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Author Details

Zheng Wang
University of Miami
2009
45
19
PMIDPaper TitleJournal TitlePublished Year
37302805scHiMe: predicting single-cell DNA methylation levels based on single-cell Hi-C data.Brief Bioinform2023
37478379HiC4D: forecasting spatiotemporal Hi-C data with residual ConvLSTM.Brief Bioinform2023
37440599DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.PLoS Comput Biol2023
35328034Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions.Genes (Basel)2022
35741810scHiCEmbed: Bin-Specific Embeddings of Single-Cell Hi-C Data Using Graph Auto-Encoders.Genes (Basel)2022
35842895Predicting residue-specific qualities of individual protein models using residual neural networks and graph neural networks.Proteins2022
36369063Placing human gene families into their evolutionary context.Hum Genomics2022
35118378PANDA2: protein function prediction using graph neural networks.NAR Genom Bioinform2022
34072879Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential.Int J Mol Sci2021
34428304The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer-promoter interaction and R-loop formation.Nucleic Acids Res2021
32191325Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi.Mol Biol Evol2020
32631256MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials.BMC Bioinformatics2020
31671634HiCNN2: Enhancing the Resolution of Hi-C Data Using an Ensemble of Convolutional Neural Networks.Genes (Basel)2019
31787081Exploring the 2D and 3D structural properties of topologically associating domains.BMC Bioinformatics2019
31872104Comprehensive climate factor characteristics and quantitative analysis of their impacts on grain yields in China's grain-producing areas.Heliyon2019
29186290scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data.Bioinformatics2018
30591009Reconstructing high-resolution chromosome three-dimensional structures by Hi-C complex networks.BMC Bioinformatics2018
30305653GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms.Sci Rep2018
29472600PANDA: Protein function prediction using domain architecture and affinity propagation.Sci Rep2018
29713370SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity.Source Code Biol Med2018
26763289Benchmarking Deep Networks for Predicting Residue-Specific Quality of Individual Protein Models in CASP11.Sci Rep2016
27604469An expanded evaluation of protein function prediction methods shows an improvement in accuracy.Genome Biol2016
27807743Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling.Adv Exp Med Biol2016
26797014Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks.Sci Rep2016
24731387Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment.BMC Struct Biol2014
25406415PCP-ML: protein characterization package for machine learning.BMC Res Notes2014
24776231SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.BMC Bioinformatics2014
23353650A large-scale evaluation of computational protein function prediction.Nat Methods2013
23507482Aberrant epigenetic gene regulation in lymphoid malignancies.Semin Hematol2013
23514381Three-level prediction of protein function by combining profile-sequence search, profile-profile search, and domain co-occurrence networks.BMC Bioinformatics2013
23536826The properties of genome conformation and spatial gene interaction and regulation networks of normal and malignant human cell types.PLoS One2013
22057943An iterative self-refining and self-evaluating approach for protein model quality estimation.Protein Sci2012
22809379Recursive protein modeling: a divide and conquer strategy for Protein Structure Prediction and its case study in CASP9.J Bioinform Comput Biol2012
22545707The MULTICOM toolbox for protein structure prediction.BMC Bioinformatics2012
22252370Evolutionary dynamics of protein domain architecture in plants.BMC Evol Biol2012
22369646Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics.BMC Genomics2012
21455299A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny.PLoS One2011
21989082A conformation ensemble approach to protein residue-residue contact.BMC Struct Biol2011
21546397APOLLO: a quality assessment service for single and multiple protein models.Bioinformatics2011
20082720SoyDB: a knowledge database of soybean transcription factors.BMC Plant Biol2010
20438647SeqRate: sequence-based protein folding type classification and rates prediction.BMC Bioinformatics2010
20150411MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8.Bioinformatics2010
19004001Evaluating the absolute quality of a single protein model using structural features and support vector machines.Proteins2009
19544564Prediction of global and local quality of CASP8 models by MULTICOM series.Proteins2009
19420062NNcon: improved protein contact map prediction using 2D-recursive neural networks.Nucleic Acids Res2009
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Collaborators

Jianlin Cheng
University of Missouri
Co-authored papers 21
Dong Xu
University of Missouri
Co-authored papers 7
Renzhi Cao
Pacific Lutheran University
Co-authored papers 5
Chenguang Zhao
Center for Cognition and Neuroergonomics, Beijing Normal University
Co-authored papers 5
Christopher Funk
University of Colorado School of Medicine
Co-authored papers 2
Qingtian Gong
Fudan University
Co-authored papers 2
Tal Ronnen Oron
Buck Institute for Research On Aging
Co-authored papers 2
Haixuan Yang
University of Galway
Co-authored papers 2
Sean D Mooney
University of Washington
Co-authored papers 2
Patricia C Babbitt
University of California san francisco
Co-authored papers 2
Hai Fang
University of Bristol
Co-authored papers 2
Stefano Toppo
University of Padova
Co-authored papers 2
Tobias Hamp
Inc. San Diego
Co-authored papers 2
Asa Ben-Hur
Colorado State University
Co-authored papers 2
Michal Linial
Institute of Life Sciences, The Hebrew University of Jerusalem
Co-authored papers 2
Karin Verspoor
National Centre for Infections in Cancer, 5Peter MacCallum Cancer Centre
Co-authored papers 2
Daisuke Kihara
Purdue University
Co-authored papers 2
Iddo Friedberg
Iowa State University
Co-authored papers 2
David T Jones
University College London
Co-authored papers 2
Nives ??kunca
ETH Zurich, Universitatstrasse 19
Co-authored papers 2
Wyatt T Clark
BioMarin Pharmaceutical Inc.
Co-authored papers 2
Steven E Brenner
University of California berkeley
Co-authored papers 2
Weidong Tian
Institute of Biostatistics, Fudan University
Co-authored papers 2
Rita Casadio
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 2
Yuanpeng Zhou
Fudan University
Co-authored papers 2
Burkhard Rost
Technical University of Munich (TUM)
Co-authored papers 2
Domenico Cozzetto
Imperial College London
Co-authored papers 2
Prajwal Bhat
Royal Holloway University of London
Co-authored papers 2
Kevin Bryson
University of Glasgow
Co-authored papers 2
Pekka Koskinen
University of Helsinki and Helsinki University Hospital
Co-authored papers 2
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