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Author Details

Yu Xia
College of Information Engineering, Zhejiang University of Technology
1996
86
31
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36871126Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader.Commun Biol2023
37788318E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning.J Chem Inf Model2023
37695768Pathfinder: Protein folding pathway prediction based on conformational sampling.PLoS Comput Biol2023
37680537Comparative Transcriptomic Analyses of a Vero Cell Line in Suspension versus Adherent Culture Conditions.Int J Cell Biol2023
36920090Inter-domain distance prediction based on deep learning for domain assembly.Brief Bioinform2023
35962986Structural analogue-based protein structure domain assembly assisted by deep learning.Bioinformatics2022
35404956Are transient protein-protein interactions more dispensable?PLoS Comput Biol2022
35850298Structural Determinants of Yeast Protein-Protein Interaction Interface Evolution at the Residue Level.J Mol Biol2022
35869699From functional genomics of vero cells to CRISPR-based genomic deletion for improved viral production rates.Biotechnol Bioeng2022
34355233Distance-guided protein folding based on generalized descent direction.Brief Bioinform2021
36303776Mutation Edgotype Drives Fitness Effect in Human.Front Bioinform2021
33826605Quantifying evolutionary importance of protein sites: A Tale of two measures.PLoS Genet2021
34525125Principal component analysis of alpha-helix deformations in transmembrane proteins.PLoS One2021
34417462Haplotype-resolved de novo assembly of the Vero cell line genome.NPJ Vaccines2021
34245242A sequential niche multimodal conformational sampling algorithm for protein structure prediction.Bioinformatics2021
34012977Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs.Front Mol Biosci2021
32296183A reference map of the human binary protein interactome.Nature2020
30759076Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes.PLoS Comput Biol2019
31325440Non-catalytic Binding Sites Induce Weaker Long-Range Evolutionary Rate Gradients than Catalytic Sites in Enzymes.J Mol Biol2019
31324802Estimating dispensable content in the human interactome.Nat Commun2019
31236007Using Pseudoenzymes to Probe Evolutionary Design Principles of Enzymes.Evol Bioinform Online2019
29112911Interactome evolution: insights from genome-wide analyses of protein-protein interactions.Curr Opin Struct Biol2018
30202983Nature of Long-Range Evolutionary Constraint in Enzymes: Insights from Comparison to Pseudoenzymes with Similar Structures.Mol Biol Evol2018
28046110Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes.PLoS One2017
28228842Worldwide malaria incidence and cancer mortality are inversely associated.Infect Agent Cancer2017
28107392Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates.PLoS One2017
28333346The Impact of Native State Switching on Protein Sequence Evolution.Mol Biol Evol2017
29038160A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome.Mol Cell Biol2017
28846689Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing.PLoS Comput Biol2017
26871637Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.Cell2016
26771498A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.Cell2016
27107014An inter-species protein-protein interaction network across vast evolutionary distance.Mol Syst Biol2016
25910212Widespread macromolecular interaction perturbations in human genetic disorders.Cell2015
24678734Research resource: EPSLiM: ensemble predictor for short linear motifs in nuclear hormone receptors.Mol Endocrinol2014
25416956A proteome-scale map of the human interactome network.Cell2014
25079789Transcriptional correlates of disease outcome in anticoagulant-treated non-human primates infected with ebolavirus.PLoS Negl Trop Dis2014
24811061A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur.PLoS One2014
24925905A computational framework for heparan sulfate sequencing using high-resolution tandem mass spectra.Mol Cell Proteomics2014
24577717Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily.Proteins2014
23192549Construction of functional linkage gene networks by data integration.Methods Mol Biol2013
24339775Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.PLoS Pathog2013
23959887Consequences of domain insertion on sequence-structure divergence in a superfold.Proc Natl Acad Sci U S A2013
23512408Quantitative residue-level structure-evolution relationships in the yeast membrane proteome.Genome Biol Evol2013
22174284Structural models for host-pathogen protein-protein interactions: assessing coverage and bias.Pac Symp Biocomput2012
23267356Toward a three-dimensional view of protein networks between species.Front Microbiol2012
23028852Multi-edge gene set networks reveal novel insights into global relationships between biological themes.PLoS One2012
23093926Regulatory network structure as a dominant determinant of transcription factor evolutionary rate.PLoS Comput Biol2012
23056364Independent effects of protein core size and expression on residue-level structure-evolution relationships.PLoS One2012
21680884Structural principles within the human-virus protein-protein interaction network.Proc Natl Acad Sci U S A2011
21987740Therapeutics of Ebola hemorrhagic fever: whole-genome transcriptional analysis of successful disease mitigation.J Infect Dis2011
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Collaborators

Mark Gerstein
Yale University
Co-authored papers 14
Michael Levitt
Stanford University
Co-authored papers 8
Jasmin Coulombe-Huntington
Institute for Research in Immunology and Cancer, Universite de Montreal
Co-authored papers 7
Marc Vidal
Blavatnik Institute, Harvard Medical School
Co-authored papers 7
Haiyuan Yu
Weill Institute for Cell and Molecular Biology, Cornell University
Co-authored papers 6
Frederick P Roth
University of Toronto
Co-authored papers 6
Sara Garamszegi
The Broad Institute of MIT and Harvard
Co-authored papers 5
Ram Samudrala
Jacobs School of Medicine and Biomedical Sciences, University at Buffalo
Co-authored papers 4
Patrick Aloy
Institucio Catalana de Recerca i Estudis Avancats (ICREA)
Co-authored papers 4
Nidhi Sahni
The University of Texas MD Anderson Cancer Center
Co-authored papers 3
Kerstin Spirohn
Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute
Co-authored papers 3
Albert-L??szl?? Barab??si
Network Science Institute, Northeastern University
Co-authored papers 3
Song Yi
Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin
Co-authored papers 3
Judith Frydman
Stanford University
Co-authored papers 3
Chetanya Pandya
Icahn School of Medicine at Mount Sinai
Co-authored papers 2
Atanas Kamburov
Broad Institute of Harvard and MIT
Co-authored papers 2
Charles DeLisi
Co-authored papers 2
Karen N Allen
Boston University
Co-authored papers 2
Gloria M Sheynkman (CM4AI)
University of Virginia
Co-authored papers 2
Javier De Las Rivas
Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL)
Co-authored papers 2
J??rg Menche
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 2
Susan Lindquist
Whitehead Institute for Biomedical Research
Co-authored papers 2
Debra Dunaway-Mariano
University of New Mexico
Co-authored papers 2
Daniel M Jordan
Icahn School of Medicine at Mount Sinai
Co-authored papers 1
Marc Brehme
Delft University of Technology
Co-authored papers 1
Zhenjun Hu
Co-authored papers 1
Adam M Deutschbauer
Lawrence Berkeley National Laboratory
Co-authored papers 1
Xianghong Jasmine Zhou
David Geffen School of Medicine, University of California at Los Angeles
Co-authored papers 1
Wen-Han Yu
Co-authored papers 1
Mandy H Y Lam
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital
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Release 1.2