Marks Lab Members and Collaborators



Lab Members   Collaborators   Alumni


Debora S. Marks
Principal Investigator
Associate Professor at Harvard Medical School
Associate member at the Broad Institute.

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Contact Kevin Chimo, Debbie's faculty assistant for all non science related questions:
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Debora is a mathematician and computational biologist with a track record of using novel algorithms and statistics to successfully address unsolved biological problems. She has a passion for interpreting genetic variation in a way that impacts biomedical applications. During her PhD, she quantified the potential pan-genomic scope of microRNA targeting and combinatorial regulation of protein expression and co-discovered the first microRNA in a virus. As a postdoc she and her colleagues cracked the classic, unsolved problem of ab initio 3D structure prediction of proteins using a maximum entropy probability model for evolutionary sequences. She has developed this approach to determine functional interactions, biomolecular structures, including the 3D structure of RNA and RNA-protein complexes and the conformational ensembles of apparently disordered proteins. Her new lab at Harvard is interested in developing methods in deep learning to address a wide range of biological challenges including predicting the effects of genetic variation and sequence design for biosynthetic applications.

NIH Biosketch


Chris Chris Sander

Professor at Dana-Farber Cancer Institute (DFCI) and Harvard Medical School (HMS)

The Marks lab works very closely with the Sander lab. Find all our collaborators from the Sander lab at: sanderlab.org

Kelly Brock
Postdoc (joint with Chris Sander)

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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.
Jonathan Frazer
Postdoc

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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.
Jonny's webpage
picture of Mafalda Figueiredo Dias Mafalda Figueiredo Dias
Postdoc

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Mafalda is a theoretical physicist who recently became interested in genomics. Before joining Debbie's lab she worked at the border between cosmology and string theory, developing computational tools and studying complex models as a way to learn about the first instants of the Universe.
picture of Nikki Thadani Nikki Thadani
Postdoc

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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 protein engineering and synthetic evolution. Outside of lab, she enjoys taking her mini-schnauzer on pup adventures around Boston.
David David Ding
Graduate Student

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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.
Eli_Weinstein Eli Weinstein
Graduate Student
Harvard Biophysics
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Eli received his undergraduate degree in Chemistry and Physics from Harvard College. He is currently writing new search algorithms to find interesting things in big sequence databases.
June June Jung-Eun Shin
Graduate Student
Harvard Systems Biology

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June is a first year Systems Biology PhD student rotating 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.
picture of Christian Dallago Nathan Rollins
Graduate Student (joint with Silver lab)
Harvard Systems Biology

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Nathan is a joint student with Debbie and Pam Silver. With Pam, he's modeled enzyme mechanisms and designed anti-cancer proteins. Lately he’s been scrounging 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.
picture of Christian Dallago Tessa D. Green
Graduate Student
Harvard Biophysics

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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.
picture of Aaron Kollasch Aaron Kollasch
Graduate Student
Systems Biology

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picture of Joshua Rollins Joshua Rollins
Software Engineer

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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.
picture of Ada Shaw Ada Shaw
Graduate Student

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Ada is a graduate student in the School of Applied Science and Engineering. She comes from UC Berkeley where she worked on raising Ammonia-Oxidizing Bacteria. After spending her first year in graduate school with atmospheric chemistry models she decided to apply her modeling experience to her original interest in biology.
picture of Amy Tam Amy Tam
Research Assistant
Lab Manager

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Amy studied Computational & Systems Biology as an undergraduate at UCLA. There, she developed a deeper appreciation for interdisciplinary approaches to advancing our understanding of biomedical sciences. Her enthusiasm for learning and desire to develop a big-picture understanding of biology and research has led her to the Marks Lab. Outside of lab, Amy can be found in a library or wandering the streets of Boston.
picture of Trenton Bricken Trenton Bricken
Summer Intern
Duke University

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Trenton is a rising senior at Duke University majoring in Biological and Artificial Intelligence. He is interested 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.
Siranush Siranush Babakhanova

Ed Boyden's Synthetic Neurobiology Group

MIT Media Lab and McGovern Institute for Brain Research

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

picture of Alan Amin Alan Amin
Graduate Student

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Alan is a first year PhD student in the Systems Biology program rotating in the Marks lab with a background in mathematics and biochemistry.
picture of Rose Orenbuch Rose Orenbuch
Graduate Student

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Coming from a background in computer science and biology, Rose is a first year Systems Biology graduate student rotating in the Marks lab.
picture of David Yang David Yang
Undergraduate Student

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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.
picture of Kasia Kready Kasia Kready
Graduate Student

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picture of Sharifa Sahai Sharifa Sahai
Graduate Student

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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.
picture of Nicolas Gort Freitas Nicolas Gort Freitas
Graduate Student

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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.
Collaborators
Alumni
Anna Anna G. Green
Graduate Student
Harvard Systems Biology

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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. During her PhD, she studied he evolutionary constraints on protein-protein interactions. After graduating, Anna began a post-doc fellowship in Maha Farhat's lab.
Hailey Hailey Cambra
Graduate Student
Harvard Systems Biology

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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.
picture of Christian Dallago Christian Dallago
Software Engineer
Rostlab

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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 memebers to the community.
Adam Adam Riesselman
Graduate Student
Harvard BIG Program

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In the Marks lab, Adam made predictive, interpretable mathematical models for biology.

DOE CSGF
Linkedin
Github
John John Ingraham
Graduate Student

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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 spent 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.
Benjamin Schubert
Postdoc (joint with Chris Sander)

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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 Postdoctoral Fellow at Harvard Medical School, Benni continued his work in cancer immunology and related areas.
Rohan Rohan Maddamsetti
Postdoc

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Rohan defended his PhD on the evolution of laboratory and natural populations of Escherichia coli at Michigan State University in 2016. His main interest is 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
picture of Ana Anastasia Leshchyk
Summer Intern
Worcester Polytechnic Institute

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Anastasia’s pursuing Master's degree in Bioinformatics and Computational Biology at Worcester Polytechnic Institute. She was a Fulbright student from Belarus and Edmund S. Muskie Internship Program Fellow
picture of David E. Rollins David E. Rollins
Summer Intern
University of Texas

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David is a student at the University of 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 potential for direct manipulation on a cellular level. In his spare time, David enjoys reading articles on the implementations of artificial intelligence (particularly in Biology), binging Netflix, and training for the U.S. Olympic Swimming Trials.
Charlotta Charlotta Schärfe
Graduate Student
Hattie Hattie Chung
Researcher

Harvard Medical School

Sophia Sophia Mersmann
Summer Intern
Bioinformatics, Imperial College in London
Chan Chan Kang
Software Engineer
Harvard Systems Biology
Thomas Thomas Hopf
Postdoc (joint with Chris Sander)
Eli Eli Draizen
Graduate Student

Currently at National Institute of Health(NIH)

Li Li Yang
Software Engineer

Currently working at Mathworks

Ruomu Ruomu Jiang
Senior Bioinformatics Scientist

Currently working at Helix

Sikander Sikander Hayat
Postdoc(2013 - 2014)

MSKCC in New York

Torsten Torsten Gross
Institute for Theoretical Biology

Humboldt University, Berlin

Jörn Jörn Schmiedel
Graduate Student

Berlin University

Centre for Genomic Regulation, Barcelona

Agnes Toth-Petroczy
Postdoc
Ben Ben Alemu
Summer Undergraduate Student
Harvard Systems Biology
Duncan Duncan Mitchison-Field
High School Intern & Summer Intern