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.

Email »


Contact Kevin Chimo, Debbie's faculty assistant for all non science related questions:
Email »

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.
Rohan Rohan Maddamsetti
Postdoc

Email »

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
Kelly Brock
Postdoc (joint with Chris Sander)

Email »

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.
Benjamin Schubert
Postdoc (joint with Chris Sander)

Email »

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.
Jonathan Frazer
Postdoc

Email »

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
Mafalda Figueiredo Dias
Postdoc

Email »

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.
David David Ding
Graduate Student

Email »

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.
John John Ingraham
Graduate Student

Email »

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.
Anna Anna G. Green
Graduate Student
Harvard Systems Biology

Email »

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.
Adam Adam Riesselman
Graduate Student
Harvard BIG Program

Email »

Adam is making predictive, interpretable mathematical models for biology.

DOE CSGF
Linkedin
Github
Eli_Weinstein Eli Weinstein
Graduate Student
Harvard Biophysics
Email »
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.
Hailey Hailey Cambra
Graduate Student
Harvard Systems Biology

Email »

Hailey is rotating 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!
June June Jung-Eun Shin
PhD Student
Harvard Systems Biology

Email »

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 Christian Dallago
Software Engineer
Rostlab

Email »

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 Markslab to spread the tools developed by fellow lab memebers to the community.
picture of Christian Dallago Nathan Rollins
Graduate Student (joint with Silver lab)
Harvard Systems Biology

Email »

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

Email »

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 Christian Dallago David E. Rollins
Summer Intern
University of Texas

Email »

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), bingeing Netflix, and training for the U.S. Olympic Swimming Trials.
picture of Christian Dallago Anastasia Leshchyk
Summer Intern
Worcester Polytechnic Institute

Email »

Anastasia’s pursuing Master's degree in Bioinformatics and Computational Biology at Worcester Polytechnic Institute. She is a Fulbright student from Belarus and Edmund S. Muskie Internship Program Fellow
Collaborators
Chris Chris Sander

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

Find all our collaborators from the Sander lab at: sanderlab.org

Chris Andrew Kruse

Harvard Medical School (HMS)

Find all our collaborators from the Kruse lab at: kruse.hms.harvard.edu

Chris David Rudner

Harvard Medical School (HMS)

Find out about David's work at: mbib.med.harvard.edu

Alumni
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
Former High School Intern