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Yates III T1 - Colander: A Probability-Based Support Vector Machine Algorithm for Automatic Screening for CID Spectra of Phosphopeptides Prior to Database Search JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 3628 EP - 3634 VL - 7 IS - 08 UR - http://dx.doi.org/10.1021/pr8001194 ER - TY - JOUR A1 - Olivier Filangi A1 - Yoann Beausse A1 - Anthony Assi A1 - Ludovic Legrand A1 - Jean-Marc Larre A1 - Veronique Martin A1 - Olivier Collin A1 - Christophe Caron A1 - Hugues Leroy A1 - David Allouche T1 - BioMAJ: a flexible framework for databanks synchronization and processing JO - Bioinformatics Y1 - 2008 SP - 1823 EP - 1825 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn325 ER - TY - JOUR A1 - Eric Deutsch T1 - mzML: A single, unifying data format for mass spectrometer output JO - PROTEOMICS Y1 - 2008 SP - 2776 EP - 2777 VL - 8 IS - 14 UR - http://dx.doi.org/10.1002/pmic.200890049 ER - TY - JOUR A1 - Junqueira M A1 - Spirin V A1 - Balbuena TS A1 - Thomas H A1 - Adzhubei I A1 - Sunyaev S A1 - Shevchenko A T1 - Protein identification pipeline for the homology-driven proteomics JO - J Proteomics Y1 - 2008 SP - 346 EP - 56 VL - 71 IS - 3 UR - http://dx.doi.org/10.1016/j.jprot.2008.07.003 ER - TY - JOUR A1 - Alexander Scherl A1 - Yihsuan Shannon Tsai A1 - Scott A. Shaffer A1 - David R. Goodlett T1 - Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses JO - PROTEOMICS Y1 - 2008 SP - 2791 EP - 2797 VL - 8 IS - 14 UR - http://dx.doi.org/10.1002/pmic.200800045 ER - TY - JOUR A1 - Lisa Berglund A1 - Erik Björling A1 - Kalle Jonasson A1 - Johan Rockberg A1 - Linn Fagerberg A1 - Cristina Al-Khalili Szigyarto A1 - Åsa Sivertsson A1 - Mathias Uhlén T1 - A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation JO - PROTEOMICS Y1 - 2008 SP - 2832 EP - 2839 VL - 8 IS - 14 UR - http://dx.doi.org/10.1002/pmic.200800203 ER - TY - JOUR A1 - Louis Ramaley A1 - Lisandra Cubero Herrera T1 - Software for the calculation of isotope patterns in tandem mass spectrometry JO - Rapid Communications in Mass Spectrometry Y1 - 2008 SP - 2707 EP - 2714 VL - 22 IS - 17 UR - http://dx.doi.org/10.1002/rcm.3668 ER - TY - JOUR A1 - A.M. Willemsen A1 - G.A. Jansen A1 - J.C. Komen A1 - S. van Hooff A1 - H.R. Waterham A1 - P.M.T. Brites A1 - R.J.A. Wanders A1 - A.H.C. van Kampen T1 - Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways JO - Bioinformatics Y1 - 2008 SP - i21 EP - i27 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn274 ER - TY - JOUR A1 - Duncan P. Brown T1 - Efficient functional clustering of protein sequences using the Dirichlet process JO - Bioinformatics Y1 - 2008 SP - 1765 EP - 1771 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn244 ER - TY - JOUR A1 - Louie B A1 - Tarczy-Hornoch P A1 - Higdon R A1 - Kolker E T1 - Validating Annotations for Uncharacterized Proteins in Shewanella oneidensis JO - OMICS Y1 - 2008/08/7 SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18687039&dopt=Abstract ER - TY - JOUR A1 - Sebastian Bocker and Florian Rasche T1 - Towards de novo identification of metabolites by analyzing tandem mass spectra JO - Bioinformatics Y1 - 2008 SP - i49 EP - i55 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn270 ER - TY - JOUR A1 - Julia E. Bandow A1 - John D. Baker A1 - Matthias Berth A1 - Cory Painter A1 - Osvaldo J. Sepulveda A1 - Kelly A. Clark A1 - Iain Kilty A1 - Ruth A. VanBogelen T1 - Improved image analysis workflow for 2-D gels enables large-scale 2-D gel-based proteomics studies - COPD biomarker discovery study JO - PROTEOMICS Y1 - 2008 SP - 3030 EP - 3041 VL - 8 IS - 15 UR - http://dx.doi.org/10.1002/pmic.200701184 ER - TY - JOUR A1 - Chia-Ying Yang A1 - Chao-Hui Chang A1 - Ya-Ling Yu A1 - Tsu-Chun Emma Lin A1 - Sheng-An Lee A1 - Chueh-Chuan Yen A1 - Jinn-Moon Yang A1 - Jin-Mei Lai A1 - Yi-Ren Hong A1 - Tzu-Ling Tseng A1 - Kun-Mao Chao A1 - Chi-Ying F. Huang T1 - PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database JO - Bioinformatics Y1 - 2008 SP - i14 EP - i20 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn297 ER - TY - JOUR A1 - Yaniv Loewenstein and Michal Linial T1 - Connect the dots: exposing hidden protein family connections from the entire sequence tree JO - Bioinformatics Y1 - 2008 SP - i193 EP - i199 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn301 ER - TY - JOUR A1 - Kosuke Hashimoto A1 - Ichigaku Takigawa A1 - Motoki Shiga A1 - Minoru Kanehisa A1 - Hiroshi Mamitsuka T1 - Mining significant tree patterns in carbohydrate sugar chains JO - Bioinformatics Y1 - 2008 SP - i167 EP - i173 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn293 ER - TY - JOUR A1 - Predrag Radivojac A1 - Peter H. Baenziger A1 - Maricel G. Kann A1 - Matthew E. Mort A1 - Matthew W. Hahn A1 - Sean D. Mooney T1 - Gain and loss of phosphorylation sites in human cancer JO - Bioinformatics Y1 - 2008 SP - i241 EP - i247 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn267 ER - TY - JOUR A1 - Gammerman A A1 - Nouretdinov I A1 - Burford B A1 - Chervonenkis A A1 - Vovk V A1 - Luo Z T1 - Clinical mass spectrometry proteomic diagnosis by conformal predictors JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18673293&dopt=Abstract ER - TY - JOUR A1 - Jardin-Mathe O A1 - Bonnel D A1 - Franck J A1 - Wisztorski M A1 - Macagno E A1 - Fournier I A1 - Salzet M T1 - MITICS (MALDI Imaging Team Imaging Computing System): A new open source mass spectrometry imaging software JO - J Proteomics Y1 - 2008 SP - 332 EP - 45 VL - 71 IS - 3 UR - http://dx.doi.org/10.1016/j.jprot.2008.07.004 ER - TY - JOUR A1 - Jung Hun Oh A1 - Young Bun Kim A1 - Prem Gurnani A1 - Kevin P. Rosenblatt A1 - Jean X. Gao T1 - Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data JO - Bioinformatics Y1 - 2008 SP - 1812 EP - 1818 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn316 ER - TY - JOUR A1 - Deukwoo Kwon A1 - Marina Vannucci A1 - Joon Jin Song A1 - Jaesik Jeong A1 - Ruth M. Pfeiffer T1 - A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise JO - PROTEOMICS Y1 - 2008 SP - 3019 EP - 3029 VL - 8 IS - 15 UR - http://dx.doi.org/10.1002/pmic.200701010 ER - TY - JOUR A1 - Andreas Quandt A1 - Patricia Hernandez A1 - Alexandre Masselot A1 - Celine Hernandez A1 - Sergio Maffioletti A1 - Cesare Pautasso A1 - Ron D. Appel A1 - Frederique Lisacek T1 - swissPIT: a novel approach for pipelined analysis of mass spectrometry data JO - Bioinformatics Y1 - 2008 SP - 1416 EP - 1417 VL - 24 IS - 11 UR - http://dx.doi.org/10.1093/bioinformatics/btn139 ER - TY - JOUR A1 - Samuel H. Payne A1 - Margaret Yau A1 - Marcus B. Smolka A1 - Stephen Tanner A1 - Huilin Zhou A1 - Vineet Bafna T1 - Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 3373 EP - 3381 VL - 7 IS - 08 UR - http://dx.doi.org/10.1021/pr800129m ER - TY - JOUR A1 - Matthiesen R A1 - Jensen ON T1 - Analysis of mass spectrometry data in proteomics JO - Methods Mol Biol Y1 - 2008 SP - 105 EP - 22 VL - 453 IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18712299&dopt=Abstract ER - TY - JOUR A1 - Goffard N A1 - Weiller G T1 - Identifying components of complexes JO - Methods Mol Biol Y1 - 2008 SP - 257 EP - 65 VL - 453 IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18712308&dopt=Abstract ER - TY - JOUR A1 - Aleksandr Morgulis A1 - George Coulouris A1 - Yan Raytselis A1 - Thomas L. Madden A1 - Richa Agarwala A1 - Alejandro A. Schaffer T1 - Database indexing for production MegaBLAST searches JO - Bioinformatics Y1 - 2008 SP - 1757 EP - 1764 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn322 ER - TY - JOUR A1 - Kristoffer Forslund and Erik L. L. Sonnhammer T1 - Predicting protein function from domain content JO - Bioinformatics Y1 - 2008 SP - 1681 EP - 1687 VL - 24 IS - 15 UR - http://dx.doi.org/10.1093/bioinformatics/btn312 ER - TY - JOUR A1 - Jayesh Pandey A1 - Mehmet Koyuturk A1 - Shankar Subramaniam A1 - Ananth Grama T1 - Functional coherence in domain interaction networks JO - Bioinformatics Y1 - 2008 SP - i28 EP - i34 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn296 ER - TY - JOUR A1 - Claus Lundegaard A1 - Ole Lund A1 - Morten Nielsen T1 - Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers JO - Bioinformatics Y1 - 2008 SP - 1397 EP - 1398 VL - 24 IS - 11 UR - http://dx.doi.org/10.1093/bioinformatics/btn128 ER - TY - JOUR A1 - Benjamin J. Cargile A1 - Joel R. Sevinsky A1 - Amal S. Essader A1 - Jerry P. Eu A1 - James L. Stephenson Jr T1 - Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects JO - ELECTROPHORESIS Y1 - 2008 SP - 2768 EP - 2778 VL - 29 IS - 13 UR - http://dx.doi.org/10.1002/elps.200700701 ER - TY - JOUR A1 - Aude Martinez A1 - José A. Traverso A1 - Benoît Valot A1 - Myriam Ferro A1 - Christelle Espagne A1 - Geneviève Ephritikhine A1 - Michel Zivy A1 - Carmela Giglione A1 - Thierry Meinnel T1 - Extent of N-terminal modifications in cytosolic proteins from eukaryotes JO - PROTEOMICS Y1 - 2008 SP - 2809 EP - 2831 VL - 8 IS - 14 UR - http://dx.doi.org/10.1002/pmic.200701191 ER - TY - JOUR A1 - Gelio Alves A1 - Wells W. Wu A1 - Guanghui Wang A1 - Rong-Fong Shen A1 - Yi-Kuo Yu T1 - Enhancing Peptide Identification Confidence by Combining Search Methods JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 3102 EP - 3113 VL - 7 IS - 08 UR - http://dx.doi.org/10.1021/pr700798h ER - TY - JOUR A1 - Maclean D A1 - Burrell MA A1 - Studholme DJ A1 - Jones AM T1 - PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18710483&dopt=Abstract ER - TY - JOUR A1 - A. D. J. van Dijk A1 - D. Bosch A1 - C. J. F. ter Braak A1 - A. R. van der Krol A1 - R. C. H. J. van Ham T1 - Predicting sub-Golgi localization of type II membrane proteins JO - Bioinformatics Y1 - 2008 SP - 1779 EP - 1786 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn309 ER - TY - JOUR A1 - Magno Junqueira A1 - Victor Spirin A1 - Tiago Santana Balbuena A1 - Patrice Waridel A1 - Vineeth Surendranath A1 - Grigoriy Kryukov A1 - Ivan Adzhubei A1 - Henrik Thomas A1 - Shamil Sunyaev A1 - Andrej Shevchenko T1 - Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 3382 EP - 3395 VL - 7 IS - 08 UR - http://dx.doi.org/10.1021/pr800140v ER - TY - JOUR A1 - Sven-Eric Schelhorn A1 - Thomas Lengauer A1 - Mario Albrecht T1 - An integrative approach for predicting interactions of protein regions JO - Bioinformatics Y1 - 2008 SP - i35 EP - i41 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn290 ER - TY - JOUR A1 - Sangtae Kim A1 - Nitin Gupta A1 - Pavel A. Pevzner T1 - Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 3354 EP - 3363 VL - 7 IS - 08 UR - http://dx.doi.org/10.1021/pr8001244 ER - TY - JOUR A1 - Lukas Kall A1 - John D. Storey A1 - William Stafford Noble T1 - Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry JO - Bioinformatics Y1 - 2008 SP - i42 EP - i48 VL - 24 IS - 16 UR - http://dx.doi.org/10.1093/bioinformatics/btn294 ER - TY - JOUR A1 - Hongzhan H A1 - Shukla HD A1 - Cathy W A1 - Satya S T1 - Challenges and solutions in proteomics JO - Curr Genomics Y1 - 2007 SP - 21 EP - 8 VL - 8 IS - 1 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18645629&dopt=Abstract ER - TY - JOUR A1 - Takashi Ishida and Kengo Kinoshita T1 - Prediction of disordered regions in proteins based on the meta approach JO - Bioinformatics Y1 - 2008 SP - 1344 EP - 1348 VL - 24 IS - 11 UR - http://dx.doi.org/10.1093/bioinformatics/btn195 ER -