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Author Details

Wei Zheng
University of Michigan ann arbor
2013
54
20
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37099469A Novel Tensor Learning Model for Joint Relational Triplet Extraction.IEEE Trans Cybern2024
36828268ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.J Mol Biol2023
37650367Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15.Proteins2023
36851671Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals.Viruses2023
35913147Characterization of Treponema denticola Major Surface Protein (Msp) by Deletion Analysis and Advanced Molecular Modeling.J Bacteriol2022
35844960Progressive assembly of multi-domain protein structures from cryo-EM density maps.Nat Comput Sci2022
35536281DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction.Nucleic Acids Res2022
35420129LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation.Nucleic Acids Res2022
35931779I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nat Protoc2022
33090512Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions.J Med Virol2021
33770072Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks.PLoS Comput Biol2021
33628593Patient-derived non-small cell lung cancer xenograft mirrors complex tumor heterogeneity.Cancer Biol Med2021
34873061Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction.Proc Natl Acad Sci U S A2021
34529671Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders.PLoS Comput Biol2021
34382712Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14.Proteins2021
34408149Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions.Nat Commun2021
34671415Emotion Recognition Based on EEG Using Generative Adversarial Nets and Convolutional Neural Network.Comput Math Methods Med2021
34012049Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin.Nat Commun2021
34331351Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14.Proteins2021
34355210Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations.Cell Rep Methods2021
33393786Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.J Proteome Res2021
32511314Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1.bioRxiv2020
31830252SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function.Bioinformatics2020
33083802Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps.bioRxiv2020
32284349The Human DNA Mismatch Repair Protein MSH3 Contains Nuclear Localization and Export Signals That Enable Nuclear-Cytosolic Shuttling in Response to Inflammation.Mol Cell Biol2020
32506493Landscape of variable domain of heavy-chain-only antibody repertoire from alpaca.Immunology2020
32109228Publisher Correction: Cryo-EM structure of the human MLL1 core complex bound to the nucleosome.Nat Commun2020
32265459Two-Level Protein Methylation Prediction using structure model-based features.Sci Rep2020
32200634Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1.J Proteome Res2020
32227201FUpred: detecting protein domains through deep-learning-based contact map prediction.Bioinformatics2020
31081035LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins.Nucleic Acids Res2019
31804488Cryo-EM structure of the human MLL1 core complex bound to the nucleosome.Nat Commun2019
31427836I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.Future Gener Comput Syst2019
31144641Incorporating User Generated Content for Drug Drug Interaction Extraction Based on Full Attention Mechanism.IEEE Trans Nanobioscience2019
27802931A large-scale comparative assessment of methods for residue-residue contact prediction.Brief Bioinform2018
30223767A document level neural model integrated domain knowledge for chemical-induced disease relations.BMC Bioinformatics2018
30572820Protein complexes identification based on go attributed network embedding.BMC Bioinformatics2018
29675426A Novel Method for Drug Screen to Regulate G Protein-Coupled Receptors in the Metabolic Network of Alzheimer's Disease.Biomed Res Int2018
29746916An effective neural model extracting document level chemical-induced disease relations from biomedical literature.J Biomed Inform2018
29534977MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.J Mol Biol2018
29077847Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths.Bioinformatics2018
27918921PrAS: Prediction of amidation sites using multiple feature extraction.Comput Biol Chem2017
29017459An attention-based effective neural model for drug-drug interactions extraction.BMC Bioinformatics2017
27899282BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts.J Mol Biol2017
27012903A graph kernel based on context vectors for extracting drug-drug interactions.J Biomed Inform2016
27378005gDNA-Prot: Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of protein sequence.J Theor Biol2016
27183223Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set.PLoS One2016
25705698Novel numerical characterization of protein sequences based on individual amino acid and its application.Biomed Res Int2015
26244562Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull.PLoS One2015
25891327Genome-wide interaction analysis of quantitative traits in outbred mice.Genet Res (Camb)2015
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Collaborators

Chengxin Zhang
University of Michigan ann arbor
Co-authored papers 15
Yang Zhang
University of Michigan ann arbor
Co-authored papers 10
Peter L Freddolino
University of Michigan ann arbor
Co-authored papers 4
Michael A Cianfrocco
Co-authored papers 2
Torsten Schwede
University of Basel
Co-authored papers 1
Stephen K Burley
The State University of New Jersey
Co-authored papers 1
Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 1
Dennis W Piehl
The State University of New Jersey
Co-authored papers 1
Gerardo Tauriello
University of Basel
Co-authored papers 1
Ivan Anischanka
and Institute for Protein Design, University of Washington
Co-authored papers 1
Augustin ????dek
Co-authored papers 1
David Baker
University of Washington
Co-authored papers 1
Michel Dumontier
Institute of Data Science, Maastricht University
Co-authored papers 1
Benjamin Webb
University of California san francisco
Co-authored papers 1
James Tolchard
European Bioinformatics Institute
Co-authored papers 1
Ian Sillitoe
University College London
Co-authored papers 1
Jeffrey C Hoch
University of Connecticut Health Center
Co-authored papers 1
Zhiheng Li
College of Materials and Chemical Engineering, Zhengzhou University of Light Industry
Co-authored papers 1
Stefan Bienert
University of Basel
Co-authored papers 1
Sameer Velankar
European Bioinformatics Institute
Co-authored papers 1
John D Westbrook
The State University of New Jersey
Co-authored papers 1
Ardan Patwardhan
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 1
Helen M Berman
The State University of New Jersey
Co-authored papers 1
Gilbert S Omenn
and School of Public Health, University of Michigan ann arbor
Co-authored papers 1
Brinda Vallat
Institute for Quantitative Biomedicine, State University of New Jersey
Co-authored papers 1
Juergen Haas
University of Basel
Co-authored papers 1
Christine Orengo
University College London, Institute of Structural and Molecular Biology
Co-authored papers 1
Ezra Peisach
The State University of New Jersey
Co-authored papers 1
Genji Kurisu
Institute for Protein Research, Osaka University
Co-authored papers 1
Mihaly Varadi
European Bioinformatics Institute
Co-authored papers 1
Release 1.2