Management
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
Evan Cofer
I work on computational techniques for analyzing large-scale sets of genomic variation. In general, I am interested in how we can develop and use machine learning models to better understand, predict, and design regulatory mechanisms.
In my free time, I like to climb rocks outside and play tabletop RPGs indoors.
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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, MIT EECS
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
Han Spinner, Biological and Biomedical Sciences
Han is a PhD student in BBS in the Marks Lab. Previously, Han studied Genetics and Plant Biology at UC Berkeley and did CRISPR protein + RNA engineering. They’re excited about the intersection of machine learning and big biological molecules. Beyond the impactful biologically-driven machine learning research, they believe this lab fosters an environment of love and inclusivity that is quite special!
embedding: funny, :), Go Bears, eats early, sleeps early, wakes early, hats, Doudna, ambitious, biology, morning person, backgammon player, wetlab, pipette, startups, Moo, protein engineering, outgoing, master cloner, plants, Berkeley, flower shirts, excited, fun, kind, sincere, self-assured, Hank the Tank
Steffanie Paul, Bioinformatics and Integrative Genomics
Steffanie studied Molecular and Cellular Biology in her undergraduate at Harvard College. After a brief time in Biotech, they crossed the river to start their PhD in the Bioinformatics and Integrative Genomics program at HMS. When away from her computer, she enjoys sipping hot coffee over a book in a local cafe.
embedding: great hair, fashionable, cool, confident, fun, interesting, responsible, awesome, union, eyeliner, sparkly eyeshadow, stylish, bubbly, creative, political, enthusiastic, kind, deep learning lover, math, biology, goss, nanobody
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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, Joint Advised with Yarin Gal from 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.
Amber Shen, Bioinformatics and Integrative Genomics
Amber is a graduate student in the Bioinformatics and Integrative Genomics program. Previously, she studied math at MIT and worked on developing single-cell methods to understand gene regulation. She enjoys playing tennis, biking, and taking walks around Boston.
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, Harvard-MIT HST 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.
Rotating Students
Rohit Arora, BIOINFORMATICS AND INTEGRATIVE GENOMICS
Rohit is a student in the Bioinformatics and Integrative Genomics PhD program. Before relocating to Boston, he studied reindeer skin regeneration in Canada and looked for therapeutic targets in a variety of diseases using multi-omic data. Now, he's venturing into AI and protein design. Outside the lab, he's usually at the gym, traveling, or taking care of his plants.
Visiting Scholars
Max Guidi, visting from ETH Zurich
Max is a master’s student at the ETH Zurich Department of Mathematics. His research at the Marks lab centers on learning compact representations of protein sequences through modern natural language processing methods.
Debora Monego, visiting from the Heidelberg Institute for Theoretical Studies
Debora Monego is a postdoctoral researcher at the Molecular Biomechanics group at the Heidelberg Institute for Theoretical Studies. Her research focuses on the mechanochemistry of structural proteins.
Undergraduates
Hailey Pan
Hailey is a Freshman at MIT studying Computer Science and is interested in exploring bioinformatics, particularly drug discovery and synthetic biology. Her current research involves using machine learning to understand motifs in immune epitopes and predict protein-protein interactions. Outside of the lab, she enjoys solving escape rooms, playing tennis, and exploring new music.
Erik Xie
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.
Staff
Dan Ritter, Software Engineer
Daniel is working as a software engineer in the Marks lab. Previously, he studied computer science and political science during his undergraduate at Brown University, and computer science during his master's at the University of Oxford. In his spare time, he enjoys overly complicated board games, playing the piano, and running.
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.
Lood van Niekerk, Associate Researcher
Lood is working as a research associate with the Marks Lab for a year. He previously collaborated with the Marks Lab while studying Masters in Computer Science at Oxford. In his spare time, he enjoys playing the piano and drums.
embedding: cheery, happy, bright, computer science, South Africa, Julius Cheesar, blond hair, games, patient, coder, friendly, enthusiastic, good with kids, chill, sporty, welcoming, musical , tennis, kubb, personable, keen
Dinko Franceschi, AI Research Engineer
Dinko’s research centers on studying the effects of genetic variation on viral evolution. Before joining the Marks Lab, Dinko worked on genomics research projects with Google Brain and the Broad Institute. He holds an undergraduate degree in Applied Mathematics from Columbia University.