Deciphering a global network of functionally associated post-translational modifications
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Peer Bork | Manuela Helmer-Citterich | Pablo Minguez | Luca Parca | Francesca Diella | Anne-Claude Gavin | P. Bork | D. Mende | A. Gavin | M. Helmer-Citterich | Runjun D. Kumar | F. Diella | V. van Noort | L. Parca | Pablo Minguez | Vera van Noort | Daniel R Mende | Runjun Kumar | P. Minguez
[1] Gary D Bader,et al. Phosphorylation sites of higher stoichiometry are more conserved , 2012, Nature Methods.
[2] Arne G. Schmeisky,et al. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium , 2012, Molecular systems biology.
[3] Zhongyi Cheng,et al. Bioinformatic Analysis and Post-Translational Modification Crosstalk Prediction of Lysine Acetylation , 2011, PloS one.
[4] Peer Bork,et al. SMART 7: recent updates to the protein domain annotation resource , 2011, Nucleic Acids Res..
[5] Chunaram Choudhary,et al. Proteome-Wide Mapping of the Drosophila Acetylome Demonstrates a High Degree of Conservation of Lysine Acetylation , 2011, Science Signaling.
[6] P. V. Balaji,et al. Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes. , 2011, Molecular bioSystems.
[7] Toni Gabaldón,et al. TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees , 2011, Nucleic acids research.
[8] L. Jensen,et al. Mass Spectrometric Analysis of Lysine Ubiquitylation Reveals Promiscuity at Site Level* , 2010, Molecular & Cellular Proteomics.
[9] Florian Gnad,et al. PHOSIDA 2011: the posttranslational modification database , 2010, Nucleic Acids Res..
[10] Feng-Chi Chen,et al. Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals. , 2010, Molecular biology and evolution.
[11] I. Talianidis,et al. Cross-talk between post-translational modifications regulates life or death decisions by E2F1 , 2010, Cell cycle.
[12] T. Pawson,et al. Post-translational modifications in signal integration , 2010, Nature Structural &Molecular Biology.
[13] Florian Gnad,et al. Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints , 2010, Cell.
[14] Richard J. Edwards,et al. SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs , 2010, Nucleic Acids Res..
[15] Ashis Kumer Biswas,et al. Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information , 2010, BMC Bioinformatics.
[16] Joaquín Dopazo,et al. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling , 2010, Nucleic Acids Res..
[17] O. Gascuel,et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.
[18] B. Harrison,et al. Protein kinase C‐related kinase targets nuclear localization signals in a subset of class IIa histone deacetylases , 2010, FEBS letters.
[19] E. Tajkhorshid,et al. Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-κB , 2010, Molecular and Cellular Biology.
[20] Peer Bork,et al. BIOINFORMATICS APPLICATIONS , 2022 .
[21] J. Shabanowitz,et al. Extensive Crosstalk Between O-GlcNAcylation and Phosphorylation Regulates Cytokinesis , 2010, Science Signaling.
[22] Damian Szklarczyk,et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations , 2009, Nucleic Acids Res..
[23] Baris E. Suzek,et al. The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..
[24] S. Gygi,et al. Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution , 2009, Science.
[25] M. Mann,et al. Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions , 2009, Science.
[26] Tony Pawson,et al. Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases , 2009, Science Signaling.
[27] Joaquín Dopazo,et al. SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks , 2009, Nucleic Acids Res..
[28] B. Benayoun,et al. A post-translational modification code for transcription factors: sorting through a sea of signals. , 2009, Trends in cell biology.
[29] C. Landry,et al. Weak functional constraints on phosphoproteomes. , 2009, Trends in genetics : TIG.
[30] Florian Gnad,et al. Large-scale Proteomics Analysis of the Human Kinome , 2009, Molecular & Cellular Proteomics.
[31] A. Shukla,et al. Histone methylation and ubiquitination with their cross-talk and roles in gene expression and stability , 2008, Cellular and Molecular Life Sciences.
[32] Sandhya Rani,et al. Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..
[33] Christian von Mering,et al. STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..
[34] Robert D. Finn,et al. InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..
[35] Jos Boekhorst,et al. Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes , 2008, Genome Biology.
[36] Rainer Malik,et al. Comparative conservation analysis of the human mitotic phosphoproteome , 2008, Bioinform..
[37] Rodrigo Lopez,et al. A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences , 2008, BMC Bioinformatics.
[38] J. Manley,et al. Sumoylation regulates multiple aspects of mammalian poly(A) polymerase function. , 2008, Genes & development.
[39] K. Basso,et al. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas , 2008, Molecular systems biology.
[40] Gregory B. Gloor,et al. Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction , 2008, Bioinform..
[41] T. Hunter. The age of crosstalk: phosphorylation, ubiquitination, and beyond. , 2007, Molecular cell.
[42] M. Mann,et al. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites , 2007, Genome Biology.
[43] John A Latham,et al. Cross-regulation of histone modifications , 2007, Nature Structural &Molecular Biology.
[44] Allegra Via,et al. Phospho.ELM: a database of phosphorylation sites—update 2008 , 2007, Nucleic Acids Res..
[45] Anders Gorm Pedersen,et al. Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation , 2007, Algorithms for molecular biology : AMB.
[46] G. Petsko. My worries are no longer behind me , 2007, Genome Biology.
[47] Richard J. Edwards,et al. The SLiMDisc server: short, linear motif discovery in proteins , 2007, Nucleic Acids Res..
[48] J. Dopazo,et al. The human phylome , 2007, Genome Biology.
[49] Ryan E. Mills,et al. Classical Nuclear Localization Signals: Definition, Function, and Interaction with Importin α* , 2007, Journal of Biological Chemistry.
[50] S. Horinouchi,et al. Multiple Histone Deacetylases and the CREB-binding Protein Regulate Pre-mRNA 3′-End Processing* , 2007, Journal of Biological Chemistry.
[51] P. Bignone,et al. Phosphorylation of a Threonine Unique to the Short C-terminal Isoform of βII-Spectrin Links Regulation of α-β Spectrin Interaction to Neuritogenesis* , 2007, Journal of Biological Chemistry.
[52] P. Bork,et al. Co-evolution of transcriptional and post-translational cell-cycle regulation , 2006, Nature.
[53] Ping Wang,et al. SUMO regulates the cytoplasmonuclear transport of its target protein Daxx , 2006, Journal of cellular biochemistry.
[54] T. Pawson,et al. Reading protein modifications with interaction domains , 2006, Nature Reviews Molecular Cell Biology.
[55] B. Snel,et al. Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.
[56] Hsien-Da Huang,et al. dbPTM: an information repository of protein post-translational modification , 2005, Nucleic Acids Res..
[57] L. C. Martin,et al. Using information theory to search for co-evolving residues in proteins , 2005, Bioinform..
[58] T. Gibson,et al. Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks , 2005, PLoS biology.
[59] Leonard Buckbinder,et al. NF-κB RelA Phosphorylation Regulates RelA Acetylation , 2005, Molecular and Cellular Biology.
[60] G. Gloor,et al. Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. , 2005, Biochemistry.
[61] Xiang-Jiao Yang,et al. Multisite protein modification and intramolecular signaling , 2005, Oncogene.
[62] J. Kornhauser,et al. PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation , 2004, Proteomics.
[63] Joaquín Dopazo,et al. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes , 2004, Bioinform..
[64] Database resources of the National Center for Biotechnology Information , 2014, Nucleic Acids Res..
[65] T. Gibson,et al. Protein disorder prediction: implications for structural proteomics. , 2003, Structure.
[66] D. Harrich,et al. Inhibition of Retinoblastoma Protein Degradation by Interaction with the Serpin Plasminogen Activator Inhibitor 2 via a Novel Consensus Motif , 2003, Molecular and Cellular Biology.
[67] Thomas W. H. Lui,et al. Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments , 2003, Bioinform..
[68] Wei Gu,et al. Ubiquitination, phosphorylation and acetylation: the molecular basis for p53 regulation. , 2003, Current opinion in cell biology.
[69] B. Peter,et al. EpsinR: an AP1/clathrin interacting protein involved in vesicle trafficking. , 2003, The Journal of cell biology.
[70] B. Dalrymple,et al. A universal protein–protein interaction motif in the eubacterial DNA replication and repair systems , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[71] R. Hay,et al. SUMO-1 Conjugation in Vivo Requires Both a Consensus Modification Motif and Nuclear Targeting* , 2001, The Journal of Biological Chemistry.
[72] S. Perrotta,et al. Reversible erythrocyte skeleton destabilization is modulated by beta-spectrin phosphorylation in childhood leukemia , 2001, Leukemia.
[73] P. Cohen,et al. The regulation of protein function by multisite phosphorylation--a 25 year update. , 2000, Trends in biochemical sciences.
[74] A. Kretsovali,et al. Acetylation by PCAF Enhances CIITA Nuclear Accumulation and Transactivation of Major Histocompatibility Complex Class II Genes , 2000, Molecular and Cellular Biology.
[75] Warren C. Lathe,et al. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. , 2000, Genome research.
[76] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[77] W. Atchley,et al. Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[78] Marius Sudol,et al. From Src Homology domains to other signaling modules: proposal of the `protein recognition code' , 1998, Oncogene.
[79] D. Lipman,et al. A genomic perspective on protein families. , 1997, Science.
[80] A. Lapedes,et al. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[81] Ruth I. Tennen,et al. Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling , 2011, Nature Immunology.
[82] María Martín,et al. The Universal Protein Resource (UniProt) in 2010 , 2010 .
[83] F. Castellino,et al. gamma-Glutamate and beta-hydroxyaspartate in proteins. , 2008, Methods in molecular biology.
[84] P. Bignone,et al. Phosphorylation of a threonine unique to the short C-terminal isoform of betaII-spectrin links regulation of alpha-beta spectrin interaction to neuritogenesis. , 2007, The Journal of biological chemistry.
[85] Leonard Buckbinder,et al. NF-kappaB RelA phosphorylation regulates RelA acetylation. , 2005, Molecular and cellular biology.
[86] Søren Brunak,et al. O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins , 1999, Nucleic Acids Res..
[87] Thomas M. Cover,et al. Elements of Information Theory , 2005 .