Author details

Full Name

Lenore J Cowen

Affiliation

Tufts University, 177 College Avenue

ORCID

Career Start Year

2001

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
37289807	Contrastive learning in protein language space predicts interactions between drugs and protein targets.	Proc Natl Acad Sci U S A	2023
37897686	TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions.	Bioinformatics	2023
34995299	Cognitive cascades: How to model (and potentially counter) the spread of fake news.	PLoS One	2022
35537462	Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience.	Annu Rev Biomed Data Sci	2022
35575379	GLIDER: function prediction from GLIDE-based neighborhoods.	Bioinformatics	2022
35758793	Topsy-Turvy: integrating a global view into sequence-based PPI prediction.	Bioinformatics	2022
36097278	Evaluation of fluorescence-based viability stains in cells dissociated from scleractinian coral Pocillopora damicornis.	Sci Rep	2022
35976727	MEDFORD: A human- and machine-readable metadata markup language.	Database (Oxford)	2022
33591921	Majority Vote Cascading: A Semi-Supervised Framework for Improving Protein Function Prediction.	IEEE/ACM Trans Comput Biol Bioinform	2022
35044538	Bioengineered models of Parkinson's disease using patient-derived dopaminergic neurons exhibit distinct biological profiles in a 3D microenvironment.	Cell Mol Life Sci	2022
34536380	D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions.	Cell Syst	2021
36699351	MUNDO: protein function prediction embedded in a multispecies world.	Bioinform Adv	2021
33691030	Bioinformatics of corals: Investigating heterogeneous omics data from coral holobionts for insight into reef health and resillience.	Pac Symp Biocomput	2021
32455252	Cell shape, and not 2D migration, predicts extracellular matrix-driven 3D cell invasion in breast cancer.	APL Bioeng	2020
32657369	GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks.	Bioinformatics	2020
29589565	Detangling PPI networks to uncover functionally meaningful clusters.	BMC Syst Biol	2018
30453938	Retraction Note: detangling PPI networks to uncover functionally meaningful clusters.	BMC Syst Biol	2018
27896958	WHEN SHOULD WE NOT TRANSFER FUNCTIONAL ANNOTATION BETWEEN SEQUENCE PARALOGS?	Pac Symp Biocomput	2017
28607512	Network propagation: a universal amplifier of genetic associations.	Nat Rev Genet	2017
26357074	MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search.	IEEE/ACM Trans Comput Biol Bioinform	2015
24931987	New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence.	Bioinformatics	2014
23331614	Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data.	BMC Bioinformatics	2013
24194834	Going the distance for protein function prediction: a new distance metric for protein interaction networks.	PLoS One	2013
23812995	Compressive genomics for protein databases.	Bioinformatics	2013
21464511	Touring protein space with Matt.	IEEE/ACM Trans Comput Biol Bioinform	2012
24806988	Molli: interactive visualization for exploratory protein analysis.	IEEE Comput Graph Appl	2012
23039758	Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.	BMC Bioinformatics	2012
22408192	SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone.	Bioinformatics	2012
22095906	STITCHER: Dynamic assembly of likely amyloid and prion Î²-structures from secondary structure predictions.	Proteins	2012
21882903	Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut.	J Comput Biol	2011
20377458	Evaluating between-pathway models with expression data.	J Comput Biol	2010
20529918	Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution.	Bioinformatics	2010
20147619	Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system.	Proc Natl Acad Sci U S A	2010
19325876	BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis.	PLoS Comput Biol	2009
19399174	Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.	PLoS One	2009
19389731	Augmented training of hidden Markov models to recognize remote homologs via simulated evolution.	Bioinformatics	2009
18193941	Matt: local flexibility aids protein multiple structure alignment.	PLoS Comput Biol	2008
18551181	Protein coding gene nucleotide substitution pattern in the apicomplexan protozoa Cryptosporidium parvum and Cryptosporidium hominis.	Comp Funct Genomics	2008
16547930	Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins.	Proteins	2006
16108716	Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils.	J Comput Biol	2005
12015881	Predicting the beta-helix fold from protein sequence data.	J Comput Biol	2002
11752429	BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens.	Proc Natl Acad Sci U S A	2001
11721928	Array-to-array transfer of an artificial nose classifier.	Anal Chem	2001

1 - 43 of 43

Jianzhu Ma

Purdue University

Career Start Year 2012

Number of shared co-authors 6

Tobias Hamp

Inc. San Diego

Career Start Year 2011

Number of shared co-authors 0

Lucy J Colwell

Google Research

Career Start Year 2009

Number of shared co-authors 0

Sheng Wang

University of Texas at Arlington

Career Start Year 2008

Number of shared co-authors 3

Aleksandar Stojmirovic

Janssen Research & Development LLC

Career Start Year 2007

Number of shared co-authors 1

Alberto Paccanaro

University of London

Career Start Year 2005

Number of shared co-authors 0

George Karypis

University of Minnesota

Career Start Year 2003

Number of shared co-authors 0

Predrag Radivojac

Indiana University

Career Start Year 2002

Number of shared co-authors 0

Dmitry Korkin

Worcester Polytechnic Institute

Career Start Year 2002

Number of shared co-authors 0

Julian Gough

Medical Research Council Laboratory of Molecular Biology

Career Start Year 2001

Number of shared co-authors 1

Dariusz Przybylski

Howard Hughes Medical Institute, Brandeis University

Career Start Year 2001

Number of shared co-authors 0

Iddo Friedberg

Iowa State University

Career Start Year 1997

Number of shared co-authors 0

Patrick Aloy

Institucio Catalana de Recerca i Estudis Avancats (ICREA)

Career Start Year 1997

Number of shared co-authors 1

Asa Ben-Hur

Colorado State University

Career Start Year 1996

Number of shared co-authors 1

Yu Xia

College of Information Engineering, Zhejiang University of Technology

Career Start Year 1996

Number of shared co-authors 3

Steven E Brenner

University of California berkeley

Career Start Year 1994

Number of shared co-authors 2

Edward M Marcotte

University of Texas

Career Start Year 1993

Number of shared co-authors 2

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 1

Erik L L Sonnhammer

Stockholm University

Career Start Year 1992

Number of shared co-authors 0

Burkhard Rost

Technical University of Munich (TUM)

Career Start Year 1992

Number of shared co-authors 1

Jaap Heringa

VU University Amsterdam

Career Start Year 1991

Number of shared co-authors 0

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 1

Robert B Russell

Heidelberg University

Career Start Year 1991

Number of shared co-authors 0

Ram Samudrala

Jacobs School of Medicine and Biomedical Sciences, University at Buffalo

Career Start Year 1990

Number of shared co-authors 0

Adam Godzik

University of California Riverside

Career Start Year 1987

Number of shared co-authors 1

Liisa Holm

Institute of Biotechnology, University of Helsinki

Career Start Year 1986

Number of shared co-authors 0

Richard Bonneau

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

Career Start Year 1983

Number of shared co-authors 0

Olivier Lichtarge

Baylor College of Medicine

Career Start Year 1981

Number of shared co-authors 1

Chris Sander

Broad Institute of MIT and Harvard

Career Start Year 1979

Number of shared co-authors 3

Rita Casadio

Department of Pharmacy and Biotechnology, University of Bologna

Career Start Year 1974

Number of shared co-authors 0

row(s) 1 - 30 of 30

Bonnie Berger

Massachusetts Institute of Technology

Co-authored papers 13

Jisoo Park

University of California San Diego san francisco

Co-authored papers 2

Jake Crawford

Perelman School of Medicine, University of Pennsylvania

Co-authored papers 2

Judith Klein-Seetharaman

School of Molecular Sciences & College of Health Solutions, Arizona State University

Co-authored papers 2

Susan Lindquist

Whitehead Institute for Biomedical Research

Co-authored papers 2

David L Kaplan

Co-authored papers 1

David R Walt

Brigham and Women's Hospital

Co-authored papers 1

Jian Peng

University of Illinois

Co-authored papers 1

Nathan Palmer

Harvard Medical School

Co-authored papers 1

Trey Ideker (CM4AI)

University of California San Diego

Co-authored papers 1

Benjamin J Raphael

Princeton University

Co-authored papers 1

Roded Sharan

Tel Aviv University

Co-authored papers 1

Bryan D Bryson

Massachusetts Institute of Technology, USA The Ragon Institute of MGH

Co-authored papers 1

1 - 13

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