Protein-protein interaction predictions using text mining methods.

[1]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[2]  Dmitrij Frishman,et al.  Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis , 2013, Nucleic Acids Res..

[3]  Evangelos Theodoridis,et al.  Reconstruction of the experimentally supported human protein interactome: what can we learn? , 2013, BMC Systems Biology.

[4]  Hongfei Lin,et al.  PPIExtractor: A Protein Interaction Extraction and Visualization System for Biomedical Literature , 2013, IEEE Transactions on NanoBioscience.

[5]  Kalpana Raja,et al.  PPInterFinder—a mining tool for extracting causal relations on human proteins from literature , 2013, Database J. Biol. Databases Curation.

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

[7]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[8]  Cathy H. Wu,et al.  The eFIP system for text mining of protein interaction networks of phosphorylated proteins , 2012, Database J. Biol. Databases Curation.

[9]  Wade H. Dunham,et al.  Affinity‐purification coupled to mass spectrometry: Basic principles and strategies , 2012, Proteomics.

[10]  Johannes Goll,et al.  Protein interaction data curation: the International Molecular Exchange (IMEx) consortium , 2012, Nature Methods.

[11]  Jinfeng Zhang,et al.  IMID: integrated molecular interaction database , 2012, Bioinform..

[12]  W. John Wilbur,et al.  PIE the search: searching PubMed literature for protein interaction information , 2012, Bioinform..

[13]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

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

[15]  Damian Szklarczyk,et al.  STITCH 3: zooming in on protein–chemical interactions , 2011, Nucleic Acids Res..

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

[17]  Sophia Ananiadou,et al.  Discovering and visualizing indirect associations between biomedical concepts , 2011, Bioinform..

[18]  Jonathan G. Lees,et al.  Systematic computational prediction of protein interaction networks , 2011, Physical biology.

[19]  Anne-Claude Gavin,et al.  Recent advances in charting protein-protein interaction: mass spectrometry-based approaches. , 2011, Current opinion in biotechnology.

[20]  Barend Mons,et al.  In silico discovery and experimental validation of new protein–protein interactions , 2011, Proteomics.

[21]  Xue-wen Chen,et al.  KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions , 2010, Nucleic Acids Res..

[22]  Haruki Nakamura,et al.  HitPredict: a database of quality assessed protein–protein interactions in nine species , 2010, Nucleic Acids Res..

[23]  Dieter Braun,et al.  Protein-binding assays in biological liquids using microscale thermophoresis. , 2010, Nature communications.

[24]  Jun'ichi Tsujii,et al.  Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[25]  Ulf Leser,et al.  A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature , 2010, PLoS Comput. Biol..

[26]  Menglong Li,et al.  PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment , 2010, BMC Research Notes.

[27]  Xingming Zhao,et al.  Predicting protein–protein interactions from protein sequences using meta predictor , 2010, Amino Acids.

[28]  R. Durbin,et al.  Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins , 2010, Science.

[29]  Dmitrij Frishman,et al.  The Negatome database: a reference set of non-interacting protein pairs , 2009, Nucleic Acids Res..

[30]  Damian Szklarczyk,et al.  STITCH 2: an interaction network database for small molecules and proteins , 2009, Nucleic Acids Res..

[31]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[32]  Carl J. Schmidt,et al.  eGIFT: Mining Gene Information from the Literature , 2010, BMC Bioinformatics.

[33]  Quan Pan,et al.  PPLook: an automated data mining tool for protein-protein interaction , 2010, BMC Bioinformatics.

[34]  Darby Tien-Hao Chang,et al.  Predicting protein-protein interactions in unbalanced data using the primary structure of proteins , 2010, BMC Bioinformatics.

[35]  Jun'ichi Tsujii,et al.  Protein-protein interaction extraction by leveraging multiple kernels and parsers , 2009, Int. J. Medical Informatics.

[36]  Raul Rodriguez-Esteban,et al.  Biomedical Text Mining and Its Applications , 2009, PLoS Comput. Biol..

[37]  Martijn J. Schuemie,et al.  Novel Protein-Protein Interactions Inferred from Literature Context , 2009, PloS one.

[38]  Jason Weston,et al.  Large Scale Application of Neural Network Based Semantic Role Labeling for Automated Relation Extraction from Biomedical Texts , 2009, PloS one.

[39]  Jinfeng Zhang,et al.  Bayesian inference of protein-protein interactions from biological literature , 2009, Bioinform..

[40]  Michael Schroeder,et al.  GoGene: gene annotation in the fast lane , 2009, Nucleic Acids Res..

[41]  Ben Lehner,et al.  Tissue specificity and the human protein interaction network , 2009, Molecular systems biology.

[42]  M. He,et al.  PPI Finder: A Mining Tool for Human Protein-Protein Interactions , 2009, PloS one.

[43]  S. Pu,et al.  Up-to-date catalogues of yeast protein complexes , 2008, Nucleic acids research.

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

[45]  Alfonso Valencia,et al.  Progress and challenges in predicting protein-protein interaction sites , 2008, Briefings Bioinform..

[46]  Geoffrey J. Barton,et al.  PIPs: human protein–protein interaction prediction database , 2008, Nucleic Acids Res..

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

[48]  Lincoln Stein,et al.  Reactome knowledgebase of human biological pathways and processes , 2008, Nucleic Acids Res..

[49]  Kenneth H. Buetow,et al.  PID: the Pathway Interaction Database , 2008, Nucleic Acids Res..

[50]  Hongfei Lin,et al.  Incorporating rich background knowledge for gene named entity classification and recognition , 2009, BMC Bioinformatics.

[51]  Huiru Zheng,et al.  GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction , 2008, Source Code for Biology and Medicine.

[52]  A. Barabasi,et al.  High-Quality Binary Protein Interaction Map of the Yeast Interactome Network , 2008, Science.

[53]  Ian M. Donaldson,et al.  iRefIndex: A consolidated protein interaction database with provenance , 2008, BMC Bioinformatics.

[54]  Sophia Ananiadou,et al.  FACTA: a text search engine for finding associated biomedical concepts , 2008, Bioinform..

[55]  David S. Wishart,et al.  Nucleic Acids Research Polysearch: a Web-based Text Mining System for Extracting Relationships between Human Diseases, Genes, Mutations, Drugs Polysearch: a Web-based Text Mining System for Extracting Relationships between Human Diseases, Genes, Mutations, Drugs and Metabolites , 2008 .

[56]  Byoung-Tak Zhang,et al.  PIE: an online prediction system for protein–protein interactions from text , 2008, Nucleic Acids Res..

[57]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[58]  Ozlem Keskin,et al.  PRISM: protein-protein interaction prediction by structural matching. , 2008, Methods in molecular biology.

[59]  Zhiyong Lu,et al.  OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression , 2008, BMC Bioinformatics.

[60]  Jun'ichi Tsujii,et al.  Corpus annotation for mining biomedical events from literature , 2008, BMC Bioinformatics.

[61]  Sara Linse,et al.  Methods for the detection and analysis of protein–protein interactions , 2007, Proteomics.

[62]  Geoffrey J. Barton,et al.  Probabilistic prediction and ranking of human protein-protein interactions , 2007, BMC Bioinformatics.

[63]  Juwen Shen,et al.  Predicting protein–protein interactions based only on sequences information , 2007, Proceedings of the National Academy of Sciences.

[64]  Zhongming Zhao,et al.  Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? , 2007, Biochemical and biophysical research communications.

[65]  Fabio Rinaldi,et al.  Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach , 2007, Artif. Intell. Medicine.

[66]  Ralf Zimmer,et al.  RelEx - Relation extraction using dependency parse trees , 2007, Bioinform..

[67]  Insuk Lee,et al.  A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality , 2007, BMC Bioinformatics.

[68]  I. Jurisica,et al.  Unequal evolutionary conservation of human protein interactions in interologous networks , 2007, Genome Biology.

[69]  Jonathan W. Bourne,et al.  Mutational data integration in gene‐oriented files of the Hermansky‐Pudlak Syndrome database , 2006, Human mutation.

[70]  Peer Bork,et al.  Extraction of regulatory gene/protein networks from Medline , 2006, Bioinform..

[71]  J. Qin,et al.  Weak protein-protein interactions as probed by NMR spectroscopy. , 2006, Trends in biotechnology.

[72]  Mei Liu,et al.  Prediction of protein-protein interactions using random decision forest framework , 2005, Bioinform..

[73]  Burr Settles,et al.  ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text , 2005 .

[74]  K. E. Ravikumar,et al.  Literature mining and database annotation of protein phosphorylation using a rule-based system , 2005, Bioinform..

[75]  Alfonso Valencia,et al.  Overview of BioCreAtIvE: critical assessment of information extraction for biology , 2005, BMC Bioinformatics.

[76]  Igor Jurisica,et al.  Online Predicted Human Interaction Database , 2005, Bioinform..

[77]  William R. Hersh,et al.  A survey of current work in biomedical text mining , 2005, Briefings Bioinform..

[78]  R. Karp,et al.  From the Cover : Conserved patterns of protein interaction in multiple species , 2005 .

[79]  William Stafford Noble,et al.  Kernel methods for predicting protein-protein interactions , 2005, ISMB.

[80]  Dmitrij Frishman,et al.  MIPS: analysis and annotation of proteins from whole genomes in 2005 , 2005, Nucleic Acids Res..

[81]  Hao Yu,et al.  Discovering patterns to extract protein-protein interactions from full texts , 2004, Bioinform..

[82]  William B. Langdon,et al.  BioRAT: extracting biological information from full-length papers , 2004, Bioinform..

[83]  L. Melton.  Protein arrays: Proteomics in multiplex , 2004, Nature.

[84]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[85]  Michael Krauthammer,et al.  GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data , 2004, J. Biomed. Informatics.

[86]  W. Willats,et al.  Phage display: practicalities and prospects , 2002, Plant Molecular Biology.

[87]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[88]  Stuart Brand,et al.  A new quantitative optical biosensor for protein characterisation. , 2003, Biosensors & bioelectronics.

[89]  Sergei Egorov,et al.  MedScan, a natural language processing engine for MEDLINE abstracts , 2003, Bioinform..

[90]  M. Campbell,et al.  PANTHER: a library of protein families and subfamilies indexed by function. , 2003, Genome research.

[91]  D. Eisenberg,et al.  Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach , 2003, Genome Biology.

[92]  Robert S. Ledley,et al.  The Protein Information Resource , 2003, Nucleic Acids Res..

[93]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[94]  Daniel Auerbach,et al.  The post‐genomic era of interactive proteomics: Facts and perspectives , 2002, Proteomics.

[95]  Jin-Dong Kim,et al.  The GENIA corpus: an annotated research abstract corpus in molecular biology domain , 2002 .

[96]  M. Vidal,et al.  Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". , 2001, Genome research.

[97]  Alfonso Valencia,et al.  Extracting Information Automatically From Biological Literature , 2001, Comparative and functional genomics.

[98]  B. Séraphin,et al.  The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.

[99]  Michael Krauthammer,et al.  GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles , 2001, ISMB.

[100]  E. Petricoin,et al.  Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front , 2001, Oncogene.

[101]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[102]  Gary D Bader,et al.  BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.

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

[104]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[105]  B. Snel,et al.  Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.

[106]  B. Alberts.  The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists , 1998, Cell.

[107]  A. Valencia,et al.  Correlated mutations contain information about protein-protein interaction. , 1997, Journal of molecular biology.

[108]  G. Naumann,et al.  Occurrence of pseudoexfoliation following penetrating keratoplasty for keratoconus. , 1992, The British journal of ophthalmology.

[109]  C. Chothia,et al.  The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.

[110]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[111]  G. P. Smith,et al.  Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. , 1985, Science.