clique appears to give more accurate results than Cnidaria, we believe RNA-clique should be the preferred method despite the latter method’s superior scalability. Still, the sources of error in Cnidaria’s distance matrix for the bluehead wrasse data are not fully known. Future work could focus on identifying these sources of error with the goal of improving the method or determining on which datasets Cnidaria can be used reliably.

Future work

In addition to the possible future directions mentioned above, we would also like to further test our method using more synthetic data designed to simulate a wider range of scenarios. Since many commonly studied organisms are diploid or polyploid, we are especially interested in simulating hybridization of closely related taxa to investigate the effect that the presence of homeologs has on the accuracy of the calculated distances and correct matching of orthologs.

Although we think using simulated data would allow us to study more precisely how the number of samples s and samples’ relatedness affect ideal component count, we also plan to test this approach on data for larger—and perhaps more diverse—sets of organisms. Such tests may better inform us of the practical limitations of the method proposed.

Finally, we would like to explore the mathematical properties of the distances we compute and possibly refine our method based on our findings. Although we often describe the quantities we compute for each pair of samples as “distances”, we have not proven that our distance, as a function of a pair of transcriptomes, satisfies all properties one expects to hold for a distance metric. In particular, we believe the distance we compute may not necessarily be symmetric; i.e., computing the distance between sample A and sample B may not give the same result as computing the distance between sample B and sample A . We also have not proved that the triangle inequality holds; we do not know that the sum of distances from A to B and B to C are never less than the distance from A to C . We have yet to observe a counterexample for either property, but we have so far only tested RNA-clique on “realistic” data that may not be likely to explore cases in which these properties would be violated.

Despite the aggressive filtering applied throughout the proposed method and the inherent limitations of considering only transcribed sequences, we find the approach described in this paper satisfactorily measures differences among closely related individuals in tests with both real and simulated data. Although the amount of data remaining after filtering depends on the number of samples used and the relatedness of those samples, the filtering process retains enough data to get useful pairwise distances for the testbed examples, provided that we set the parameter n sufficiently high.

The method has been tested on a hexaploid grass, a vertebrate animal, and simulated data with satisfactory results that suggest RNA-clique may be equipped to handle other organisms of practical interest that possess similarly complex genomes, including humans and many other animals. The method is not without some limitations. Applying RNA-clique to simulated data generated using a high mutation rate (data not shown) revealed that samples may be too distantly related to compare with this method. Likewise, there may be some datasets where samples are too closely related to distinguish above the noise. Comparisons for time and memory usage for RNA-clique versus Cnidaria suggests that the latter may sometimes be preferable for very large sets of samples with the caveat that Cnidaria may not produce as accurate results depending on the nature of the sample sets. Therefore, if the data set is too large for RNA-clique, it may be a useful strategy to check results of Cnidaria against results of RNA-clique on a subset of samples.

Although further work is required to determine how distantly or closely related the samples may be in order for RNA-clique to be practical, we nevertheless think that the results of our tests indicate the method proposed here is useful for generating pairwise distance matrices based on multiple RNA-seq datasets for a wide range of organisms and experiments.

Data availability

The tall fescue RNA-seq data analyzed during the current study are available from the NCBI Sequence Read Archive at https://www.ncbi.nlm.nih.gov/sra using the accessions provided in Tables 11 and 12 . The bluehead wrasse data are likewise available from the Sequence Read Archive and may be found using the BioSample accessions provided in Table 13 The simulated transcriptomes analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

We acknowledge Dr. Padmaja Nagabhyru for providing advice and suggesting and providing the tall fescue datasets used in this work.

This work was supported by U.S. National Science Foundation grant DEB 2030225, U.S. Department of Agriculture National Institute of Food and Agriculture Multi-state project 7003566, and the Harry E. Wheeler endowment to the University of Kentucky.

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ACT, JWJ, NM, and CLS contributed to the conceptualization of the methods used and reviewed and edited the manuscript. ACT prepared the manuscript and wrote new software used.

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Tapia, A.C., Jaromczyk, J.W., Moore, N. et al. RNA-clique: a method for computing genetic distances from RNA-seq data. BMC Bioinformatics 25 , 205 (2024). https://doi.org/10.1186/s12859-024-05811-9

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DOI : https://doi.org/10.1186/s12859-024-05811-9

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