Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins.

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

[2]  B. Kuster,et al.  Mass-spectrometry-based draft of the human proteome , 2014, Nature.

[3]  A Keith Dunker,et al.  Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. , 2013, Current opinion in structural biology.

[4]  M. Bucan,et al.  From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes , 2013, PLoS genetics.

[5]  TaeHyung Kim,et al.  Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing , 2013, PLoS Comput. Biol..

[6]  J. Eng,et al.  Comet: An open‐source MS/MS sequence database search tool , 2013, Proteomics.

[7]  Philip M. Kim,et al.  The Evolutionary Landscape of Alternative Splicing in Vertebrate Species , 2012, Science.

[8]  C. Burge,et al.  Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues , 2012, Science.

[9]  Christie S. Chang,et al.  The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..

[10]  Alfonso Valencia,et al.  APPRIS: annotation of principal and alternative splice isoforms , 2012, Nucleic Acids Res..

[11]  Xinchen Wang,et al.  Tissue-specific alternative splicing remodels protein-protein interaction networks. , 2012, Molecular cell.

[12]  Alfonso Valencia,et al.  Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function , 2012, Molecular biology and evolution.

[13]  J. Rinn,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[14]  Varodom Charoensawan,et al.  RNA sequencing reveals two major classes of gene expression levels in metazoan cells , 2011, Molecular systems biology.

[15]  Richard J. Edwards,et al.  SLiMSearch 2.0: biological context for short linear motifs in proteins , 2011, Nucleic Acids Res..

[16]  Aalt DJ van Dijk,et al.  Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data , 2011, BMC Plant Biology.

[17]  Massimiliano Orsini,et al.  MAISTAS: a tool for automatic structural evaluation of alternative splicing products , 2011, Bioinform..

[18]  A. Tramontano,et al.  Coding potential of the products of alternative splicing in human , 2011, Genome Biology.

[19]  Peter Tompa,et al.  Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder , 2010, Nucleic acids research.

[20]  Mingming Jia,et al.  COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer , 2010, Nucleic Acids Res..

[21]  Jennifer A. Siepen,et al.  Investigating protein isoforms via proteomics: A feasibility study , 2010, Proteomics.

[22]  Peter Tompa,et al.  Intrinsic Structural Disorder Confers Cellular Viability on Oncogenic Fusion Proteins , 2009, PLoS Comput. Biol..

[23]  M. Tress,et al.  Proteomics studies confirm the presence of alternative protein isoforms on a large scale , 2008, Genome Biology.

[24]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[25]  Charles Elkan,et al.  Learning classifiers from only positive and unlabeled data , 2008, KDD.

[26]  R. Zimmer,et al.  Alternative splicing and protein structure evolution , 2007, Nucleic acids research.

[27]  Robert D. Finn,et al.  The Pfam protein families database , 2007, Nucleic Acids Res..

[28]  Hagen Blankenburg,et al.  The implications of alternative splicing in the ENCODE protein complement , 2007, Proceedings of the National Academy of Sciences.

[29]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[30]  A Keith Dunker,et al.  Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Michelle S. Scott,et al.  Global Survey of Organ and Organelle Protein Expression in Mouse: Combined Proteomic and Transcriptomic Profiling , 2006, Cell.

[32]  P. Tompa,et al.  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..

[33]  I. Rafalska,et al.  Function of alternative splicing. , 2005, Gene.

[34]  Robertson Craig,et al.  Open source system for analyzing, validating, and storing protein identification data. , 2004, Journal of proteome research.

[35]  Robertson Craig,et al.  TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.

[36]  Andrew Emili,et al.  PRISM, a Generic Large Scale Proteomic Investigation Strategy for Mammals*S , 2003, Molecular & Cellular Proteomics.

[37]  N. Grishin.  Fold change in evolution of protein structures. , 2001, Journal of structural biology.

[38]  C. Ponting,et al.  Protein repeats: structures, functions, and evolution. , 2001, Journal of structural biology.

[39]  A. Koromilas,et al.  Dominant Negative Function by an Alternatively Spliced Form of the Interferon-inducible Protein Kinase PKR* , 2001, The Journal of Biological Chemistry.

[40]  M. Röllinghoff,et al.  Two distinct stimulus-dependent pathways lead to production of soluble murine interleukin-4 receptor. , 1996, Journal of immunology.

[41]  Corinna Cortes,et al.  Support-Vector Networks , 1995, Machine Learning.

[42]  J. Spring,et al.  Tenascin variants: differential binding to fibronectin and distinct distribution in cell cultures and tissues. , 1991, Cell regulation.

[43]  Philip M. Kim,et al.  An omics perspective of protein disorder. , 2012, Molecular bioSystems.

[44]  E. Deutsch.  The PeptideAtlas Project , 2010, Proteome Bioinformatics.

[45]  Alfonso Valencia,et al.  Determination and validation of principal gene products , 2008, Bioinform..

[46]  Nucleic Acids Research Advance Access published June 22, 2009 Stochastic noise in splicing machinery , 2008 .

[47]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[48]  Trevor Hastie,et al.  The Elements of Statistical Learning , 2001 .

[49]  L. Breiman.  Random Forests , 2001, Machine Learning.