Author details

Full Name

Jianzhu Ma

Affiliation

Purdue University

ORCID

Career Start Year

2012

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
35238654	Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization.	Proc Natl Acad Sci U S A	2022
35853872	Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma.	Cell Discov	2022
35684708	MobilePrune: Neural Network Compression via <i>â¿¿</i><sub>0</sub> Sparse Group Lasso on the Mobile System.	Sensors (Basel)	2022
36070863	Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data.	Brief Bioinform	2022
34999749	scPretrain: multi-task self-supervised learning for cell-type classification.	Bioinformatics	2022
34223192	Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients.	Nat Cancer	2021
34819669	A multi-scale map of cell structure fusing protein images and interactions.	Nature	2021
34729476	ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways.	NAR Genom Bioinform	2021
34252957	Disease gene prediction with privileged information and heteroscedastic dropout.	Bioinformatics	2021
34252932	Predicting MHC-peptide binding affinity by differential boundary tree.	Bioinformatics	2021
32619550	Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome.	Cell Syst	2020
33096023	Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells.	Cancer Cell	2020
32657383	Artificial-cell-type aware cell-type classification in CITE-seq.	Bioinformatics	2020
30878356	DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.	Cell Syst	2019
31235599	Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation.	Proc Natl Acad Sci U S A	2019
30726869	Classifying tumors by supervised network propagation.	Bioinformatics	2019
29218918	Annotating gene sets by mining large literature collections with protein networks.	Pac Symp Biocomput	2018
29906441	Visible Machine Learning for Biomedicine.	Cell	2018
29949979	Classifying tumors by supervised network propagation.	Bioinformatics	2018
30297789	Typing tumors using pathways selected by somatic evolution.	Nat Commun	2018
29505029	Using deep learning to model the hierarchical structure and function of a cell.	Nat Methods	2018
28881999	DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields.	Bioinformatics	2017
26752681	Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.	Sci Rep	2016
27587688	AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields.	Bioinformatics	2016
27587686	ModuleAlign: module-based global alignment of protein-protein interaction networks.	Bioinformatics	2016
26230689	DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields.	Int J Mol Sci	2015
26275894	Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.	Bioinformatics	2015
26339631	AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model.	Biomed Res Int	2015
24675572	MRFalign: protein homology detection through alignment of Markov random fields.	PLoS Comput Biol	2014
24573471	RaptorX server: a resource for template-based protein structure modeling.	Methods Mol Biol	2014
24629187	Algorithms, applications, and challenges of protein structure alignment.	Adv Protein Chem Struct Biol	2014
23486213	Protein structure alignment beyond spatial proximity.	Sci Rep	2013
23812991	Protein threading using context-specific alignment potential.	Bioinformatics	2013
22689779	A conditional neural fields model for protein threading.	Bioinformatics	2012

1 - 34 of 34

Brian Hie

Stanford University

Career Start Year 2016

Number of shared co-authors 1

Jie Hou

Saint Louis University

Career Start Year 2015

Number of shared co-authors 0

Chen Li

Biomedicine Discovery Institute, Monash 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

Renzhi Cao

Pacific Lutheran University

Career Start Year 2013

Number of shared co-authors 0

Lucy J Colwell

Google Research

Career Start Year 2009

Number of shared co-authors 0

Zheng Wang

University of Miami

Career Start Year 2009

Number of shared co-authors 0

Xin Gao

King Abdullah University of Science and Technology (KAUST)

Career Start Year 2007

Number of shared co-authors 2

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

Xiuzhen Huang

Cedars-Sinai Medical Center.

Career Start Year 2006

Number of shared co-authors 0

Yanjun Qi

University of Virginiagrid.27755.32

Career Start Year 2005

Number of shared co-authors 1

Jianlin Cheng

University of Missouri

Career Start Year 2005

Number of shared co-authors 0

Shanfeng Zhu

Shanghai Qi Zhi Institute

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 1

Dukka B Kc

Michigan Technological University

Career Start Year 2002

Number of shared co-authors 0

Predrag Radivojac

Indiana University

Career Start Year 2002

Number of shared co-authors 1

Dmitry Korkin

Worcester Polytechnic Institute

Career Start Year 2002

Number of shared co-authors 0

Chun-Nan Hsu

University of California, C.N.H.) and Veterans Affairs San Diego Healthcare System

Career Start Year 2001

Number of shared co-authors 1

Lenore J Cowen

Tufts University, 177 College Avenue

Career Start Year 2001

Number of shared co-authors 6

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 2

Volkan Atalay

Middle East Technical University

Career Start Year 1999

Number of shared co-authors 0

Zoran Obradovic

Center for Data Analytics and Biomedical Informatics, Temple University

Career Start Year 1998

Number of shared co-authors 0

Dong Xu

University of Missouri

Career Start Year 1998

Number of shared co-authors 1

Asa Ben-Hur

Colorado State University

Career Start Year 1996

Number of shared co-authors 1

Hiroshi Mamitsuka

Institute for Chemical Research, Kyoto University

Career Start Year 1994

Number of shared co-authors 0

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 4

Richard Bonneau

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

Career Start Year 1983

Number of shared co-authors 0

row(s) 1 - 30 of 30

Sheng Wang

University of Texas at Arlington

Co-authored papers 14

Trey Ideker (CM4AI)

University of California San Diego

Co-authored papers 11

Jinbo Xu

Toyota Technological Institute at Chicago

Co-authored papers 9

Jian Peng

University of Illinois

Co-authored papers 8

Samson H Fong

University of California San Diego

Co-authored papers 5

Michael Ku Yu

University of California San Diego

Co-authored papers 4

Jason F Kreisberg

University of California San Diego

Co-authored papers 4

Fan Zheng

University of California San Diego

Co-authored papers 3

Wei Zhang

University of California San Diego

Co-authored papers 3

Jisoo Park

University of California San Diego san francisco

Co-authored papers 2

Roded Sharan

Tel Aviv University

Co-authored papers 2

Keiichiro Ono

university of california san diego

Co-authored papers 2

Jingtian Zhou

Co-authored papers 2

Barry Demchak

University of California

Co-authored papers 2

Yunan Luo

Georgia Institute of Technology

Co-authored papers 2

Katherine Licon

University of California San Diego

Co-authored papers 2

John Paul Shen

The University of Texas MD Anderson Cancer Center

Co-authored papers 2

John Lee

University of California San Diego

Co-authored papers 2

Tina Wang

Harvard University

Co-authored papers 1

Adriana Pitea

University of California San Diego

Co-authored papers 1

Edward W Huang

University of Illinois at Urbana-Champaign

Co-authored papers 1

Jing Chen

University of Science and Technology of China

Co-authored papers 1

Soufiane Mourragui

Oncode Institute, The Netherlands Cancer Institute

Co-authored papers 1

Brent M Kuenzi

Moffitt Cancer Center

Co-authored papers 1

Michael Chen

University of California San Diego

Co-authored papers 1

Tian Zhang

Harvard Medical School

Co-authored papers 1

Dexter Pratt (CM4AI)

UC San Diego

Co-authored papers 1

Joseph R Ecker

The Salk Institute for Biological Studies

Co-authored papers 1

Eric Sage

University of California San Diego

Co-authored papers 1

Marc Hafner

Harvard Medical School

Co-authored papers 1

1 - 30

Author Details

Column Actions

Recommended Authors

Collaborators