Postdocs
Noor Youssef
Noor's background is in math and biology and she has been working at the interface of these two disciplines since her undergrad. Her PhD work was on understanding how epistasis shapes protein evolution and how it might bias our inference of evolutionary parameters. She's looking forward to joining the Marks' lab in the Fall and decoding more of nature's hidden messages.
embedding: proteins, lifting, Halifax, strawberry licorice, kind, thoughtful, hard working, leader, fitness, chicken chip, friendly, Canadian!, dog, chill, warm, greyhound, calm, work-out buddy, quick, polite, Blake, genuine, confident
Pascal Notin
Pascal is leading the subunit focusing on protein engineering in the Marks lab. He is passionate about the transformative potential of AI to support the design of novel biomolecules that address problems in medicine, new material and sustainability. He did his PhD in the Oxford Applied & Theoretical Machine Learning (OATML) group where he developed deep generative models for applications in protein fitness modeling, viral escape prediction and protein design. Before returning to academia, he was a senior manager at McKinsey & Company, advising clients in the healthcare and pharmaceutical industries on AI and analytics strategy.
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Aaron Kollasch
Aaron is a postdoc in the Marks lab. He is interested in learning from observed sequences to design new biomolecules.
embedding: wavenet, 'I have a script for that', BBS, tuxedo cat, computers, NLP, protiens, helpful, knowledgeable, ML, calm, coding, night owl, Hera, Colorado, unix expert, O2 whisperer, sweet, composed, stoic, gentle
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Graduate Students
Rose Orenbuch, Systems, Synthetic, and Quantitative Biology
Coming from a background in computer science and biology, Rose is a Systems Biology graduate student in the Marks Lab.
embedding: genetic diseases, baking, cooking, CAKE DAY, computer science, talented, art, drawing, lifting, bad ass, cool shades, clever, spy, organized, nyt reader, artsy, calm, competent, artistic, out-spoken, direct, amazing cook, funny, math
Sam Berry, Biophysics
Sam is a Biophysics PhD student interested in relating protein structure and evolution. When not daydreaming about proteins, he likes to write, escape to the mountains, and spend quality time with his cat, Linus Pawling.
embedding: cool hair, wet lab, co-advised, membrane, biochemistry, ions, Manganese, glasses, cat, GPCR, enthusiastic, fun, curious, transporters, berries, structures, actually does experiments, genuinely likes science, funny, friendly
Sarah Gurev, Electrical Engineering and Computer Science - MIT
Sarah Gurev is a PhD student at MIT in EECS. She studied computer science as an undergraduate at Stanford, where she focused on projects in structural biology and healthcare. She enjoys reading in her free time.
embedding: calm, structured, Stanford, virus, puppy, sweet, dog lover, board gamer, bananagrams, outgoing, night owl, friendly, outgoing, MIT, Wall-e, Sacramento, California, laugh, competent, engaged, quiet, focused, genuine, funny
Courtney Shearer, Systems, Synthetic, and Quantitative Biology
Courtney explored computer science and genomics at Clemson University, Zymergen, and CRISPRtx before joining the Systems Biology Program at Harvard. She is excited to continue research on machine learning for genomics and improve approaches for experimental design for high throughput assays.
embedding: runner, biology, sugar, southern, colorful, python, coder, South Carolina, hungry mode, bioinformatics, hardcore, cool socks, bio, python, awesome, loafers, fashionable, espresso, vintage, coffee, artisan, persistent, focused, kind, animated, inquisItive, technological, fast
Ruben Weitzman, Jointly Advised with Yarin Gal, University of Oxford
Ruben is a PhD student in machine learning and computational biology working on protein sequence generative models and bayesian optimisation for sequence design with Prof Debbie Marks and Prof. Yarin Gal at the University of Oxford
Fiona Qu, Systems, Synthetic, and Quantitative Biology
Fiona studied Chemistry at the University of Illinois where she did protein biochemistry and antibiotic drug discovery. After a few years in industry as a protein engineer, she joined the Systems Biology program at Harvard where she’s excited to dive further into protein design and synthetic biology. Outside of science, she likes playing bassoon in community orchestras, making functional pottery, and knitting/crocheting.
Sam Huang, Biomedical Informatics Master Student
Sam is a graduate student in Master of Biomedical Informatics at Harvard Medical School. He obtained his BS in computer science and statistics from Northwestern. His research interest lies at the intersection of machine learning and drug design. Beyond the lab, he enjoys cooking and exploring the finest food in the town.
Abigail Jackson, Medical Engineering and Medical Physics (bioengineerings concentration) - Harvard-MIT Health Sciences and Technology program
Abigail is a Ph.D. student in the Harvard-MIT HST program in the Marks Lab. She previously graduated from the University of Southern California with degrees in Computational Neuroscience and Philosophy and conducted research in structural virology and immunology at The Scripps Research Institute under Andrew Ward. Abigail is interested in studying how viral evolution can inform gene therapy and vaccine design.
Tomás Lio Grudny, Computational Systems Biology - MIT
Tomás is a student in the Computational and Systems Biology PhD Program at MIT. He previously worked on various aspects of microbial ecology and evolution as an RA at ETH Zurich and master’s student at the University of Copenhagen. He is interested in applying AI methods for understanding and predicting viral evolution
Rotating Students
Murphy Angelo, Biological & Biomedical Sciences
Murphy is a Biological & Biomedical Sciences Ph.D. student. Previously, he studied computer science at Northwestern, explored the game industry, and then completed a post-bac at Indiana University School of Medicine. He’s interested in using molecular modeling and evolution to understand and exploit the behavior of complex systems.
Embedding: food, Hank, music, matcha, biophysics, game dev, wildcat, mental health advocate, kimchi, drug discovery
Visiting Scholars
Leo Chen, Duke University
Leo is a master's student in Biomedical Engineering at Duke University. His research focuses on protein design, causal inference, and microbiology. Outside the lab, he enjoys exploring culinary delights and watching MMA.
Undergraduates
Aarushi Mehrotra, MIT
Aarushi is an undergrad at MIT double majoring in Bioengineering and Computer Science. Her research focuses on using evolutionary viral influenza sequences to computationally predict flu vaccines for every season. Outside of academics, you will find her hanging out with her friends, probably laughing at something really funny that one of them said.
Erik Xie, MIT
Erik is an MIT undergrad working towards a degree in bioengineering and computer science. His interest in genomics has prompted him to explore bioinformatics and machine learning. Outside of academics, he plays drums in a fusion band but also loves black metal.
Hannah Boen, Harvard University
Hannah is a senior at Harvard studying Applied Math & Computer Science. Her research focuses on statistical analysis of rare variants using evolutionary generative sequence models. Outside of lab, she enjoys knitting/crocheting and music.
Seojean Kim, Wellesley College
Seojean is a student at Wellesley College studying chemistry and computer science. Her primary research interests lie in harnessing the power of computation in biological and chemical research. In her free time, she often spends it dancing, hiking with her mother, and crocheting.
Aoi Otani, Harvard University
Aoi is a senior at Harvard studying Integrative Biology & Computer Science. Her research focuses on MSA clustering based on protein language model embeddings for improved fitness prediction. Outside of academics, she enjoys trying new restaurants, art, and watching movies.
Staff
Jake Reardon, Project Manager
Jake has been a project manager for various university and healthcare systems in the US and Europe since 2016. He has a background in Dramatic Art, Chemistry, and Higher Education Student Affairs. He has enjoyed expanding his network in biology, computer science, mathematics, and education-based research projects.
Dinko Franceschi, DOCTORAL RESEARCHER
Dinko Franceschi is a doctoral researcher at Harvard working with the Marks Lab.
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Artem Gazizov, RESEARCH ASSOCIATE
Artem has been working in artificial intelligence and protein design in both industry and academic settings. Previously, he worked on identifying protein-ligand binding sites and developing large language models (LLMs) for various wet lab applications. Outside the lab, he enjoys pottery and yoga.