Author details

Full Name

Jian Peng

Affiliation

University of Illinois

ORCID

Career Start Year

2009

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
37129358	Metabolic activity organizes olfactory representations.	Elife	2023
35238654	Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization.	Proc Natl Acad Sci U S A	2022
33957083	Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains.	Mol Cell	2021
34873599	A large-scale systematic survey of SARS-CoV-2 antibodies reveals recurring molecular features.	bioRxiv	2021
34593817	ECNet is an evolutionary context-integrated deep learning framework for protein engineering.	Nat Commun	2021
34795232	Jumper enables discontinuous transcript assembly in coronaviruses.	Nat Commun	2021
34252956	Bayesian information sharing enhances detection of regulatory associations in rare cell types.	Bioinformatics	2021
34223192	Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients.	Nat Cancer	2021
33214279	A marine microbiome antifungal targets urgent-threat drug-resistant fungi.	Science	2020
30893303	Identification of pathways associated with chemosensitivity through network embedding.	PLoS Comput Biol	2019
30010790	Metagenomic binning through low-density hashing.	Bioinformatics	2019
31235599	Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation.	Proc Natl Acad Sci U S A	2019
31483777	Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction.	PLoS Comput Biol	2019
29218868	Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action.	Pac Symp Biocomput	2018
29936184	Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks.	Cell Syst	2018
30138580	Principles of Systems Biology, No. 31.	Cell Syst	2018
30745791	DPPred: An Effective Prediction Framework with Concise Discriminative Patterns.	IEEE Trans Knowl Data Eng	2018
30297789	Typing tumors using pathways selected by somatic evolution.	Nat Commun	2018
30423083	Learning structural motif representations for efficient protein structure search.	Bioinformatics	2018
29725668	Generalizable visualization of mega-scale single-cell data.	Res Comput Mol Biol	2018
29408992	Reconstructing spatial organizations of chromosomes through manifold learning.	Nucleic Acids Res	2018
29275173	Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks.	Cell Syst	2018
29218918	Annotating gene sets by mining large literature collections with protein networks.	Pac Symp Biocomput	2018
27896959	PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION.	Pac Symp Biocomput	2017
28131822	Genome-Scale Networks Link Neurodegenerative Disease Genes to Î±-Synuclein through Specific Molecular Pathways.	Cell Syst	2017
28570104	Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining.	J Comput Biol	2017
28924171	A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information.	Nat Commun	2017
28574983	Network-assisted target identification for haploinsufficiency and homozygous profiling screens.	PLoS Comput Biol	2017
27897012	SCALABLE VISUALIZATION FOR HIGH-DIMENSIONAL SINGLE-CELL DATA.	Pac Symp Biocomput	2017
26752681	Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.	Sci Rep	2016
28163983	DPClass: An Effective but Concise Discriminative Patterns-Based Classification Framework.	Proc SIAM Int Conf Data Min	2016
28299178	DWCox: A density-weighted Cox model for outlier-robust prediction of prostate cancer survival.	F1000Res	2016
28127592	Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning.	Res Comput Mol Biol	2016
28174677	MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance.	Proc SIAM Int Conf Data Min	2016
27889536	Compact Integration of Multi-Network Topology for Functional Analysis of Genes.	Cell Syst	2016
26930205	Reconstructing Causal Biological Networks through Active Learning.	PLoS One	2016
27054987	Compressive mapping for next-generation sequencing.	Nat Biotechnol	2016
25748910	Quality score compression improves genotyping accuracy.	Nat Biotechnol	2015
28748230	Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks.	Res Comput Mol Biol	2015
26098139	Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.	J Comput Biol	2015
26072504	Exploiting ontology graph for predicting sparsely annotated gene function.	Bioinformatics	2015
25910212	Widespread macromolecular interaction perturbations in human genetic disorders.	Cell	2015
24675685	HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.	PLoS Comput Biol	2014
25036637	A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.	Cell	2014
23486213	Protein structure alignment beyond spatial proximity.	Sci Rep	2013
23594911	Computational solutions for omics data.	Nat Rev Genet	2013
23812995	Compressive genomics for protein databases.	Bioinformatics	2013
22095743	Modeling large regions in proteins: applications to loops, termini, and folding.	Protein Sci	2012
22937800	A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.	Genome Biol	2012
22689779	A conditional neural fields model for protein threading.	Bioinformatics	2012

1 - 50 of 61

Chengxin Zhang

University of Michigan ann arbor

Career Start Year 2017

Number of shared co-authors 0

Jie Hou

Saint Louis University

Career Start Year 2015

Number of shared co-authors 0

Wei Zheng

University of Michigan ann arbor

Career Start Year 2013

Number of shared co-authors 0

Lucy J Colwell

Google Research

Career Start Year 2009

Number of shared co-authors 1

Zheng Wang

University of Miami

Career Start Year 2009

Number of shared co-authors 0

Stefan R Maetschke

Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics

Career Start Year 2007

Number of shared co-authors 0

Yuanfang Guan

University of Michigan ann arbor

Career Start Year 2007

Number of shared co-authors 1

Xin Gao

King Abdullah University of Science and Technology (KAUST)

Career Start Year 2007

Number of shared co-authors 2

Yanjun Qi

University of Virginiagrid.27755.32

Career Start Year 2005

Number of shared co-authors 2

Jianlin Cheng

University of Missouri

Career Start Year 2005

Number of shared co-authors 0

Jiangning Song

Monash Data Futures Institute, Monash University

Career Start Year 2004

Number of shared co-authors 0

George Karypis

University of Minnesota

Career Start Year 2003

Number of shared co-authors 0

Dongsup Kim

Korea Advanced Institute of Science and Technology

Career Start Year 2003

Number of shared co-authors 2

Dmitry Korkin

Worcester Polytechnic Institute

Career Start Year 2002

Number of shared co-authors 3

Kyle Ellrott

Oregon Health & Science University

Career Start Year 2002

Number of shared co-authors 1

Predrag Radivojac

Indiana University

Career Start Year 2002

Number of shared co-authors 2

Haiyuan Yu

Weill Institute for Cell and Molecular Biology, Cornell University

Career Start Year 2001

Number of shared co-authors 10

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 3

Marc A Marti-Renom

Universitat Pompeu Fabra (UPF)

Career Start Year 1998

Number of shared co-authors 0

Dong Xu

University of Missouri

Career Start Year 1998

Number of shared co-authors 2

Patrick Aloy

Institucio Catalana de Recerca i Estudis Avancats (ICREA)

Career Start Year 1997

Number of shared co-authors 12

Asa Ben-Hur

Colorado State University

Career Start Year 1996

Number of shared co-authors 2

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 4

Hiroshi Mamitsuka

Institute for Chemical Research, Kyoto University

Career Start Year 1994

Number of shared co-authors 1

Steven E Brenner

University of California berkeley

Career Start Year 1994

Number of shared co-authors 5

Burkhard Rost

Technical University of Munich (TUM)

Career Start Year 1992

Number of shared co-authors 1

Zhiping Weng

University of Massachusetts Medical School

Career Start Year 1992

Number of shared co-authors 3

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 8

Ram Samudrala

Jacobs School of Medicine and Biomedical Sciences, University at Buffalo

Career Start Year 1990

Number of shared co-authors 1

Richard Bonneau

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

Career Start Year 1983

Number of shared co-authors 2

row(s) 1 - 30 of 30

Bonnie Berger

Massachusetts Institute of Technology

Co-authored papers 22

Jinbo Xu

Toyota Technological Institute at Chicago

Co-authored papers 16

Sheng Wang

University of Texas at Arlington

Co-authored papers 13

Jianzhu Ma

Purdue University

Co-authored papers 8

Yunan Luo

Georgia Institute of Technology

Co-authored papers 8

Hyunghoon Cho

Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Stanford University, Yale University

Co-authored papers 8

Jiawei Han

University of Illinois at Urbana-Champaign

Co-authored papers 6

Susan Lindquist

Whitehead Institute for Biomedical Research

Co-authored papers 3

Trey Ideker (CM4AI)

University of California San Diego

Co-authored papers 3

Tobin R Sosnick

Institute for Biophysical Dynamics, The University of Chicago

Co-authored papers 3

Karl F Freed

University of Chicago

Co-authored papers 3

Edward W Huang

University of Illinois at Urbana-Champaign

Co-authored papers 2

Roded Sharan

Tel Aviv University

Co-authored papers 2

Marc Vidal

Blavatnik Institute, Harvard Medical School

Co-authored papers 2

Jingtian Zhou

Co-authored papers 2

Jadwiga Bienkowska

Pfizer Global Research and Development La Jolla

Co-authored papers 2

John Paul Shen

The University of Texas MD Anderson Cancer Center

Co-authored papers 2

Mandy H Y Lam

Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital

Co-authored papers 2

Anne-Claude Gingras

Lunenfeld-Tanenbaum Research Institute

Co-authored papers 2

Yu Xia

College of Information Engineering, Zhejiang University of Technology

Co-authored papers 1

Guangyu Zhou

Peking University

Co-authored papers 1

Liewei Wang

Mayo Clinic

Co-authored papers 1

Rainer Spang

University of Regensburg

Co-authored papers 1

Song Yi

Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin

Co-authored papers 1

Soufiane Mourragui

Oncode Institute, The Netherlands Cancer Institute

Co-authored papers 1

Pavan K Auluck

Co-authored papers 1

Zhemin Zhou

Pasteurien College, Suzhou Medical College of Soochow University

Co-authored papers 1

Norbert Perrimon

Co-authored papers 1

Fabio Vandin

University of Padova

Co-authored papers 1

Justin Nelson

Co-authored papers 1

1 - 30

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