Navami Jain, Bioinformatics and Integrative Genomics
Navami is a PhD student in the Bioinformatics and Integrative Genomics Program at Harvard Medical School completing a rotation in the Marks Lab. She is interested in applying machine learning to improve potency of vaccines and therapeutic antibodies.
Alexandra Ferrante, Systems, Synthetic, and Quantitative Biology
Alexandra is a Systems, Synthetic, and Quantitative Biology PhD student rotating in the Marks lab. She is broadly interested in developing machine learning frameworks that bridge the gap between biological and computational experiments.
Felix Teufel, University of Copenhagen
Felix is a PhD student at the University of Copenhagen, advised by Ole Winther. His research is focused on peptide discovery and engineering as well as protein sorting prediction.
Willis Chow, Max Planck Institute of Molecular Cell Biology and Genetics
Willis is a PhD student at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, supervised by Agnes Toth-Petroczy (a former Marks lab alumni!). His research is focussed on developing new computational tools to study intrinsically disordered protein regions.
Liv Eboreime, Harvard University
Liv is an undergraduate at Harvard College studying bioengineering on the premedical track. She is interested in studying how technology can fuel the treatment of various health conditions. Outside of the lab, you can find her dancing or exploring the diverse food in Boston.
Sahil Sood, Harvard University
Sahil is a Harvard undergrad studying Molecular/Cellular Bio and Government on the pre-medical track. Broadly, he is interested in infectious disease work and understanding how research can be used to better understand viruses and pathogens. In his free time, you can often find him watching basketball or football!
Sage Widder, Wellesley College
Sage is a student at Wellesley College with a variety of interests from biology and math to linguistics and philosophy. She has worked on research projects in physical chemistry, design, materials science, and computational biology, and is hoping to do a PhD in theoretical biology. She spends her free time painting and drawing, hiking, and exploring Boston with her friends.
Hailey Pan, MIT
Hailey was an undergraduate in the Marks Lab, as a first year student at MIT studying Computer Science and is interested in exploring bioinformatics, particularly drug discovery and synthetic biology. Her research involved 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.
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
Website
Dan Ritter, Software Engineer
Daniel was a software engineer in the Marks lab, before heading to Cornell to pursue a PhD. 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.
Rohit Arora, BIOINFORMATICS AND INTEGRATIVE GENOMICS
Rohit was a student in the Bioinformatics and Integrative Genomics PhD program and rotated in the Marks Lab. 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.
Jio Jeong, Chemistry and Chemical Biology
Jio is a graduate student in the Chemistry and Chemical Biology (CCB) department at Harvard University. She graduated from University of Pennsylvania with a bachelor’s degree, majoring in chemistry and computer science. During undergrad, she worked in Prof. Jeffery Saven’s lab, and studied self-assembling peptide “bundlemers” that can be linked together into customizable polymers with click chemistry. Outside of the lab, she enjoys exploring the city and discovering new music.
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.
Lood van Niekerk, Associate Researcher
Lood was a research associate with the Marks Lab, before departing to join Ginkgo Bioworks. 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
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.
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 centered on learning compact representations of protein sequences through modern natural language processing methods.
Evan Cofer, Postdoc
Evan worked on computational techniques for analyzing large-scale sets of genomic variation. In general, he was interested in how we can develop and use machine learning models to better understand, predict, and design regulatory mechanisms.
He like to climb rocks outside and play tabletop RPGs indoors.
Website
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Hannah Pierce-Hoffman, Biomedical Informatics Master Student
Hannah is a master’s degree student in the Department of Biomedical Informatics at Harvard Medical School. She completed her undergraduate degree in computer science at Columbia University, then worked professionally as both a software engineer and a molecular biologist before coming to Harvard.
Benjamin Chang, undergraduate intern
Benjamin was a junior at Harvard studying Chemical and Physical Biology and Computer Science. He was interested in using machine learning to advance the possibilities of biology. Outside of lab, you can find him skateboarding around campus, shooting astrophotography, or reading about giant pumpkins.
Sunny Eom, Albany High School intern
Sunny (Sunwoo) was a high school student engineering de novo proteins using generative models in the Marks lab. She has experience conducting biomedical research utilizing multimodal deep learning and self-supervised learning. Outside of the lab, Sunny enjoys writing poetry and creating art, capturing the musicality and color of life!
Annie Eom, Albany High school intern
Annie (Sunmin) was a high school student interested in the intersection of machine learning and proteins, nature’s building blocks of life. She had previously worked on predicting stress using ML. Her current research centers on applying ML to generate novel in silico proteins. In her spare time, Annie likes to create playlists about each of the 27 possible states of human emotion!
Tessa D. Green, Biophysics
Tessa studied Physics as an undergraduate at MIT, where she spent far too much time in dark rooms trapping ions. After a brief flirtation with molecular biology and some quality time spent pipetting, she decided to return to her mathematical roots. She is now a Biophysics graduate student interested in how cells and scientists interpret noisy data.
embedding: cool hair, rings, single cell, rare genetic diseases, collaborative, knitting, pink, quantum, reader, union, e-bike, independent, empathetic, tall, RNA, union, activist, Colorado, MIT, physics, biology
Alissa Hummer, Visiting PhD student, Oxford
Alissa was a visiting Ph.D. student from the Oxford Protein Informatics Group at the University of Oxford. In her research, she is developing machine-learning methods for antibody design and optimization.
Nikki Thadani, postdoc
Nikki spent her PhD applying synthetic biology principles to the task of engineering viruses for gene therapy. Years of synthesizing and testing capsid mutants inspired her interest in data-driven prtoein engineering and synthetic evolution. Outside of lab, she enjoys taking her mini-schnauzer on pup adventures around Boston.
embedding: virus, leader, apples and peanut butter, Texas, snacks, omnipotent, calming, statistics, reasonable, AAV, reason, math, driven, focused, Lincoln, methodical, reassuring, helpful
Japheth Gado, visiting from National Renewable Energy Laboratory
Japheth’s PhD is in chemical engineering, where he worked on understanding cellulose-degrading enzymes with molecular dynamics simulations and machine learning. Currently, at the National Renewable Energy Laboratory and the BOTTLE consortium, he develops deep-learning models to enable the discovery and engineering of enzymes that deconstruct plastics.
Alan Amin, Systems, Synthetic, and Quantitative Biology
Alan was a PhD student in the Systems Biology program in the Marks lab with a background in mathematics and biochemistry.
embedding: funny, Canadian, cnfident, stylish, supportive, Hipster, energetic, math, perplexity, mis-specification, nice, Toronto, loud, passionate, fast, biking, pure math, cicada, chaos, stats, backgammon, Hell Yeah, Let's Go, I'm Back, BEAR
Daniel Kassler, Bioinformatics and Integrative Genomics
Daniel used to be a theoretical mathematician, but after a brief stint in public policy research and a bite from a radioactive geneticist he has now fully embraced the life sciences. He’s interested in using statistics and synthetic biology to tackle the most important environmental, health, and climate issues facing the planet. Outside of lab, Daniel is an avid bird lover, board gamer, and nature enthusiast.
embedding: explorer, curious, biking, nature, birds, sustainability, mother earth, outside, Zelda, plants, facts, talkative, careful, cat, energy, trivia, ornithologist, long hair, environment
Rachapun (Gear) Rotrattanadumrong, visiting from Okinawa Insititute of Science and Technology
Gear was a PhD student currently at the Okinawa Insititute of Science and Technology in Japan. He worked on high-throughput experimental and computational methods for the study and evaluation of functional RNA. Outside the lab he enjoys scuba diving, ice coffee and recently got into cocktail making!
Srihari Ganesh, Harvard
Srihari is an undergraduate studying Chemical and Physical Biology & Statistics at Harvard College. He's interested in computational approaches to macromolecular structure. Outside (and inside) of lab, you can find him watching an endless stream of YouTube videos and snacking on anything within walking distance.
embedding: undergrad, clout, content, biology, math, Michigan, two pairs of shoes, stats, nba, bananagrams, pyro fanatic, ambitious, puns, kubb, energetic, easy going
Kalyan Palepu, Harvard
Chenzhang (Henry) Zhou, Rotation Student from Bioinformatics and Integrative Genomics
Chenzhang (Henry) is a G2 in the Bioinformatics and Integrative Genomics program. He is interested in applying machine learning models to accelerate protein designs. When away from the computer, he enjoys playing badminton and watching soccer.
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Davy Deng, Rotation Student from MIT
Davy is a PhD student in the Harvard-MIT HST program rotating in the Marks lab. Previously Davy graduated with degrees in Chemistry, Genetics and Psychology from UC Berkeley and conducted research on novel electron transport chain systems in anaerobic pathogens. He is excited about the tremendous potential of forecasting viral evolution and hopes to one day extend such technique to microbial and mammalian cells using machine learning. Outside of the lab, he spends most of his time learning the Boston venture creation ecosystem, volunteering for research efforts for global health and humanitarian response and experimenting cocktail recipes with his roommates and friends.
Ada Fang, Rotation Student from Chemistry
Ada is PhD student in Chemistry at Harvard rotating in the Marks lab, and originally from Sydney, Australia. In her spare time, she enjoys being outdoors and on the water.
Kelly Brock, Associate Research Director
Kelly spent her PhD studying the evolution of protein stress response in the England group at MIT. As a joint postdoc between the Marks and Sander groups, she applies evolutionary couplings analysis both to predict protein structures de novo and to enable better fold and alternate conformation analysis from NMR and X-ray crystallography. Additionally, she works on Pathway Commons biological applications and analysis tools. When not trying to bend computers to do her bidding, she enjoys playing pub trivia and coaching cheerleading.
embedding: hero, lab glue, South Carolina, knowledgable, bioinformatics, Frodo, kind, comedy, , de-stresser, jazz hands, peaceful, queen, friendly, helpful, boss, warm, efficient, loves cute dogs, protein expert, EV Couplings, MIT, proactive, communicative, approachable, kind, sweet, caring, math
Jonathan Frazer
Jonny's background is in theoretical physics. His previous work included developing computational tools for testing theories of the very early universe, as well as pioneering the use of information theory and probabilistic modelling for studying cosmic inflation in string theory. His love of high-dimensional probability and information theory has now brought him to the data-rich world of genomics.
embedding: curly, glasses, kind, supportive, athletic, pet parrot, string theory, pleasant accent, curious, enthusiastic, Luis, EVE, physics, calm, strawberry licorice, runner, strava, high dimensional, plants
Mafalda Dias
Mafalda is a theoretical physicist who recently became interested in computational biology. Before joining Debbie’s lab she worked at the border between cosmology and string theory. She now develops new probabilistic models of sequence data to understand the map from sequence to function and the effect of genetic variation.
embedding: fashionable, EVE, physics, beautiful, math, flowy, massive styles, art, brilliant, mom, plants, Portuguese, cool, outgoing, biology, hobbies, multilingual, honest, paintings, lemon pants, great hair, kind, fashionable, caring, lively, easy going, Luis, funny
Kasper Einarson, Visiting PhD Student
Kasper was a PhD student visiting the lab from Danish Technical University in spring 2022. His background is in computer science and current research focus on applications for biological property prediction using deep learning. In his free time he enjoys playing piano and guitar.
Javier Marchena, Associate Researcher
Javier was an Associate working in the Marks lab for a year. Originally from Spain, he studied his MSc in Bioinformatics in Copenhagen. He loves structural bioinformatics and now works on predicting the effects of mutations in proteins. In his free time, he can be found at the local chess club pushing some wooden pieces.
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Joe Min, Software Engineer
Joe studied biomedical engineering and computer science during his undergraduate years at Johns Hopkins. After working for four years as a software engineer in industry, he is excited to apply what he has learned to the world of computational biology!
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Nathan Rollins
Nathan was a joint student with Debbie and Pam Silver. With Pam, he's modeled enzyme mechanisms and designed anti-cancer proteins. Lately he's been scroungin around in viral genomes with Debbie. Outside the lab, he can be found in the middle of a biking accident, compulsively acquiring more craigslist furniture, or hanging too many things from his ceiling.
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Eli Weinstein, Biophysics
Eli received his undergraduate degree in Chemistry and Physics from Harvard College. He's interested in Bayesian statistics and machine learning, and is currently focused on generative models of complex mutational processes.
Harvard Biophysics
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Joshua Rollins, Software Engineer
Joshua studied applied and computational math sciences along with electrical engineering at University of Washington. He now absorbs knowledge of our tiny friends the tardigrades, while creating bioinformatics software. Enticed by candles, bamboo, and coconuts he can often be found drawn into Filipino folk dance.
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Mrunali Manjrekar, Undergraduate Intern
Mrunali is a rising sophomore at the University of California, Berkeley, majoring in Bioengineering and Electrical Engineering and Computer Sciences (EECS). She is intrigued by the interface between computing and biological problems, especially ones involving multi-omics, and hopes to pursue a PhD in a related field upon graduation. When away from the keyboard, Mrunali enjoys reading nonfiction, journaling, exploring new places, and playing the occasional board game.
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Jean Disset, Postdoc
Jean has a background in high performance computing with a PhD in Artificial Life. He has a passion for complex systems, evolution theory and well written code. He’s done research on evolutionary computations, cell simulation, synthetic biology, morphogenetics engineering, and the emergence of complex morphologies and behavior.
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June Jung-Eun Shin, Graduate Student
June is a Systems Biology PhD student in the Marks lab. Broadly, she is interested in the use of computational methods applied to therapeutics-related research and intends to spend her rotation working on computational drug screens.
Harvard Systems Biology
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David Ding, Graduate Student
Contrary to appearance, David was born and raised in idyllic Austria, and educated in even more idyllic Oxford. David somehow ended up being interested in how protein interactions evolve, and travelled across the pond to work with Debbie. When David is not troubleshooting experiments, he likes to move around even more, preferably on a bike and somewhere in nature.
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Darius Russell Kish, Rotation Student
Darius attended Boston College where he studied computer science and German studies. At BC, he worked on computational models for chemistry and systems biology. He is excited to continue working at the interface of computer science and biology.
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Amy Tam, Lab manager
Amy's zest for learning drives her to study systems biology with an interdisciplinary approach and brought her first pit stop at UCLA, where she studied Computational and Systems Biology. From there, she was inspired to take a more data-driven, computational path. When Amy's not in lab, she can be found wandering the streets of Boston or the pages of a book.
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Joe Hurley, Rotation Student
Joe is a first-year PhD student in the BBS program rotating in the Marks lab, and he is interested in teasing apart relationships between protein sequences, structures, and functions. Before coming to Harvard, Joe studied biochemistry at Northwestern University, researched bacterial outer membrane proteins at the NIH, and worked in drug discovery at several biotech companies. In his free time, he likes climbing, playing music, and cooking spicy food.
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Siranush Babakhanova
Siranush is studying Physics and CS at MIT'20. She is interested in creating new tools to study and augment complex biological systems. Outside of lab she can be found trying to marry physics, neuroscience and art, engaging in work on human enhancement, or spotted dancing or writing in books.
LinkedIn
Ethan Jones, Graduate Student
Ethan Jones is a first year PhD student in Systems Biology who rotated in the Marks Lab
Email >>29: mailto:ethan_jones@g.harvard.edu
Kasia Kready, Graduate Student
Kasia is a first year PhD student in the Systems Biology program rotating in the Marks lab.
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Sharifa Sahai, Graduate Student
Sharifa was born and raised in Queens, New York. She went to Union College for her Bachelor's and was a dual major in Computer Science and Biology. Before starting her PhD, she did a one-year software-engineering residency at Google in NYC. Sharifa has previously done summer research in the Jarosz Lab at Stanford University School of Medicine and in the Planetary Protection Group at the NASA Jet Propulsion Laboratory. She is also scuba certified and did marine conservation research in Fiji at the Shark Reef Marine Reserve. Sharifa enjoys cycling, weightlifting, playing board games and listening to podcasts / audiobooks.
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Nicolas Gort Freitas, Graduate Student
Nico studied biology and data science at Minerva, a traveling university that allowed him to live in six countries throughout his undergrad studies. His previous work includes inferring the presence of post-translational modifications from mass-spectrometry data and modeling the evolution of cell composition in bacteria. Nico’s interests range from systems and synthetic biology to linguistics and philosophy. In his free time, Nico sings at the Longwood Chorus and plays soccer. He also enjoys hiking, dancing tango, playing board games, and making high-quality memes.
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David Yang, Undergraduate Student
David is an undergraduate at Harvard studying Statistics and Biology and joining the Marks lab for his senior thesis. He is broadly interested in using statistical methods to guide protein design. When he’s not in the lab, you can find him ballroom dancing or biking along the Charles.
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Trenton Bricken, Summer Intern - Duke University
Trenton is a rising senior at Duke University majoring in Biological and Artificial Intelligence. He is interesed in applications of machine learning to pressing problems in biology and hopes to contribute to the Biostasis and FunGCAT projects this summer. If the world was free of pathogens, you'd find him backpacking around the world with his Grandfather's vintage Leica M3 film camera taking mediocre photos.
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Irina Ponamareva, Summer Intern, Higher School of Economics(Moscow)
Irina is a computer science student from Moscow who’s fascinated by machine learning applications in biology. She hopes to contribute to testing and developing deep generative models for protein sequence generation problem.
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Anna G. Green, Graduate Student
Anna received her undergraduate degree in molecular and cell biology from the University of Connecticut, where she worked on the evolution of optimal growth temperature and gene flow in thermophilic bacteria. She is interested in the evolution of biological systems and the use of computational tools to understand biological questions. Her current work involves the evolutionary constraints on protein-protein interactions. In her spare time she enjoys softball, homebrewing, and science fiction.
Harvard Systems Biology
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Adam Riesselman, Graduate Student
Adam is making predictive, interpretable mathematical models for biology.
DOE CSGF
Linkedin
Github
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John Ingraham, Graduate Student
John studied Applied Math and Biochemistry at Arizona State University, somehow avoiding proteins with research on vaccines, howler monkeys, and brain cancer. The flash cards of biochemistry class got back at him eventually, though, as he now spends his PhD in the Marks Lab developing predictive, interpretable models for sequence variation that are grounded in biophysics and genetics. Away from the keyboard & whiteboard, John likes being outside, in the forest or desert, and preferably on a bike.
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Hailey Cambra, Graduate Student
Hailey rotated in the Marks Lab working to understand how evolutionary couplings can be used to predict protein structure. In her spare time, Hailey likes to read, cook, run, hike, watch Netflix programs, and learn new things. Right now Hailey is learning about world geography, since she has never formally learned the subject!
Harvard Systems Biology
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Christian Dallago, Software Engineer
Christian completed his Master of Science at the Technical University of Munich (TUM), in Germany. He has spent two years working on different software tools for Rostlab, the chair of Bioinformatics at TUM, and wrote his master thesis on adverse drug reaction prediction. Passionate about software engineering in the field of Bioinformatics, Christian joined the Marks lab to spread the tools developed by fellow lab members to the community.
Rostlab
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Benjamin Schubert, Postdoc (joint with Chris Sander)
Benni’s background is in computer science and computational biology. In his undergraduate studies, Benni became interested in applying advanced optimization and machine learning approaches to tackle immunological questions. During his PhD at the Univesity of Tübingen, he continued his undergraduate work in computational immunology and made important algorithmic contributions to NGS-based HLA genotyping and to personalized cancer vaccines design. He also became fascinated by co-evolutionary models used for protein structure inference. He combined these models with his previous work to tackle the problem of anti-drug antibody formation in biotherapeutics in close collaboration with the Marks Lab at Harvard Medical School. As a new Postdoctoral Fellow at Harvard Medical School, Benni will continue his work in cancer immunology and related areas.
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Rohan Maddamsetti, Postdoc
Rohan defended his PhD on the evolution of laboratory and natural populations of Escherichia coli at Michigan State University in 2016. His main interest ins molecular evolution. Rohan is especially interested in whether coevolution at the molecular scale is sufficient(or not) in driving the evolution of complex cellular lifeforms.
Rohan's Weebly page
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Anastasia Leshchyk, Summer Intern - Worcester Polytechnic Institute
Anastasia is pursuing a Master's degree in Bioinormatics and Computational Biology at Worcester Polytechnic Institute. She is a Fulbright student from Belarus and Edmund S. Muskie Internship Program Fellow.
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David E. Rollins, Summer Intern - University of Texas
David is a student at the Universityof Texas at Austin double-majoring in Software Engineering and Nanotechnology. He is particularly interested in the development of algorithms for Biology applications as well as the production of microscopic electronics that hold potentail for direct manipulation on a cellular level. In his spare time, David enjoys reading articles on the implementations of artificial intelligence (particularly in Biology), bingeing Netflix, and training for the U.S. Olympic Swimming Trials.
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Charlotta Schärfe, Graduate Student
Hattie Chung, Researcher - Harvard Medical School
Sophia Mersmann, Summer Intern - Bioinformatics, Imperial College in London
Chan Kang, Software Engineer
Thomas Hopf, Postdoc (joint with Chris Sander)
Eli Draizen, Graduate Student
Currently at National Institute of Health (NIH)
Li Yang, Software Engineer
Currently working at Mathworks
Ruomu Jiang, Senior Bioinformatics Scientist
Sikander Hayat, Postdoc
Currently Working at Memorial Sloan Kettering Cancer Center (MSKCC) in New York
Torsten Gross
Institute for Theoretical Biology, Humboldt University, Berlin
Jörn Schmiedel, Graduate Student
Berlin University
Centre for Genomic Regulation, Barcelona
Agnes Toth-Petroczy, Postdoc
Ben Alemu, Summer Undergraduate Student
Duncan Mitchison-Field, High School and Undergraduate Intern
