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Author Details

Sheng Wang
University of Texas at Arlington
2008
65
28
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
35972373Molecule Sequence Generation with Rebalanced Variational Autoencoder Loss.J Comput Biol2023
36977053Effect of Soil Washing with an Amino-Acid-Derived Ionic Liquid on the Properties of Cd-Contaminated Paddy Soil.Toxics2023
36291662Shared Genetic Regulatory Networks Contribute to Neuropathic and Inflammatory Pain: Multi-Omics Systems Analysis.Biomolecules2022
35740899Deep Ensemble Learning with Atrous Spatial Pyramid Networks for Protein Secondary Structure Prediction.Biomolecules2022
34473376When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14-(tFold for CASP14 contact prediction).Proteins2021
31593235Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing.Bioinformatics2020
31913436DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing.Bioinformatics2020
32831134Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs.Genome Biol2020
31583631A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning.Methods Mol Biol2020
31077312Correction to: Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning.Gigascience2019
29931155Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.Brief Bioinform2019
30010792AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.Bioinformatics2019
30084960PredMP: a web server for de novo prediction and visualization of membrane proteins.Bioinformatics2019
31471916Analysis of distance-based protein structure prediction by deep learning in CASP13.Proteins2019
30893303Identification of pathways associated with chemosensitivity through network embedding.PLoS Comput Biol2019
28845538Analysis of deep learning methods for blind protein contact prediction in CASP12.Proteins2018
29959357Marine microalgae bioengineered Schizochytrium sp. meal hydrolysates inhibits acute inflammation.Sci Rep2018
29854161Framing Electronic Medical Records as Polylingual Documents in Query Expansion.AMIA Annu Symp Proc2018
29949980Protein threading using residue co-variation and deep learning.Bioinformatics2018
30297789Typing tumors using pathways selected by somatic evolution.Nat Commun2018
30423085An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing.Bioinformatics2018
30413241A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.Biophys J2018
29648610Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning.Gigascience2018
29423650PRIM: An Efficient Preconditioning Iterative Reweighted Least Squares Method for Parallel Brain MRI Reconstruction.Neuroinformatics2018
29745828RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning.BMC Bioinformatics2018
29790960ComplexContact: a web server for inter-protein contact prediction using deep learning.Nucleic Acids Res2018
29659695DeepSimulator: a deep simulator for Nanopore sequencing.Bioinformatics2018
29310625Monocular lens dislocation due to vomiting-a case report.BMC Ophthalmol2018
29218918Annotating gene sets by mining large literature collections with protein networks.Pac Symp Biocomput2018
29218916VisAGE: Integrating external knowledge into electronic medical record visualization.Pac Symp Biocomput2018
29218868Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action.Pac Symp Biocomput2018
29069344DEEPre: sequence-based enzyme EC number prediction by deep learning.Bioinformatics2018
27896959PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION.Pac Symp Biocomput2017
29208709Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome.Proc Natl Acad Sci U S A2017
28957654Folding Membrane Proteins by Deep Transfer Learning.Cell Syst2017
28881999DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields.Bioinformatics2017
28807790The functional domains for Baxâ¿¿2 aggregate-mediated caspase 8-dependent cell death.Exp Cell Res2017
28669749Extracellular vesicles in gastrointestinal cancer in conjunction with microbiota: On the border of Kingdoms.Biochim Biophys Acta Rev Cancer2017
28849559Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.Methods Mol Biol2017
28574983Network-assisted target identification for haploinsufficiency and homozygous profiling screens.PLoS Comput Biol2017
28056090Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.PLoS Comput Biol2017
26752681Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.Sci Rep2016
28299178DWCox: A density-weighted Cox model for outlier-robust prediction of prostate cancer survival.F1000Res2016
28884168AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling.Mach Learn Knowl Discov Databases2016
26590263Lynx: a knowledge base and an analytical workbench for integrative medicine.Nucleic Acids Res2016
27587688AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields.Bioinformatics2016
27307635CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.Bioinformatics2016
27112573RaptorX-Property: a web server for protein structure property prediction.Nucleic Acids Res2016
27112569CoinFold: a web server for protein contact prediction and contact-assisted protein folding.Nucleic Acids Res2016
26230689DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields.Int J Mol Sci2015
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Collaborators

Jinbo Xu
Toyota Technological Institute at Chicago
Co-authored papers 24
Jianzhu Ma
Purdue University
Co-authored papers 14
Jian Peng
University of Illinois
Co-authored papers 13
Xin Gao
King Abdullah University of Science and Technology (KAUST)
Co-authored papers 8
Edward W Huang
University of Illinois at Urbana-Champaign
Co-authored papers 4
Chengxiang Zhai
University of Illinois Urbana-Champaign
Co-authored papers 3
Lachlan J M Coin
The Peter Doherty Institute for Infection and Immunity, The University of Melbourne
Co-authored papers 2
Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 2
Tobin R Sosnick
Institute for Biophysical Dynamics, The University of Chicago
Co-authored papers 2
Jiawei Han
University of Illinois at Urbana-Champaign
Co-authored papers 2
Zhen Li
Co-authored papers 2
Michael Ku Yu
University of California San Diego
Co-authored papers 1
Bonnie Berger
Massachusetts Institute of Technology
Co-authored papers 1
Saurabh Sinha
Georgia Institute of Technology
Co-authored papers 1
Fan Zheng
University of California San Diego
Co-authored papers 1
Liewei Wang
Mayo Clinic
Co-authored papers 1
Fa Zhang
University of Chinese Academy of Sciences
Co-authored papers 1
Inna Dubchak
Lawrence Berkeley National Laboratory
Co-authored papers 1
John Paul Shen
The University of Texas MD Anderson Cancer Center
Co-authored papers 1
Hyunghoon Cho
Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Stanford University, Yale University
Co-authored papers 1
Yunan Luo
Georgia Institute of Technology
Co-authored papers 1
Xiaohua Wan
Beijing Institute of Technology
Co-authored papers 1
Yanyi Huang
Co-authored papers 1
Justin K Huang
The University of Texas MD Anderson Cancer Center
Co-authored papers 1
Karl F Freed
University of Chicago
Co-authored papers 1
Wei Zhang
University of California San Diego
Co-authored papers 1
Albert Lawrence
National Center for Microscopy and Imaging Research, University of California
Co-authored papers 1
Release 1.2