Dynamic rewiring of the human interactome by interferon signaling

[1]  Marco Y. Hein,et al.  Functional single-cell genomics of human cytomegalovirus infection , 2019, Nature Biotechnology.

[2]  Daniel D. T. Andrews,et al.  Dynamic rewiring of the human interactome by interferon signaling , 2019, Genome Biology.

[3]  Gary D Bader,et al.  EPIC: software toolkit for elution profile-based inference of protein complexes , 2019, Nature Methods.

[4]  M. Crow,et al.  Type I Interferons in Autoimmune Disease. , 2019, Annual review of pathology.

[5]  Andreas Ruepp,et al.  CORUM: the comprehensive resource of mammalian protein complexes—2019 , 2018, Nucleic Acids Res..

[6]  S. Quake,et al.  Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue , 2018, Proceedings of the National Academy of Sciences.

[7]  Melvin A. Park,et al.  Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer* , 2018, Molecular & Cellular Proteomics.

[8]  Michael Lässig,et al.  Gene expression variability across cells and species shapes innate immunity , 2018, Nature.

[9]  L. Foster,et al.  Context-specific interactions in literature-curated protein interaction databases , 2018, BMC Genomics.

[10]  Mark Gerstein,et al.  Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci , 2018, Nature Genetics.

[11]  Leonard J Foster,et al.  Genomic data integration systematically biases interactome mapping , 2018, PLoS Comput. Biol..

[12]  K. Sakaguchi,et al.  Interferon stimulation creates chromatin marks and establishes transcriptional memory , 2018, Proceedings of the National Academy of Sciences.

[13]  M. Barna,et al.  The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life. , 2018, Molecular cell.

[14]  R. Greg Stacey,et al.  An atlas of protein-protein interactions across mammalian tissues , 2018, bioRxiv.

[15]  I. Amit,et al.  Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing , 2018, Cell Systems.

[16]  Pär Nordlund,et al.  Modulation of Protein-Interaction States through the Cell Cycle , 2018, Cell.

[17]  Peer Bork,et al.  Pervasive Protein Thermal Stability Variation during the Cell Cycle , 2018, Cell.

[18]  Chern Han Yong,et al.  Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells , 2018, Science.

[19]  The Uniprot Consortium.  UniProt: the universal protein knowledgebase , 2018, Nucleic acids research.

[20]  Astrid Gall,et al.  Ensembl 2018 , 2017, Nucleic Acids Res..

[21]  Thawfeek M. Varusai,et al.  The Reactome Pathway Knowledgebase , 2017, Nucleic acids research.

[22]  Johanna R. McEntyre,et al.  The BioStudies database—one stop shop for all data supporting a life sciences study , 2017, Nucleic Acids Res..

[23]  Joshua B. Singer,et al.  Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses , 2017, PLoS biology.

[24]  R. Green,et al.  Ribosomopathies: There’s strength in numbers , 2017, Science.

[25]  Christian L. Müller,et al.  Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets , 2017, PLoS Comput. Biol..

[26]  P. Pavlidis,et al.  Can we predict protein from mRNA levels? , 2017, Nature.

[27]  K. Fujii,et al.  Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. , 2017, Molecular cell.

[28]  P. Bork,et al.  Capturing protein communities by structural proteomics in a thermophilic eukaryote , 2017, Molecular systems biology.

[29]  R. Greg Stacey,et al.  A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE) , 2017, BMC Bioinformatics.

[30]  Heike Hofmann,et al.  Network Visualization with ggplot2 , 2017, R J..

[31]  P. Pavlidis,et al.  Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein–Protein Interactions , 2017, Molecular & Cellular Proteomics.

[32]  S. McWeeney,et al.  A MicroRNA Screen Identifies the Wnt Signaling Pathway as a Regulator of the Interferon Response during Flavivirus Infection , 2017, Journal of Virology.

[33]  M. Lee-Kirsch.  The Type I Interferonopathies. , 2017, Annual review of medicine.

[34]  Nichollas E. Scott,et al.  Interactome disassembly during apoptosis occurs independent of caspase cleavage , 2017, Molecular systems biology.

[35]  Ernest Turro,et al.  ontologyX: a suite of R packages for working with ontological data , 2016, Bioinform..

[36]  Kara Dolinski,et al.  The BioGRID interaction database: 2017 update , 2016, Nucleic Acids Res..

[37]  Finn Drabløs,et al.  Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals , 2016, Nucleic Acids Res..

[38]  Martin H. Schaefer,et al.  HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks , 2016, Nucleic Acids Res..

[39]  Francesco Vallania,et al.  Methods to increase reproducibility in differential gene expression via meta-analysis , 2016, Nucleic acids research.

[40]  Edoardo M. Airoldi,et al.  Post-transcriptional regulation across human tissues , 2015, bioRxiv.

[41]  S. Brunak,et al.  A scored human protein–protein interaction network to catalyze genomic interpretation , 2017, Nature Methods.

[42]  T. Weichhart,et al.  Effects of Interferons and Viruses on Metabolism , 2016, Front. Immunol..

[43]  C. Rice,et al.  Supplemental Information Identification of Interferon-stimulated Genes with Antiretroviral Activity , 2022 .

[44]  Winston Haynes,et al.  Empowering Multi-Cohort Gene Expression Analysis to Increase Reproducibility , 2016, bioRxiv.

[45]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[46]  Maxim N. Artyomov,et al.  Type 1 Interferons Induce Changes in Core Metabolism that Are Critical for Immune Function. , 2016, Immunity.

[47]  Alexey Sergushichev,et al.  An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation , 2016 .

[48]  R. Aebersold,et al.  On the Dependency of Cellular Protein Levels on mRNA Abundance , 2016, Cell.

[49]  Sara Ballouz,et al.  Positive and negative forms of replicability in gene network analysis , 2016, Bioinform..

[50]  Chun Jimmie Ye,et al.  Parsing the Interferon Transcriptional Network and Its Disease Associations , 2016, Cell.

[51]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.

[52]  José A. Dianes,et al.  2016 update of the PRIDE database and its related tools , 2015, Nucleic Acids Res..

[53]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[54]  Igor Jurisica,et al.  Integrated interactions database: tissue-specific view of the human and model organism interactomes , 2015, Nucleic Acids Res..

[55]  Ryan Miller,et al.  WikiPathways: capturing the full diversity of pathway knowledge , 2015, Nucleic Acids Res..

[56]  Seongho Kim.  ppcor: An R Package for a Fast Calculation to Semi-partial Correlation Coefficients. , 2015, Communications for statistical applications and methods.

[57]  P. X. Dinh,et al.  Trim21 regulates Nmi-IFI35 complex-mediated inhibition of innate antiviral response. , 2015, Virology.

[58]  Greg W. Clark,et al.  Panorama of ancient metazoan macromolecular complexes , 2015, Nature.

[59]  William Stafford Noble.  Mass spectrometrists should search only for peptides they care about , 2015, Nature Methods.

[60]  M. Mann,et al.  The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics* , 2015, Molecular & Cellular Proteomics.

[61]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[62]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[63]  M. Vidal,et al.  Selecting causal genes from genome-wide association studies via functionally coherent subnetworks , 2014, Nature Methods.

[64]  Erik L. L. Sonnhammer,et al.  InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic , 2014, Nucleic Acids Res..

[65]  Rhiju Das,et al.  RNA regulons in Hox 5′UTRs confer ribosome specificity to gene regulation , 2014, Nature.

[66]  Prudence Mutowo-Meullenet,et al.  The GOA database: Gene Ontology annotation updates for 2015 , 2014, Nucleic Acids Res..

[67]  Sylvie Ricard-Blum,et al.  MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities , 2014, Nucleic Acids Res..

[68]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease , 2014, Nucleic Acids Res..

[69]  Shane J. Neph,et al.  A comparative encyclopedia of DNA elements in the mouse genome , 2014, Nature.

[70]  M. Tress,et al.  Analyzing the First Drafts of the Human Proteome , 2014, Journal of proteome research.

[71]  Marco Y. Hein,et al.  Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ * , 2014, Molecular & Cellular Proteomics.

[72]  Gary D Bader,et al.  A draft map of the human proteome , 2014, Nature.

[73]  C. Rice,et al.  Interferon-stimulated genes: a complex web of host defenses. , 2014, Annual review of immunology.

[74]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

[75]  M. Diamond,et al.  Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity , 2013, Nature.

[76]  Arnaud Céol,et al.  3did: a catalog of domain-based interactions of known three-dimensional structure , 2013, Nucleic Acids Res..

[77]  Jürgen Cox,et al.  MaxQuant for in-depth analysis of large SILAC datasets. , 2014, Methods in molecular biology.

[78]  Debasis Panda,et al.  Interferon-Inducible Protein IFI35 Negatively Regulates RIG-I Antiviral Signaling and Supports Vesicular Stomatitis Virus Replication , 2013, Journal of Virology.

[79]  L. Ivashkiv,et al.  Regulation of type I interferon responses , 2013, Nature Reviews Immunology.

[80]  Andrei L. Turinsky,et al.  Protein-protein interaction networks: the puzzling riches. , 2013, Current opinion in structural biology.

[81]  L. Castagnoli,et al.  mentha: a resource for browsing integrated protein-interaction networks , 2013, Nature Methods.

[82]  Amber L. Couzens,et al.  The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data , 2013, Nature Methods.

[83]  Rona S. Gertner,et al.  Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells , 2013, Nature.

[84]  Karin Breuer,et al.  InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation , 2012, Nucleic Acids Res..

[85]  Andrei L. Turinsky,et al.  A Census of Human Soluble Protein Complexes , 2012, Cell.

[86]  L. Foster,et al.  A high-throughput approach for measuring temporal changes in the interactome , 2012, Nature Methods.

[87]  Shifeng Xue,et al.  Specialized ribosomes: a new frontier in gene regulation and organismal biology , 2012, Nature Reviews Molecular Cell Biology.

[88]  Thao Nguyen,et al.  The interferons and their receptors—distribution and regulation , 2012, Immunology and cell biology.

[89]  G. Cheng,et al.  Systematic identification of type I and type II interferon-induced antiviral factors , 2012, Proceedings of the National Academy of Sciences.

[90]  Ali Pinar,et al.  Are We There Yet? When to Stop a Markov Chain while Generating Random Graphs , 2012, WAW.

[91]  T. Ideker,et al.  Differential network biology , 2012, Molecular systems biology.

[92]  Livia Perfetto,et al.  MINT, the molecular interaction database: 2012 update , 2011, Nucleic Acids Res..

[93]  Jianmin Wu,et al.  PINA v2.0: mining interactome modules , 2011, Nucleic Acids Res..

[94]  Haiyuan Yu,et al.  HINT: High-quality protein interactomes and their applications in understanding human disease , 2012, BMC Systems Biology.

[95]  Albert J. Vilella,et al.  A high-resolution map of human evolutionary constraint using 29 mammals , 2011, Nature.

[96]  Shifeng Xue,et al.  Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning , 2011, Cell.

[97]  Christopher T. Jones,et al.  A diverse array of gene products are effectors of the type I interferon antiviral response , 2011, Nature.

[98]  Jesse Gillis,et al.  The Impact of Multifunctional Genes on "Guilt by Association" Analysis , 2011, PloS one.

[99]  Sourav Bandyopadhyay,et al.  Rewiring of Genetic Networks in Response to DNA Damage , 2010, Science.

[100]  Gary D Bader,et al.  Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.

[101]  Javier De Las Rivas,et al.  Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks , 2010, PLoS Comput. Biol..

[102]  Linheng Li,et al.  Interferon-gamma regulates intestinal epithelial homeostasis through converging beta-catenin signaling pathways. , 2010, Immunity.

[103]  Hans-Werner Mewes,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[104]  Gary D Bader,et al.  NetPath: a public resource of curated signal transduction pathways , 2010, Genome Biology.

[105]  Michael S. Livstone,et al.  Recurated protein interaction datasets , 2009, Nature Methods.

[106]  S. Fox,et al.  Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers , 2009, Nature Medicine.

[107]  J. Irgon,et al.  Quantitative genome-scale analysis of protein localization in an asymmetric bacterium , 2009, Proceedings of the National Academy of Sciences.

[108]  A. Barabasi,et al.  An empirical framework for binary interactome mapping , 2008, Nature Methods.

[109]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[110]  M. Vidal,et al.  Literature-curated protein interaction datasets , 2009, Nature Methods.

[111]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[112]  Peer Bork,et al.  Not Comparable, But Complementary , 2008, Science.

[113]  Bryan R. G. Williams,et al.  Interferon-inducible antiviral effectors , 2008, Nature Reviews Immunology.

[114]  P. Robinson,et al.  Walking the interactome for prioritization of candidate disease genes. , 2008, American journal of human genetics.

[115]  Arun Siddharth Konagurthu,et al.  On the origin of distribution patterns of motifs in biological networks , 2008, BMC Systems Biology.

[116]  Robert Gentleman,et al.  Using GOstats to test gene lists for GO term association , 2007, Bioinform..

[117]  M. Mann,et al.  Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips , 2007, Nature Protocols.

[118]  Thomas Lengauer,et al.  Improved scoring of functional groups from gene expression data by decorrelating GO graph structure , 2006, Bioinform..

[119]  Xiaohui S. Xie,et al.  A Mammalian Organelle Map by Protein Correlation Profiling , 2006, Cell.

[120]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[121]  Dmitrij Frishman,et al.  The MIPS mammalian protein?Cprotein interaction database , 2005, Bioinform..

[122]  Ian M. Donaldson,et al.  The Biomolecular Interaction Network Database and related tools 2005 update , 2004, Nucleic Acids Res..

[123]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[124]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[125]  Colin Cooper,et al.  Algorithms and Models for the Web-Graph , 2004, Lecture Notes in Computer Science.

[126]  M. Mann,et al.  Proteomic characterization of the human centrosome by protein correlation profiling , 2003, Nature.

[127]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[128]  L. Naumovski,et al.  Intracellular redistribution of interferon-inducible proteins Nmi and IFP 35 in apoptotic cells. , 2002, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

[129]  Ioannis Xenarios,et al.  DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..

[130]  L. Naumovski,et al.  Interferon-inducible Myc/STAT-interacting Protein Nmi Associates with IFP 35 into a High Molecular Mass Complex and Inhibits Proteasome-mediated Degradation of IFP 35* , 2000, The Journal of Biological Chemistry.

[131]  M. Omary,et al.  Interferon-α Induces Nmi-IFP35 Heterodimeric Complex Formation That Is Affected by the Phosphorylation of IFP35* , 2000, The Journal of Biological Chemistry.

[132]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[133]  M. Rohde,et al.  A Cytoplasmic Structure Resembling Large Protein Aggregates Induced by Interferons , 1999, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[134]  W. Leonard,et al.  Functional Association of Nmi with Stat5 and Stat1 in IL-2- and IFN γ-Mediated Signaling , 1999, Cell.

[135]  B. Williams,et al.  Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays , 1998 .

[136]  B. Williams,et al.  Identification of genes differentially regulated by interferon alpha, beta, or gamma using oligonucleotide arrays. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[137]  Edward M. Reingold,et al.  Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..

[138]  Clifford M. Hurvich,et al.  Regression and time series model selection in small samples , 1989 .