WoW Woman in BioTech I Molly Gibson, Ph.D., co-founder and Chief Strategy and Innovation Officer of Generate Biomedicines

Dr. Molly Gibson serves as co-founder and chief strategy and chief innovation officer of Generate Biomedicines, a machine-learning-powered biotech in Cambridge, Mass., where she oversees corporate strategy as well as platform and data strategy. She is also a senior principal at Flagship Pioneering, working as part of a venture-creation team to found and grow companies at the intersection of biology and machine learning. 

Her work has resulted in multiple pending patents and publications, including articles in Science and Nature, as well as several honors, including Endpoints News' 20 under 40 biopharma list in 2020 and Business Insiders’ list of 12 young serial entrepreneurs building the next generation of biotech startups in 2021. 

As a graduate student at Washington University in Saint Louis, she developed a curriculum for incoming Ph.D. biology students to learn basic programming and analysis skills and also stewarded an all-volunteer program for underrepresented minorities in scientific careers, which reached approximately 2,000 students per year under her tenure. She continues to fulfill her interest in teaching and mentoring by lecturing at Harvard University and its medical school.

Generate Biomedicines is the first drug generation company, pioneering a machine learning-powered generative biology platform with the ability to generate new drugs on demand across a wide range of biologic modalities. The platform can drastically improve the speed at which targets and therapeutics are identified and validated, the specificity of target engagement by generated proteins, and the cost of identifying and developing clinical candidates. The company’s platform represents a potentially fundamental shift in what’s possible in the field of therapeutic development, addressing key challenges of drug discovery and drastically expanding the available search space for novel biomedicines.


Tell us a bit about your background and your projects so far.

I’ve always been passionate about engineering and math and learning how things work. I am formally trained as a computer scientist, and I love how logic and math underpin everything about how we interact with computational systems. I began my career as a software engineer building flight simulators for the F-15 at Boeing. I was constantly tasked with new challenges on how to simulate the feeling of flying as close to reality as possible. In many ways, it was magical; in other ways, I felt I was missing the chance to make an impact. I was constantly thinking back to my biology classes in grad school and realizing how, just like computers, math and statistics underly almost every biological process. If that’s true, we could apply the same type of engineering principles I was trained to do not only to airplanes but to living cells and biology too.

I pursued a Ph.D. in Computational & Systems Biology at Washington University in Saint Louis, where my passion for innovating at the intersection of biology and machine learning began. I soon joined the venture creation team at Flagship Pioneering in Boston, the firm that founded Moderna, to found and grow new biotechnology companies. While there, I co-founded Generate Biomedicines in 2018 to bring the revolution of Generative AI (the technology that underpins things like ChatGPT and DALL-E) to bear on some of the most long-standing and pressing challenges in drug discovery and development. 

How did you get into this industry? Has it been an easy industry to get into or have you had many challenges?

Following graduate school, I knew I wanted to find ways to make an impact and get as close to the end goal as possible, so I began looking for opportunities in biotech. Instead of applying for open jobs, I shared my CV with anyone who would look at it and asked for more connections along the way. I found that the most interesting jobs weren’t the ones that were posted online, and I continued to network until I found the role that was most interesting to me. I talked to a wide variety of companies, from Google to Genentech, but I ultimately joined a small start-up in Boston as one of the first 10 employees. Although unaware at the time, it began my passion for company building, entrepreneurship, and applying ML in new and innovative ways to solve some of society’s most pressing challenges.   

After almost two years at my first start-up, I joined the venture creation team that founded it at Flagship Pioneering. It was an opportunity to join a team of scientist entrepreneurs who are constantly exploring, founding, and building the next generation of first-in-class bioplatform companies.

The biotech industry is not an easy one to navigate, and had I been set on a specific or defined career path, it would have been much harder to get into. My approach was to take the most interesting opportunity at the moment and do everything I could to crush it. Although I have generally been successful, the road has been windy with many ups, downs, and left turns. Through those experiences that knocked me back, I’ve learned and grown the most.

How long did it take you to be where you are now? What was the biggest obstacle? What are the challenges of being in the industry you are in? 

Since graduating in 2015, I’ve often felt the pressures of being a young female in a largely male-dominated industry, especially while starting a family. I’ve been lucky to be supported by mentors and work for people who believe in the value of strong families actually enhancing rather than distracting from work. I’ve never been more efficient with time than when I became a mom! Simultaneously, we need to talk more about the challenges to help young women exploring careers in the field understand that what they are experiencing is normal. Being more open about our aspirations, and challenges and balancing family with work will allow more young women to continue to rise into positions of leadership in entrepreneurship and the biotech field. 

What are your biggest achievements to date?

As a scientist entrepreneur at Flagship Pioneering and part of a venture-creation team, I have contributed to the launch and growth of Generate Biomedicines, Tessera Therapeutics, and Cobalt Biomedicines, which is currently part of Sana Biotechnology.

Overall, I am most proud of founding, building, and growing Generate Biomedicines for the past four years. At Generate, we are leading the application of Generative AI, not to images or text, but to the physical machines that drive almost everything that happens in biology – proteins. I am more confident than ever that the future of drug development will be generated medicines versus discovered. I am constantly humbled by the tenacity, brilliance, and humility of the team at Generate Biomedicines to make that future a reality. I share more about our vision at Generate here

What are the projects you are currently working on?

At Generate, we’re focused on pioneering generative biology to revolutionize drug development. Instead of “discovering” treatments as is typically done in biotech today, we’ll be able to create them, specifically proteins, purpose-built for the patient’s need or disease. We’ll be able to engineer better medications with, we hope, few side effects more quickly, which we believe will expand access to much-needed treatments worldwide.

Through my work at Flagship Pioneering, I’m also working on building other innovative companies at the intersection of AI and science. I believe AI has the power to change the world for good, and I’m most passionate about building companies that have the potential to disrupt entire industries and ultimately solve some of humanity's most pressing problems, including climate change and affordable health care.

Is the #WomenInTech movement important to you and if yes, why?

Education is essential to bringing more women into STEM and tech in particular. As an undergrad, I was fortunate to have a professor and, ultimately, a mentor who introduced me to research and offered me a role in his lab. Previously I had no idea what “research” was, and the concept of graduate school or a Ph.D. was completely foreign. Without this opportunity, I’d never have been accepted into graduate school and be living an alternative career. Even after that experience, my imposter syndrome was flowing strongly. I remember a conversation with him, deciding if I should go to graduate school. I was, of course, looking around the room at the sea of confident male colleagues and drawing every comparison I could to help him see why I wasn’t cut out for a Ph.D. I’ll never forget his face of complete shock and disbelief when he fully grasped how I felt. At that moment, I began to feel his confidence in me was much deeper than a mentor trying to encourage his student, and maybe I needed to challenge my perceptions.   

We must provide these opportunities for young women and girls at an earlier age to be exposed to all types of careers in technology, challenge perceptions that have been seeded by society, and allow them to realize – and truly internalize - their full potential. 

What will be the key trends in your industry in the next five years and where do you see them heading?

Over the next few years, AI and machine learning will play an even more critical role in biotech. AI will become a staple in the origination of new medicines, and the differentiating factors for new biotechs in the drug discovery space will not be IF they use AI and machine learning, but HOW they use it and the culture they build to foster an integrated AI-first team. 

More importantly, this evolution will lead to fewer molecules will be discovered using today’s trial-and-error approach. AI-generated molecules will outnumber them due to their many advantages. These new treatments will be produced more quickly and efficiently with fewer side effects, ultimately increasing access to patients around the globe.

What is the most important piece of advice you could give to anyone who wants to start a career in this industry?

Think about what’s really important to you and what you value. Once you’ve figured out your true north, use it as your guide, remain faithful to it, and stay humble.

Who are three inspirational women in your respective industry you admire?

Since my first conversation with Frances Arnold, Ph.D. (Nobel Laureate and Professor at CalTech), I’ve been inspired by her story and persistence in a scientific discipline that was even more hostile and challenging for rising women at the start of her career. Frances signed up to be on the board of Generate Biomedicines when the company only had four people, little data, and a bold vision. She, fortunately, shared that vision and signed up to take this wild ride with us for the past four years! 

More recently, I’ve been inspired by our own Chief Medical Officer at Generate, Alex Snyder, M.D. As I’ve gotten to know her, I’ve come to realize she has the brilliance, humility, and unwavering grit required to tackle the hardest challenges in drug development. She’s fiercely dedicated to patients and her teammates, balancing that with raising two wonderful daughters along the way.  

From a distance, I’ve always admired Daphne Koller, Ph.D. and Founder/CEO of Insitro. She has built a broadly respected reputation in machine learning and has put out transformative visions for how AI will transform biology and bold perspectives on what it takes to get there – and as an entrepreneur, she is working tirelessly to make that vision a reality.  

Find out more about Generate Biomedicines on their website.

Follow Generate Biomedicines on LinkedIn and Twitter.


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This interview was conducted by Marija Butkovic, Digital Marketing and PR strategist, founder, and CEO of Women of Wearables. She regularly writes and speaks on topics of wearable tech, fashion tech, IoT, entrepreneurship, and diversity. Follow Marija on Twitter @MarijaButkovic and read her stories for Forbes here.

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