List of works - Yu Xia

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

scientific article published on 16 October 2017

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

scientific article

A computational framework for heparan sulfate sequencing using high-resolution tandem mass spectra

scientific article published on 12 June 2014

A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur.

scientific article

A proteome-scale map of the human interactome network

scientific article

A reference map of the human binary protein interactome

scientific article published on 08 April 2020

Ab initio construction of protein tertiary structures using a hierarchical approach

scientific article (publication date: 30 June 2000)

An inter-species protein-protein interaction network across vast evolutionary distance

scientific article (publication date: 22 April 2016)

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

scientific article

Are transient protein-protein interactions more dispensable?

scientific article published on 11 April 2022

Assessing the limits of genomic data integration for predicting protein networks

scientific article published in July 2005

Bioinformatics analysis of macrophages exposed to Porphyromonas gingivalis: implications in acute vs. chronic infections

scientific article

Consequences of domain insertion on sequence-structure divergence in a superfold

scientific article published on 19 August 2013

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

scientific article published on 13 February 2019

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

scientific article

Design of an optimal Chebyshev-expanded discrimination function for globular proteins

scientific article

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

scientific article published on January 2006

Discovering causal signaling pathways through gene-expression patterns

scientific article

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches

scientific article

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

scientific article published on 28 August 2017

Estimating dispensable content in the human interactome

scientific article published on 19 July 2019

Finding local communities in protein networks

scientific article published on 18 September 2009

Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution

scientific article published on April 2004

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

scientific article published on 3 September 2009

Haplotype-resolved de novo assembly of the Vero cell line genome

scientific article published on 20 August 2021

Heterozygous yeast deletion collection screens reveal essential targets of Hsp90

scientific article published in 2011

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

scientific article

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

scientific article published on October 3, 2012

Integrated assessment of genomic correlates of protein evolutionary rate

scientific article

Integrated prediction of the helical membrane protein interactome in yeast

scientific article

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

scientific article published on 4 November 2017

Molecular modeling and design of invariant chain peptides with altered dissociation kinetics from class II MHC.

scientific article published in November 1996

Multi-edge gene set networks reveal novel insights into global relationships between biological themes

scientific article

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

scientific article published on 01 November 2018

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

scientific article

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

scientific article published on 17 July 2019

Precipitation patterns with polygonal boundaries between electrolytes

scientific article published on 13 October 2009

Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data

scientific article

Quantitative residue-level structure-evolution relationships in the yeast membrane proteome

scientific article published on January 2013

Regulatory network structure as a dominant determinant of transcription factor evolutionary rate

scientific article

Research resource: EPSLiM: ensemble predictor for short linear motifs in nuclear hormone receptors.

scientific article

Roles of mutation and recombination in the evolution of protein thermodynamics

scientific article

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

scientific article

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

scientific article

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

scientific article

Simulating protein evolution in sequence and structure space

scientific article published on April 2004

Spectral affinity in protein networks

scientific article

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

scientific article published on 13 July 2009

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

scientific article published on June 16, 2011

Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily.

scientific article published on 2 May 2014

The Impact of Native State Switching on Protein Sequence Evolution.

scientific article

The role of disorder in interaction networks: a structural analysis

scientific article published on 25 March 2008

Therapeutics of Ebola hemorrhagic fever: whole-genome transcriptional analysis of successful disease mitigation

scientific article published in November 2011

Transcriptional correlates of disease outcome in anticoagulant-treated non-human primates infected with ebolavirus

scientific article

Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates.

scientific article

Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation

scientific article published on May 2005

Using Pseudoenzymes to Probe Evolutionary Design Principles of Enzymes

scientific article published on 13 June 2019

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

scientific article published on February 2016

Widespread macromolecular interaction perturbations in human genetic disorders

scientific journal article

List of works by Yu Xia

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

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

A computational framework for heparan sulfate sequencing using high-resolution tandem mass spectra

A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur.

A proteome-scale map of the human interactome network

A reference map of the human binary protein interactome

Ab initio construction of protein tertiary structures using a hierarchical approach

An inter-species protein-protein interaction network across vast evolutionary distance

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

Are transient protein-protein interactions more dispensable?

Assessing the limits of genomic data integration for predicting protein networks

Bioinformatics analysis of macrophages exposed to Porphyromonas gingivalis: implications in acute vs. chronic infections

Consequences of domain insertion on sequence-structure divergence in a superfold

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

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

Design of an optimal Chebyshev-expanded discrimination function for globular proteins

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

Discovering causal signaling pathways through gene-expression patterns

Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches

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

Estimating dispensable content in the human interactome

Finding local communities in protein networks

Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

Haplotype-resolved de novo assembly of the Vero cell line genome

Heterozygous yeast deletion collection screens reveal essential targets of Hsp90

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

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

Integrated assessment of genomic correlates of protein evolutionary rate

Integrated prediction of the helical membrane protein interactome in yeast

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

Molecular modeling and design of invariant chain peptides with altered dissociation kinetics from class II MHC.

Multi-edge gene set networks reveal novel insights into global relationships between biological themes

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

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

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

Precipitation patterns with polygonal boundaries between electrolytes

Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data

Quantitative residue-level structure-evolution relationships in the yeast membrane proteome

Regulatory network structure as a dominant determinant of transcription factor evolutionary rate

Research resource: EPSLiM: ensemble predictor for short linear motifs in nuclear hormone receptors.

Roles of mutation and recombination in the evolution of protein thermodynamics

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

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

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

Simulating protein evolution in sequence and structure space

Spectral affinity in protein networks

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

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

Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily.

The Impact of Native State Switching on Protein Sequence Evolution.

The role of disorder in interaction networks: a structural analysis

Therapeutics of Ebola hemorrhagic fever: whole-genome transcriptional analysis of successful disease mitigation

Transcriptional correlates of disease outcome in anticoagulant-treated non-human primates infected with ebolavirus

Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates.

Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation

Using Pseudoenzymes to Probe Evolutionary Design Principles of Enzymes

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Widespread macromolecular interaction perturbations in human genetic disorders