Yu Xia

发表

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

M. Gerstein, M. Vidal, Haiyuan Yu, 2004, Genome research.

Assessing the Limits of Genomic Data Integration for Predicting Protein-Protein Interactions

M. Gerstein, A. Paccanaro, Haiyuan Yu, 2005 .

Assessing the limits of genomic data integration for predicting protein networks.

M. Gerstein, A. Paccanaro, Haiyuan Yu, 2005, Genome research.

Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights

Philip M. Kim, M. Gerstein, Yu Xia, 2006, Science.

A Proteome-Scale Map of the Human Interactome Network

Bridget E. Begg, Ann M. Scholz, A. Barabasi, 2014, Cell.

The role of disorder in interaction networks: a structural analysis

Philip M. Kim, M. Gerstein, A. Sboner, 2008, Molecular systems biology.

A reference map of the human protein interactome

Gary D. Bader, Yang Wang, Gary D Bader, 2019, bioRxiv.

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

István A. Kovács, Alexander T. Leighton, A. Barabasi, 2015, Cell.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Gloria M. Sheynkman, Alyce A. Chen, Bridget E. Begg, 2016, Cell.

Diverse Cellular Functions of the Hsp90 Molecular Chaperone Uncovered Using Systems Approaches

M. Gerstein, A. Deutschbauer, Yu Xia, 2007, Cell.

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms

M. Gerstein, S. Balasubramanian, Yu Xia, 2005, Nucleic acids research.

A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome

Brian Raught, Mike Tyers, Yu Xia, 2017, Molecular and Cellular Biology.

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human

Minoru Yoshida, Yu Xia, Frederick P. Roth, 2016, Cell.

Protein evolution in yeast transcription factor subnetworks

Yu Xia, Yong Wang, Xiang-Sun Zhang, 2010, Nucleic acids research.

Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly-made proteins with complex topologies

M. Gerstein, A. Burlingame, Yu Xia, 2008, Nature Structural &Molecular Biology.

Annotation transfer for genomics : assessing the transferability of protein-protein and protein-DNA interactions between organisms

M. Gerstein, M. Vidal, Haiyuan Yu, 2004 .

, and Protein – DNA Regulogs Annotation Transfer Between Genomes : Protein – Protein Interologs data

M. Gerstein, M. Vidal, Haiyuan Yu, 2004 .

Analyzing cellular biochemistry in terms of molecular networks.

Mark Gerstein, Dov Greenbaum, Yu Xia, 2003, Annual review of biochemistry.

Design principles of molecular networks revealed by global comparisons and composite motifs

M. Gerstein, V. Trifonov, Haiyuan Yu, 2006, Genome Biology.

Use of Thioredoxin as a Reporter To Identify a Subset of Escherichia coli Signal Sequences That Promote Signal Recognition Particle-Dependent Translocation

M. Gerstein, Yu Xia, Michael H. Olma, 2005, Journal of bacteriology.

Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes

Yu Xia, J. Coulombe-Huntington, 2017, PloS one.

Nature of Long-Range Evolutionary Constraint in Enzymes: Insights from Comparison to Pseudoenzymes with Similar Structures

Yu Xia, Avital Sharir-Ivry, 2018, Molecular biology and evolution.

A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome

M. Tyers, Yu Xia, A. Chatr-aryamontri, 2017, Molecular and Cellular Biology.

Computationalanalysisofmembraneproteins: genomicoccurrence,structurepredictionand helixinteractions

M. Gerstein, Haiyuan Yu, D. Engelman, 2004 .

Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions

Mark Gerstein, Yang Liu, Yu Xia, 2004, Quarterly Reviews of Biophysics.

Active Clustering of Biological Sequences

Maria-Florina Balcan, Shang-Hua Teng, Heiko Röglin, 2012, J. Mach. Learn. Res..

Efficient Clustering with Limited Distance Information

Maria-Florina Balcan, Shang-Hua Teng, Heiko Röglin, 2010, UAI.

Independent Effects of Protein Core Size and Expression on Residue-Level Structure-Evolution Relationships

E. Franzosa, Yu Xia, 2012, PloS one.

Structural determinants of protein evolution are context-sensitive at the residue level.

Yu Xia, Eric A Franzosa, E. Franzosa, 2009, Molecular biology and evolution.

Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor.

M. Gerstein, D. Engelman, Yu Xia, 2004, Journal of molecular biology.

Selection and Characterization of Small Random Transmembrane Proteins That Bind and Activate the Platelet-derived Growth Factor B Receptor

M. Gerstein, D. Engelman, Yu Xia, 2022 .

Interactome evolution: insights from genome-wide analyses of protein-protein interactions.

Yu Xia, Jasmin Coulombe-Huntington, Mohamed A. Ghadie, 2018, Current opinion in structural biology.

Quantitative Residue-Level Structure–Evolution Relationships in the Yeast Membrane Proteome

E. Franzosa, Yu Xia, Ran Xue, 2013, Genome biology and evolution.

Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate

Mark Gerstein, Yu Xia, Eric A. Franzosa, 2009, PLoS Comput. Biol..

Chapter 1 – Structural Perspectives on Protein Evolution

Yu Xia, Eric A. Franzosa, E. Franzosa, 2008 .

Regulatory Network Structure as a Dominant Determinant of Transcription Factor Evolutionary Rate

Yu Xia, Jasmin Coulombe-Huntington, Yu Xia, 2012, PLoS Comput. Biol..

The Impact of Native State Switching on Protein Sequence Evolution

Yu Xia, Avital Sharir-Ivry, 2017, Molecular biology and evolution.

An inter‐species protein–protein interaction network across vast evolutionary distance

Albert-László Barabási, Yu Xia, David E Hill, 2016, Molecular systems biology.

Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs

Yu Xia, Y. Chen, 2021, Frontiers in Molecular Biosciences.

Toward a three-dimensional view of protein networks between species

Yu Xia, Eric A. Franzosa, Sara Garamszegi, 2012, Front. Microbio..

Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis

Mark Gerstein, Falk Schubert, Yu Xia, 2005, Data Analysis and Visualization in Genomics and Proteomics.

Integrated prediction of the helical membrane protein interactome in yeast.

Mark Gerstein, Yu Xia, M. Gerstein, 2006, Journal of molecular biology.

Computational reconstruction of protein-protein interaction networks: algorithms and issues.

Yu Xia, Bolan Linghu, Eric Franzosa, 2009, Methods in molecular biology.

Heterozygous Yeast Deletion Collection Screens Reveal Essential Targets of Hsp90

E. Franzosa, Yu Xia, J. Frydman, 2011, PloS one.

Estimating dispensable content in the human interactome

Yu Xia, Mohamed A. Ghadie, Yu Xia, 2019, Nature Communications.

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing

Yu Xia, Luke Lambourne, Marc Vidal, 2017, PLoS Comput. Biol..

Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks

Yu Xia, Eric A. Franzosa, Sara Garamszegi, 2013, PLoS pathogens.

Structural principles within the human-virus protein-protein interaction network

Yu Xia, Eric A Franzosa, E. Franzosa, 2011, Proceedings of the National Academy of Sciences.

A reference map of the human binary protein interactome

Gary D Bader, István A. Kovács, Robert J. Weatheritt, 2020, Nature.

Quantifying evolutionary importance of protein sites: A Tale of two measures

Yu Xia, Avital Sharir-Ivry, 2020, bioRxiv.

Use of Thioredoxin as a Reporter To Identify a Subset of Escherichia coli Signal Sequences That Promote Signal Recognition Particle-Dependent Translocation

M. Gerstein, Yu Xia, Michael H. Olma, 2005, Journal of Bacteriology.

Finding local communities in protein networks

Shang-Hua Teng, Yu Xia, Konstantin Voevodski, 2009, BMC Bioinformatics.

Spectral affinity in protein networks

Shang-Hua Teng, Yu Xia, Konstantin Voevodski, 2009, BMC Systems Biology.

Using Functional Linkage Gene Networks to Study Human Diseases

Guohui Liu, Yu Xia, Bolan Linghu, 2011, Handbook of Research on Computational and Systems Biology.

Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes

Yu Xia, Yangchun Frank Chen, Yu Xia, 2019, PLoS Comput. Biol..

High-precision high-coverage functional inference from integrated data sources

Charles DeLisi, Yu Xia, Evan S. Snitkin, 2008, BMC Bioinformatics.

Resource A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human Graphical

Haiyuan Yu, Yu Xia, Xiaomu Wei, 2022 .

Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor.

M. Gerstein, D. Engelman, Yu Xia, 2004, Journal of molecular biology.

Non-catalytic Binding Sites Induce Weaker Long-Range Evolutionary Rate Gradients than Catalytic Sites in Enzymes.

Yu Xia, Avital Sharir-Ivry, 2019, Journal of molecular biology.

Non-catalytic binding sites induce weaker long-range evolutionary rate gradients than catalytic sites in enzymes

Yu Xia, Avital Sharir-Ivry, 2019, bioRxiv.

viability screen reveals structural features and 1 contextual diversity of the human cell-essential

M. Tyers, Yu Xia, A. Chatr-aryamontri, 2017 .

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Gloria M. Sheynkman, Alyce A. Chen, Bridget E. Begg, 2016, Cell.

Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks

E. Franzosa, Yu Xia, Sara Garamszegi, 2013, PLoS pathogens.

Interactome evolution: insights from genome-wide analyses of protein-protein interactions.

Mohamed A. Ghadie, Yu Xia, J. Coulombe-Huntington, 2018, Current opinion in structural biology.

Structural Models for Host-Pathogen Protein-Protein Interactions: Assessing Coverage and Bias

Yu Xia, Eric A. Franzosa, E. Franzosa, 2011, Pacific Symposium on Biocomputing.

Construction of functional linkage gene networks by data integration.

Yu Xia, Bolan Linghu, Eric A Franzosa, 2013, Methods in molecular biology.

A reference map of the human binary protein interactome

Patrick Aloy, Gary D. Bader, Yang Wang, 2020, Nature.

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

M. Gerstein, M. Vidal, Haiyuan Yu, 2004, Genome research.

The role of disorder in interaction networks: a structural analysis

Philip M. Kim, M. Gerstein, A. Sboner, 2008, Molecular systems biology.