Marks Lab Members and Collaborators



Lab Members   Collaborators   Alumni


Debora S. Marks
Principal Investigator

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Bio
Jennie Jennie Epp
Faculty Assistant

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Jennie is responsible for assisting Debbie and the Marks lab with all things not directly related to the science. Including, but not limited to, reimbursements, travel booking, calendar scheduling, and---perhaps most importantly of all---knowing where all of the good candy in the Sysbio main office is located. Before coming to the Marks Lab, she spent ten years living in Tennessee, attending graduate school, and writing about The X Files.
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
Thomas Thomas Hopf
Postdoc (joint with Chris Sander)

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Thomas is a computational biologist interested in studying the coevolution of protein sequences to predict phenotypes from constraints on the sequence level. After his bioinformatics degree in Munich, he crossed the Atlantic just at the right time to work with Debbie and Chris Sander on the prediction of protein 3D structure using evolutionary couplings. When not folding proteins or troubleshooting pipelines, Thomas likes to write music on his piano and enjoy life in a Bavarian beer garden.
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, and is now very excited to study RNA structure and protein amyloid formation as a joint postdoc in Debbie Marks' and Chris Sander's labs! 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)

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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 new Postdoctoral Fellow at Harvard Medical School, Benni will continue his work in cancer immunology and related areas.
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.
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 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.
Charlotta Charlotta Schärfe
Graduate Student

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Charlotta is a Bioinformatics PhD student from the University of Tübingen and she is interested in the effects of genetic variation on drug efficacy, personalized medicine and drug repurposing. Charlotta is also working on coevolution based prediction of protein structure and interactions.

Blogs that Charlotta reads:
Science Mag
Lior Pachter Blog
Information is Beautiful
Cureffi.org
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. 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

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Adam is making predictive, interpretable mathematical models for biology.

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

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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

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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.
Chan Chan Kang
Software Engineer
Harvard Systems Biology
Chan recently graduated from Harvard University with a degree in Computer Science, and has joined the Marks lab as a software developer.
Sophia Sophia Mersmann
Summer Intern
Bioinformatics, Imperial College in London

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Sophia studied Bioinformatics at the University of Tübingen and concluded her undergraduate studies with a thesis in the field of computational immunology. In the thesis she developed a computational pipeline to de-immunize antibody sequences using the evolutionary history of a protein. Fascinated by co-evolutionary models, Sophia spent the summer in Boston trying to find a way to detect functional and, more specifically, allosteric sites in proteins. She is excited to continue her studies in the field of Bioinformatics at the Imperial College in London and is looking forward to continuing her work on co-evolution based prediction of allostery.
picture of Christian Dallago Christian Dallago
Software Engineer
Harvard Systems Biology

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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 Markslab to spread the tools developed by fellow lab memebers to the community.
Collaborators
Chris Chris Sander
Professor

Dana-Farber Cancer Institute (DFCI)

Harvard Medical School

Dwana Dwana Agosto
Program Administrator

cBio Center @ DFCI and Chris Sander Lab

Nick Nicholas Paul Gauthier
Senior Scientist

Chris Sander lab, Dana-Farber Cancer Institute (DFCI)

Frank Frank Poelwijk
Staff Scientist

Chris Sander lab, Dana-Farber Cancer Institute (DFCI)

Elin Elin Nyman
Research Fellow

Chris Sander lab, Dana-Farber Cancer Institute (DFCI)

Richard Richard Stein
Research Associate

Department of Biostatistics, Harvard School of Public Health

Chris Sander lab, Computational Biology at Dana-Farber Cancer Institute (DFCI)

Perry Perry Palmedo
Graduate Student

Bioinformatics and Integrative Genomics (BIG) program at Harvard University

Professor Bonnie Berger's group at MIT

Hattie Hattie Chung
Researcher

Harvard Medical School

Alumni
Eli Eli Draizen
Graduate Student

Currently at National Institute of Health(NIH)

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Li Li Yang
Software Engineer

Currently working at Mathworks

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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

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Jörn Jörn Schmiedel
Graduate Student

Berlin University

Centre for Genomic Regulation, Barcelona

Agnes Toth-Petroczy
Postdoc

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Ben Ben Alemu
Summer Undergraduate Student
Harvard Systems Biology
Ben is a senior at UC San Diego studying Biochemistry & Cell Biology. He teaches, researches and runs a national nonprofit that designs educational programs for underserved K-12 schools. Most of his academic research focuses on identifying metabolites through mass spectrometry and computational approaches for drug discovery. Ben will soon be pursuing graduate school and hopes to further study Systems / Computational Biology in the near future. In his free time, he likes to play basketball.

LinkedIn
Nonprofit Website
Duncan Duncan Mitchison-Field
Former High School Intern

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Duncan is an intern from the local Brookline Highschool.