Author details

Full Name

Debora S Marks

Affiliation

Blavatnik Institute, Harvard Medical School

ORCID

Career Start Year

1995

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36859542	Coordination of bacterial cell wall and outer membrane biosynthesis.	Nature	2023
37591202	How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design?	Cell Syst	2023
37394429	An Atlas of Variant Effects to understand the genome at nucleotide resolution.	Genome Biol	2023
37156936	A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories.	Nat Med	2023
37214973	Simultaneous enhancement of multiple functional properties using evolution-informed protein design.	bioRxiv	2023
37081311	The relaxin receptor RXFP1 signals through a mechanism of autoinhibition.	Nat Chem Biol	2023
37292845	GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway.	bioRxiv	2023
35176859	Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells.	ACS Synth Biol	2022
35857511	Mechanical gating of the auditory transduction channel TMC1 involves the fourth and sixth transmembrane helices.	Sci Adv	2022
35361892	Co-evolution of interacting proteins through non-contacting and non-specific mutations.	Nat Ecol Evol	2022
35388191	Democratizing the mapping of gene mutations to protein biophysics.	Nature	2022
35654455	The SpoVA membrane complex is required for dipicolinic acid import during sporulation and export during germination.	Genes Dev	2022
36477674	An in silico method to assess antibody fragment polyreactivity.	Nat Commun	2022
35319251	High-Content Screening and Computational Prediction Reveal Viral Genes That Suppress the Innate Immune Response.	mSystems	2022
33373583	CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy.	Cell Syst	2021
33654096	Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences.	Nat Commun	2021
33893299	Protein design and variant prediction using autoregressive generative models.	Nat Commun	2021
34824238	Dormant spores sense amino acids through the B subunits of their germination receptors.	Nat Commun	2021
34707284	Disease variant prediction with deep generative models of evolutionary data.	Nature	2021
34168368	Rapid generation of potent antibodies by autonomous hypermutation in yeast.	Nat Chem Biol	2021
32152588	Structural coordination of polymerization and crosslinking by a SEDS-bPBP peptidoglycan synthase complex.	Nat Microbiol	2020
33200136	Rapid generation of potent antibodies by autonomous hypermutation in yeast.	bioRxiv	2020
32870157	Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact.	Elife	2020
30611430	Combining Evolutionary Covariance and NMR Data for Protein Structure Determination.	Methods Enzymol	2019
31209393	Inferring protein 3D structure from deep mutation scans.	Nat Genet	2019
31431536	Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis.	Proc Natl Acad Sci U S A	2019
30510172	Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings.	Nat Microbiol	2019
30304492	The EVcouplings Python framework for coevolutionary sequence analysis.	Bioinformatics	2019
29590088	Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis.	Nature	2018
30193102	A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.	Mol Cell	2018
29891673	Structure and mutagenic analysis of the lipid II flippase MurJ from <i>Escherichia coli</i>.	Proc Natl Acad Sci U S A	2018
30152871	Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature.	Evolution	2018
30250057	Deep generative models of genetic variation capture the effects of mutations.	Nat Methods	2018
29979965	A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.	Mol Cell	2018
30403663	Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis.	PLoS Genet	2018
30617828	A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data.	Adv Exp Med Biol	2018
30327422	Cryo-electron microscopy structure of the lipid droplet-formation protein seipin.	J Cell Biol	2018
29499035	Population-specific design of de-immunized protein biotherapeutics.	PLoS Comput Biol	2018
29273096	Genetic variation in human drug-related genes.	Genome Med	2017
28379360	Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli.	Genome Biol Evol	2017
28092658	Mutation effects predicted from sequence co-variation.	Nat Biotechnol	2017
27087444	3D RNA and Functional Interactions from Evolutionary Couplings.	Cell	2016
27638945	Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013.	J Infect Dis	2016
27662088	Structured States of Disordered Proteins from Genomic Sequences.	Cell	2016
27472898	Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4.	Elife	2016
25584517	Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors.	Nat Commun	2015
26481813	Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.	Structure	2015
26125594	Pathway and network analysis of cancer genomes.	Nat Methods	2015
26121406	Protein structure determination by combining sparse NMR data with evolutionary couplings.	Nat Methods	2015
26225866	Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.	PLoS Comput Biol	2015

1 - 50 of 86

Angela D Wilkins

Baylor College of Medicine

Career Start Year 2010

Number of shared co-authors 1

Michael T Zimmermann

Medical College of Wisconsin

Career Start Year 2009

Number of shared co-authors 0

Fergal Casey

Biogen Inc.

Career Start Year 2006

Number of shared co-authors 0

Noah Ollikainen

California Institute of Technology

Career Start Year 2006

Number of shared co-authors 2

Vladimir Vacic

Stanley Institute for Cognitive Genomics

Career Start Year 2005

Number of shared co-authors 3

Yana Bromberg

Rutgers University

Career Start Year 2003

Number of shared co-authors 4

Vera van Noort

Leiden University, Institute of Biology Leiden

Career Start Year 2003

Number of shared co-authors 0

Manolis Kellis

Massachusetts Institute of Technology

Career Start Year 2003

Number of shared co-authors 12

Madan Mohan Babu

St. Jude Children's Research Hospital

Career Start Year 2002

Number of shared co-authors 1

Zhaolei Zhang

University of Toronto

Career Start Year 2002

Number of shared co-authors 0

Predrag Radivojac

Indiana University

Career Start Year 2002

Number of shared co-authors 4

Dmitry Korkin

Worcester Polytechnic Institute

Career Start Year 2002

Number of shared co-authors 4

Maricel G Kann

University of Maryland

Career Start Year 2000

Number of shared co-authors 2

Wei Wang

IBM Thomas J Watson Research Center, University of California Los Angeles, University of North Carolina at Chapel Hill

Career Start Year 1999

Number of shared co-authors 1

Marc A Marti-Renom

Universitat Pompeu Fabra (UPF)

Career Start Year 1998

Number of shared co-authors 6

Shamil R Sunyaev

Harvard Medical School

Career Start Year 1997

Number of shared co-authors 7

Yu Xia

College of Information Engineering, Zhejiang University of Technology

Career Start Year 1996

Number of shared co-authors 3

Sarah A Teichmann

Wellcome Sanger Institute

Career Start Year 1996

Number of shared co-authors 8

Steven E Brenner

University of California berkeley

Career Start Year 1994

Number of shared co-authors 8

Edward M Marcotte

University of Texas

Career Start Year 1993

Number of shared co-authors 2

Joel S Bader

Johns Hopkins University

Career Start Year 1993

Number of shared co-authors 3

Zhiping Weng

University of Massachusetts Medical School

Career Start Year 1992

Number of shared co-authors 6

Robert B Russell

Heidelberg University

Career Start Year 1991

Number of shared co-authors 2

Miguel A Andrade-Navarro

Institute of Organismic and Molecular Evolution, Johannes Gutenberg University

Career Start Year 1991

Number of shared co-authors 6

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 17

Chris P Ponting

The University of Edinburgh

Career Start Year 1989

Number of shared co-authors 4

David Haussler

Genomics Institute, University of California Santa Cruz

Career Start Year 1986

Number of shared co-authors 11

Richard Bonneau

Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation

Career Start Year 1983

Number of shared co-authors 6

Olivier Lichtarge

Baylor College of Medicine

Career Start Year 1981

Number of shared co-authors 5

Richard Durbin

University of Cambridge

Career Start Year 1964

Number of shared co-authors 6

row(s) 1 - 30 of 30

Chris Sander

Broad Institute of MIT and Harvard

Co-authored papers 35

Andrew C Kruse

Blavatnik Institute, Harvard Medical School

Co-authored papers 11

Bino John

University of Pittsburgh School of Medicine

Co-authored papers 5

Oliver Kohlbacher

Max Planck Institute for Developmental Biology

Co-authored papers 4

Erik Larsson

Co-authored papers 3

Yuanpeng J Huang

Center for Advanced Biotechnology and Medicine, The State University of New Jersey

Co-authored papers 3

Mihaela Zavolan

Co-authored papers 3

Gaetano T Montelione

Rensselaer Polytechnic Institute

Co-authored papers 3

Douglas M Fowler

University of Washington, USA Brotman Baty Institute for Precision Medicine

Co-authored papers 2

Chang C Liu

University of California irvine

Co-authored papers 2

Frederick P Roth

University of Toronto

Co-authored papers 2

Alexei A Aravin

Co-authored papers 2

Assaf Alon

Harvard Medical School

Co-authored papers 2

Anders Jacobsen Skanderup

Co-authored papers 2

Christina S Leslie

Co-authored papers 2

Burkhard Rost

Technical University of Munich (TUM)

Co-authored papers 2

Lucy J Colwell

Google Research

Co-authored papers 2

Aashish Manglik

Department of Pharmaceutical Chemistry, University of California San Francisco

Co-authored papers 2

Eran Segal

Weizmann Institute of Science

Co-authored papers 2

Pamela A Silver

Harvard Medical School

Co-authored papers 2

John J Fak

Co-authored papers 1

Julian Mintseris

Co-authored papers 1

Stephanie J Spielman

Alex's Lemonade Stand Foundation

Co-authored papers 1

Matthew E Hurles

Wellcome Sanger Institute

Co-authored papers 1

Masayori Inouye

Robert Wood Johnson Medical School, Rutgers University

Co-authored papers 1

William C Hahn

Broad Institute of MIT and Harvard, USA Dana-Farber Cancer Institute

Co-authored papers 1

Bonnie Berger

Massachusetts Institute of Technology

Co-authored papers 1

Jeremy F Reiter

Cardiovascular Research Institute

Co-authored papers 1

Ville Mustonen

University of Helsinki

Co-authored papers 1

Ishan Deshpande

Department of Pharmaceutical Chemistry, University of California san francisco

Co-authored papers 1

1 - 30

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