The functional landscape of the human phosphoproteome
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Juan Antonio Vizcaíno | Andrew F. Jarnuczak | Pedro Beltrao | David Ochoa | P. Beltrão | Luz Garcia-Alonso | J. Vizcaíno | D. Ochoa | Cristina Viéitez | D. Swaney | A. Mateus | K. Noh | Maja Gehre | M. Soucheray | Askar A. Kleefeldt | Anthony Hill | Kyung-Min Noh | Cristina Viéitez | Maja Gehre | Margaret Soucheray | Anthony Hill | Luz Garcia-Alonso | Danielle L. Swaney | N. Krogan | Margaret Soucheray | Frank Stein | Mikhail M. Savitski
[1] David E. James,et al. Illuminating the dark phosphoproteome , 2019, Science Signaling.
[2] M. Pellegrini,et al. Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set , 2019, Nature Communications.
[3] Bin Zhang,et al. 15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms , 2018, Nucleic Acids Res..
[4] Maria Jesus Martin,et al. SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins , 2018, Nucleic Acids Res..
[5] Cole H. Christie,et al. Protein Data Bank: the single global archive for 3D macromolecular structure data , 2018, Nucleic acids research.
[6] Emmanuel Paradis,et al. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..
[7] Omar Wagih,et al. A resource of variant effect predictions of single nucleotide variants in model organisms , 2018, Molecular systems biology.
[8] M. Mann,et al. Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis. , 2018, Developmental cell.
[9] A. Gavin,et al. Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes* , 2018, Molecular & Cellular Proteomics.
[10] V. G. Panse,et al. Conserved phosphorylation hotspots in eukaryotic protein domain families , 2018, Nature Communications.
[11] M. Savitski,et al. Thermal proteome profiling in bacteria: probing protein state in vivo , 2018, Molecular systems biology.
[12] Matthias Mann,et al. In vivo brain GPCR signaling elucidated by phosphoproteomics , 2018, Science.
[13] Peer Bork,et al. Pervasive Protein Thermal Stability Variation during the Cell Cycle , 2018, Cell.
[14] The Uniprot Consortium. UniProt: the universal protein knowledgebase , 2018, Nucleic acids research.
[15] Chunlei Liu,et al. ClinVar: improving access to variant interpretations and supporting evidence , 2017, Nucleic Acids Res..
[16] Astrid Gall,et al. Ensembl 2018 , 2017, Nucleic Acids Res..
[17] Nuno A. Fonseca,et al. Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer. , 2018, Cancer research.
[18] Sudhir Kumar,et al. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.
[19] Matthew J. Betts,et al. Systematic identification of phosphorylation-mediated protein interaction switches , 2017, PLoS Comput. Biol..
[20] Thomas A. Hopf,et al. Mutation effects predicted from sequence co-variation , 2017, Nature Biotechnology.
[21] Julio Saez-Rodriguez,et al. OmniPath: guidelines and gateway for literature-curated signaling pathway resources , 2016, Nature Methods.
[22] Uwe Sauer,et al. Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae , 2016, BMC Systems Biology.
[23] Judit Villén,et al. Evolution of protein phosphorylation across 18 fungal species , 2016, Science.
[24] Pedro Beltrão,et al. Benchmarking substrate-based kinase activity inference using phosphoproteomic data , 2016, bioRxiv.
[25] Matthew P Torres,et al. Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease , 2016, Molecular & Cellular Proteomics.
[26] Ruedi Aebersold,et al. Mass-spectrometric exploration of proteome structure and function , 2016, Nature.
[27] Joel Selkrig,et al. An atlas of human kinase regulation , 2016, Molecular Systems Biology.
[28] Mariano J. Alvarez,et al. Network-based inference of protein activity helps functionalize the genetic landscape of cancer , 2016, Nature Genetics.
[29] Michael L. Gatza,et al. Proteogenomics connects somatic mutations to signaling in breast cancer , 2016, Nature.
[30] Albert J. Vilella,et al. Ensembl comparative genomics resources , 2016, Database : the journal of biological databases and curation.
[31] José A. Dianes,et al. 2016 update of the PRIDE database and its related tools , 2016, Nucleic Acids Res..
[32] Toby J. Gibson,et al. ELM 2016—data update and new functionality of the eukaryotic linear motif resource , 2015, Nucleic Acids Res..
[33] James Y. Zou. Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.
[34] P. Ng,et al. SIFT missense predictions for genomes , 2015, Nature Protocols.
[35] J. Mesirov,et al. The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .
[36] Debora S. Marks,et al. Quantification of the effect of mutations using a global probability model of natural sequence variation , 2015, 1510.04612.
[37] J. Chin,et al. Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog. , 2015, Nature chemical biology.
[38] M. Taira,et al. The Inner Nuclear Membrane Protein Nemp1 Is a New Type of RanGTP-Binding Protein in Eukaryotes , 2015, PloS one.
[39] Steven L Salzberg,et al. HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.
[40] Damian Szklarczyk,et al. Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines , 2015, Proteomics.
[41] S. Michnick,et al. A cell-signaling network temporally resolves specific versus promiscuous phosphorylation. , 2015, Cell reports.
[42] Gary D Bader,et al. Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes , 2015, PLoS genetics.
[43] Bin Zhang,et al. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations , 2014, Nucleic Acids Res..
[44] David T. Jones,et al. DISOPRED3: precise disordered region predictions with annotated protein-binding activity , 2014, Bioinform..
[45] J. Mesirov,et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.
[46] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[47] G. Baillie,et al. PKA phosphorylation of p62/SQSTM1 regulates PB1 domain interaction partner binding. , 2014, Biochimica et biophysica acta.
[48] G. Drewes,et al. Tracking cancer drugs in living cells by thermal profiling of the proteome , 2014, Science.
[49] M. Mann,et al. Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. , 2014, Cell reports.
[50] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[51] L. Jensen,et al. KinomeXplorer: an integrated platform for kinome biology studies , 2014, Nature Methods.
[52] Guomin Liu,et al. SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. , 2014, Journal of proteomics.
[53] C. Orengo,et al. Stability-activity tradeoffs constrain the adaptive evolution of RubisCO , 2014, Proceedings of the National Academy of Sciences.
[54] Pornpimol Charoentong,et al. High STAT1 mRNA levels but not its tyrosine phosphorylation are associated with macrophage infiltration and bad prognosis in breast cancer , 2014, BMC Cancer.
[55] P. Bork,et al. Evolution and functional cross‐talk of protein post‐translational modifications , 2013, Molecular systems biology.
[56] G. Crabtree,et al. Creating a neural specific chromatin landscape by npBAF and nBAF complexes , 2013, Current Opinion in Neurobiology.
[57] David A. Scott,et al. Genome engineering using the CRISPR-Cas9 system , 2013, Nature Protocols.
[58] David A. Scott,et al. Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity , 2013, Cell.
[59] R. Jaenisch,et al. One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.
[60] J. Frahm,et al. Chromatin regulation by BAF170 controls cerebral cortical size and thickness. , 2013, Developmental cell.
[61] W. Shi,et al. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote , 2013, Nucleic acids research.
[62] P. Aloy,et al. Interactome3D: adding structural details to protein networks , 2013, Nature Methods.
[63] Steven J. M. Jones,et al. Comprehensive molecular portraits of human breast tumours , 2013 .
[64] R. Yasuda,et al. Modified SH2 domain to phototrap and identify phosphotyrosine proteins from subcellular sites within cells , 2012, Proceedings of the National Academy of Sciences.
[65] W. Lim,et al. Systematic Functional Prioritization of Protein Posttranslational Modifications , 2012, Cell.
[66] Steven J. M. Jones,et al. Comprehensive molecular portraits of human breast tumors , 2012, Nature.
[67] Evan T. Geller,et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders , 2012, Nature.
[68] John H. Morris,et al. Global landscape of HIV–human protein complexes , 2011, Nature.
[69] A. Panchenko,et al. Phosphorylation in protein-protein binding: effect on stability and function. , 2011, Structure.
[70] R. Bago,et al. Binding to Syntenin-1 Protein Defines a New Mode of Ubiquitin-based Interactions Regulated by Phosphorylation* , 2011, The Journal of Biological Chemistry.
[71] N. Delhomme,et al. Seamless Gene Tagging by Endonuclease-Driven Homologous Recombination , 2011, PloS one.
[72] Y. Jang,et al. Phosphorylation of Ran-binding Protein-1 by Polo-like Kinase-1 Is Required for Interaction with Ran and Early Mitotic Progression* , 2011, The Journal of Biological Chemistry.
[73] Vanessa E. Gray,et al. Rampant purifying selection conserves positions with posttranslational modifications in human proteins. , 2011, Molecular biology and evolution.
[74] M. Mann,et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.
[75] N. Hernandez,et al. mTORC1 Directly Phosphorylates and Regulates Human MAF1 , 2010, Molecular and Cellular Biology.
[76] N. Schork,et al. Kinase mutations in human disease: interpreting genotype–phenotype relationships , 2010, Nature Reviews Genetics.
[77] J. Chelly,et al. Tubulin-related cortical dysgeneses: microtubule dysfunction underlying neuronal migration defects. , 2009, Trends in genetics : TIG.
[78] J. Olson,et al. Comparative Genome-Wide Screening Identifies a Conserved Doxorubicin Repair Network That Is Diploid Specific in Saccharomyces cerevisiae , 2009, PloS one.
[79] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[80] A. Represa,et al. Mutations in the β-tubulin gene TUBB2B result in asymmetrical polymicrogyria , 2009, Nature Genetics.
[81] C. Landry,et al. Weak functional constraints on phosphoproteomes. , 2009, Trends in genetics : TIG.
[82] C. Worby,et al. The fic domain: regulation of cell signaling by adenylylation. , 2009, Molecular cell.
[83] 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.
[84] Susan S. Taylor,et al. Congenital disease SNPs target lineage specific structural elements in protein kinases , 2008, Proceedings of the National Academy of Sciences.
[85] Y. Xing,et al. A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function , 2008, The Journal of Neuroscience.
[86] Hermann Schindelin,et al. Studies on peptide:N-glycanase–p97 interaction suggest that p97 phosphorylation modulates endoplasmic reticulum-associated degradation , 2007, Proceedings of the National Academy of Sciences.
[87] Steven P Gygi,et al. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.
[88] Carolina Perez-Iratxeta,et al. Gene function in early mouse embryonic stem cell differentiation , 2007, BMC Genomics.
[89] M. Mann,et al. Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks , 2006, Cell.
[90] Michael R. Seringhaus,et al. Predicting essential genes in fungal genomes. , 2006, Genome research.
[91] Pierre Baldi,et al. SCRATCH: a protein structure and structural feature prediction server , 2005, Nucleic Acids Res..
[92] V. Staiger,et al. Differentiation of mouse embryonic stem cells into a defined neuronal lineage , 2004, Nature Neuroscience.
[93] Conrad C. Huang,et al. MODBASE, a database of annotated comparative protein structure models, and associated resources. , 2004, Nucleic acids research.
[94] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[95] E. Wingender,et al. MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.
[96] C. Marth,et al. Prognostic significance of signal transducer and activator of transcription 1 activation in breast cancer. , 2002, Clinical cancer research : an official journal of the American Association for Cancer Research.
[97] L. Serrano,et al. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.
[98] P. Baldi,et al. Prediction of coordination number and relative solvent accessibility in proteins , 2002, Proteins.
[99] Pierre Baldi,et al. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles , 2002, Proteins.
[100] J. Friedman. Stochastic gradient boosting , 2002 .
[101] Alex E. Lash,et al. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..
[102] Alexander E. Kel,et al. MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..
[103] Ronald W. Davis,et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.
[104] W. V. van Blitterswijk,et al. Diacylglycerol Kinase θ Binds to and Is Negatively Regulated by Active RhoA* , 1999, The Journal of Biological Chemistry.
[105] Thorsten Joachims,et al. Making large scale SVM learning practical , 1998 .
[106] J. Darnell,et al. Maximal activation of transcription by statl and stat3 requires both tyrosine and serine phosphorylation , 1995, Cell.
[107] B. Lee,et al. The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.