TY - JOUR A1 - Navratil V A1 - de Chassey B A1 - Meyniel L A1 - Delmotte S A1 - Gautier C A1 - Andre P A1 - Lotteau V A1 - Rabourdin-Combe C T1 - VirHostNet: a knowledge base for the management and the analysis of virus-host interaction networks JO - Nucleic Acids Res Y1 - 2008 Nov 4 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn794 ER - TY - JOUR A1 - Elmer A. Ferna;ndez A1 - Maria R. Girotti A1 - Juan A. Lopez del Olmo A1 - Andrea S. Llera A1 - Osvaldo L. Podhajcer A1 - Rodolfo J. C. Cantet A1 - Monica Balzarini T1 - Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study JO - Bioinformatics Y1 - 2008 SP - 2706 EP - 2712 VL - 24 IS - 23 UR - http://dx.doi.org/10.1093/bioinformatics/btn508 ER - TY - JOUR A1 - Ying Ding A1 - Hyungwon Choi A1 - Alexey I. Nesvizhskii T1 - Adaptive Discriminant Function Analysis and Reranking of MS/MS Database Search Results for Improved Peptide Identification in Shotgun Proteomics JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4878 EP - 4889 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800484x ER - TY - JOUR A1 - Marcel P. Stoop A1 - Robert-Jan A. N. Lamers A1 - Peter C. Burgers A1 - Peter A. E. Sillevis Smitt A1 - Rogier Q. Hintzen A1 - Theo M. Luider T1 - The Rate of False Positive Sequence Matches of Peptides Profiled by MALDI MS and Identified by MS/MS JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4841 EP - 4847 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800489a ER - TY - JOUR A1 - Francesco Sirocco and Silvio C. E. Tosatto T1 - TESE: generating specific protein structure test set ensembles JO - Bioinformatics Y1 - 2008 SP - 2632 EP - 2633 VL - 24 IS - 22 UR - http://dx.doi.org/10.1093/bioinformatics/btn488 ER - TY - JOUR A1 - Michael Heymann A1 - David Paramelle A1 - Gilles Subra A1 - Eric Forest A1 - Jean Martinez A1 - Christophe Geourjon A1 - Gilbert Deleage T1 - MSX-3D: a tool to validate 3D protein models using mass spectrometry JO - Bioinformatics Y1 - 2008 SP - 2782 EP - 2783 VL - 24 IS - 23 UR - http://dx.doi.org/10.1093/bioinformatics/btn510 ER - TY - JOUR A1 - Thanh Hai Dang A1 - Koenraad Van Leemput A1 - Alain Verschoren A1 - Kris Laukens T1 - Prediction of kinase-specific phosphorylation sites using conditional random fields JO - Bioinformatics Y1 - 2008 SP - 2857 EP - 2864 VL - 24 IS - 24 UR - http://dx.doi.org/10.1093/bioinformatics/btn546 ER - TY - JOUR A1 - Ahmad Y A1 - Boisvert FM A1 - Gregor P A1 - Cobley A A1 - Lamond AI T1 - NOPdb: Nucleolar Proteome Database--2008 update JO - Nucleic Acids Res Y1 - 2008 Nov 4 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn804 ER - TY - JOUR A1 - Montazery-Kordy H A1 - Miran-Baygi MH A1 - Moradi MH T1 - A data-mining approach to biomarker identification from protein profiles discrete stationary wavelet transform JO - J Zhejiang Univ Sci B Y1 - 2008 SP - 863 EP - 70 VL - 9 IS - 11 UR - http://dx.doi.org/10.1631/jzus.B0820163 ER - TY - JOUR A1 - Eizadora T. Yu A1 - Arie Hawkins A1 - Irwin D. Kuntz A1 - Larry A. Rahn A1 - Andrew Rothfuss A1 - Kenneth Sale A1 - Malin M. Young A1 - Christine L. Yang A1 - Carmen M. Pancerella A1 - Daniele Fabris T1 - The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and Their Assemblies Using Mass Spectrometry-Based Approaches JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4848 EP - 4857 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800443f ER - TY - JOUR A1 - Troshin PV A1 - Morris C A1 - Prince SM A1 - Papiz MZ T1 - Laboratory information management system for membrane protein structure initiative - from gene to crystal JO - Mol Membr Biol Y1 - 2008 SP - 639 EP - 52 VL - 25 IS - 8 UR - http://dx.doi.org/10.1080/09687680802511766 ER - TY - JOUR A1 - Prasad TS A1 - Goel R A1 - Kandasamy K A1 - Keerthikumar S A1 - Kumar S A1 - Mathivanan S A1 - Telikicherla D A1 - Raju R A1 - Shafreen B A1 - Venugopal A A1 - Balakrishnan L A1 - Marimuthu A A1 - Banerjee S A1 - Somanathan DS A1 - Sebastian A A1 - Rani S A1 - Ray S A1 - Kishore CJ A1 - Kanth S A1 - Ahmed M A1 - Kashyap MK A1 - Mohmood R T1 - Human Protein Reference Database--2009 update JO - Nucleic Acids Res Y1 - 2008 Nov 6 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn892 ER - TY - JOUR A1 - Croning MD A1 - Marshall MC A1 - McLaren P A1 - Armstrong JD A1 - Grant SG T1 - G2Cdb: the Genes to Cognition database JO - Nucleic Acids Res Y1 - 2008 Nov 4 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn700 ER - TY - JOUR A1 - Katie Cottingham T1 - Proteomics researchers now agree on some aspects of data sharing JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4612 EP - 4612 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800781d ER - TY - JOUR A1 - Manually Validating Selected Results T1 - Peptizer, a Tool for Assessing False Positive Peptide Identifications and JO - Mol Cell Proteomics Y1 - 2008 SP - 2364 EP - 2372 VL - 7 IS - 12 UR - http://www.mcponline.org/cgi/content/abstract/7/12/2364?etoc ER - TY - JOUR A1 - Corey E. Bakalarski A1 - Joshua E. Elias A1 - Judit Villén A1 - Wilhelm Haas A1 - Scott A. Gerber A1 - Patrick A. Everley A1 - Steven P. Gygi T1 - The Impact of Peptide Abundance and Dynamic Range on Stable-Isotope-Based Quantitative Proteomic Analyses JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4756 EP - 4765 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800333e ER - TY - JOUR A1 - Minyue Ma A1 - Xuejiang Guo A1 - Fuqiang Wang A1 - Chun Zhao A1 - Zichuan Liu A1 - Zhonghua Shi A1 - Yufeng Wang A1 - Ping Zhang A1 - Kemei Zhang A1 - Ningling Wang A1 - Min Lin A1 - Zuomin Zhou A1 - Jiayin Liu A1 - Qingzhang Li A1 - Liu Wang A1 - Ran Huo A1 - Jiahao Sha A1 - Qi Zhou T1 - Protein Expression Profile of the Mouse Metaphase-II Oocyte JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4821 EP - 4830 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800392s ER - TY - JOUR A1 - Seesandra V. Rajagopala A1 - Johannes Goll A1 - N.D. Deve Gowda A1 - Kumar C. Sunil A1 - Bjorn Titz A1 - Arnab Mukherjee A1 - Sharmila S. Mary A1 - Naresh Raviswaran A1 - Chetan S. Poojari A1 - Srinivas Ramachandra A1 - Svetlana Shtivelband A1 - Stephen M. Blazie A1 - Julia Hofmann A1 - Peter Uetz T1 - MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions JO - Bioinformatics Y1 - 2008 SP - 2622 EP - 2627 VL - 24 IS - 22 UR - http://dx.doi.org/10.1093/bioinformatics/btn481 ER - TY - JOUR A1 - Li SJ A1 - Peng M A1 - Li H A1 - Liu BS A1 - Wang C A1 - Wu JR A1 - Li YX A1 - Zeng R T1 - Sys-BodyFluid: a systematical database for human body fluid proteome research JO - Nucleic Acids Res Y1 - 2008 Oct 31 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn849 ER - TY - JOUR A1 - Jayson A. Falkner A1 - Jarret W. Falkner A1 - Anastasia K. Yocum A1 - Philip C. Andrews T1 - A Spectral Clustering Approach to MS/MS Identification of Post-Translational Modifications JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4614 EP - 4622 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800226w ER - TY - JOUR A1 - Gabriele Cavallaro A1 - Leonardo Decaria A1 - Antonio Rosato T1 - Genome-Based Analysis of Heme Biosynthesis and Uptake in Prokaryotic Systems JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4946 EP - 4954 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr8004309 ER - TY - JOUR A1 - Aleksey V. Tolmachev A1 - Matthew E. Monroe A1 - Samuel O. Purvine A1 - Ronald J. Moore A1 - Navdeep Jaitly A1 - Joshua N. Adkins A1 - Gordon A. Anderson A1 - Richard D. Smith T1 - Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS Instruments JO - ANALYTICAL CHEMISTRY Y1 - 2008 SP - 8514 EP - 8525 VL - 80 IS - 22 UR - http://dx.doi.org/10.1021/ac801376g ER - TY - JOUR A1 - Daniel B. Martin A1 - Ted Holzman A1 - Damon May A1 - Amelia Peterson A1 - Ashley Eastham A1 - Jimmy Eng A1 - Martin McIntosh T1 - MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments JO - Mol Cell Proteomics Y1 - 2008 SP - 2270 EP - 2278 VL - 7 IS - 11 UR - http://www.mcponline.org/cgi/content/abstract/7/11/2270?etoc ER - TY - JOUR A1 - Simon Rogers A1 - Mark Girolami A1 - Walter Kolch A1 - Katrina M. Waters A1 - Tao Liu A1 - Brian Thrall A1 - H. Steven Wiley T1 - Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models JO - Bioinformatics Y1 - 2008 SP - 2894 EP - 2900 VL - 24 IS - 24 UR - http://dx.doi.org/10.1093/bioinformatics/btn553 ER - TY - JOUR A1 - Bhasi A A1 - Philip P A1 - Manikandan V A1 - Senapathy P T1 - ExDom: an integrated database for comparative analysis of the structures of protein domains in eukaryotes JO - Nucleic Acids Res Y1 - 2008 Nov 4 SP - EP - VL - IS - UR - http://dx.doi.org/10.1093/nar/gkn746 ER - TY - JOUR A1 - Quanhu Sheng A1 - Yehia Mechref A1 - Yixue Li A1 - Milos V. Novotny A1 - Haixu Tang T1 - A computational approach to characterizing bond linkages of glycan isomers using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry JO - Rapid Communications in Mass Spectrometry Y1 - 2008 SP - 3561 EP - 3569 VL - 22 IS - 22 UR - http://dx.doi.org/10.1002/rcm.3765 ER - TY - JOUR A1 - Kelli G. Kline A1 - Barbara Frewen A1 - Michael R. Bristow A1 - Michael J. MacCoss A1 - Christine C. Wu T1 - High Quality Catalog of Proteotypic Peptides from Human Heart JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 5055 EP - 5061 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800239e ER - TY - JOUR A1 - Llewellyn R A1 - Eisenberg DS T1 - Annotating proteins with generalized functional linkages JO - Proc Natl Acad Sci U S A Y1 - 2008 SP - 17700 EP - 5 VL - 105 IS - 46 UR - http://dx.doi.org/10.1073/pnas.0809583105 ER - TY - JOUR A1 - Gu J A1 - Hilser VJ T1 - Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome JO - Structure Y1 - 2008 SP - 1627 EP - 37 VL - 16 IS - 11 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19000815&dopt=Abstract ER - TY - JOUR A1 - Melanie Osl A1 - Stephan Dreiseitl A1 - Bernhard Pfeifer A1 - Klaus Weinberger A1 - Helmut Klocker A1 - Georg Bartsch A1 - Georg Schafer A1 - Bernhard Tilg A1 - Armin Graber A1 - Christian Baumgartner T1 - A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry JO - Bioinformatics Y1 - 2008 SP - 2908 EP - 2914 VL - 24 IS - 24 UR - http://dx.doi.org/10.1093/bioinformatics/btn506 ER - TY - JOUR A1 - Shiyong Liu A1 - Ying Gao A1 - Ilya A. Vakser T1 - DOCKGROUND protein-protein docking decoy set JO - Bioinformatics Y1 - 2008 SP - 2634 EP - 2635 VL - 24 IS - 22 UR - http://dx.doi.org/10.1093/bioinformatics/btn497 ER - TY - JOUR A1 - Sheila J. Barton A1 - John C. Whittaker T1 - Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors JO - Mass Spectrometry Reviews Y1 - 2009 SP - 177 EP - 187 VL - 28 IS - 1 UR - http://dx.doi.org/10.1002/mas.20188 ER - TY - JOUR A1 - Lustgarten JL A1 - Visweswaran S A1 - Grover H A1 - Kimmel CP A1 - Ryberg HL A1 - Bowser RP A1 - Gopalakrishnan V A1 - Hogan W T1 - Using a novel resource to decrease proteomic biomarker identification time JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18999243&dopt=Abstract ER - TY - JOUR A1 - Alves G A1 - Ogurtsov AY A1 - Yu YK T1 - RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration JO - Y1 - SP - EP - VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18954448&dopt=Abstract ER - TY - JOUR A1 - Daehee Hwang A1 - Ning Zhang A1 - Hookeun Lee A1 - Eugene Yi A1 - Hui Zhang A1 - Inyoul Y. Lee A1 - Leroy Hood A1 - Ruedi Aebersold T1 - MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis JO - Bioinformatics Y1 - 2008 SP - 2641 EP - 2642 VL - 24 IS - 22 UR - http://dx.doi.org/10.1093/bioinformatics/btn491 ER - TY - JOUR A1 - Cruz-Monteagudo M A1 - Munteanu CR A1 - Borges F A1 - Cordeiro MN A1 - Uriarte E A1 - González-Díaz H T1 - Quantitative Proteome-Property Relationships (QPPRs). Part 1: Finding biomarkers of organic drugs with mean Markov connectivity indices of spiral networks of blood mass spectra JO - Bioorg Med Chem Y1 - 2008 SP - 9684 EP - 93 VL - 16 IS - 22 UR - http://dx.doi.org/10.1016/j.bmc.2008.10.004 ER - TY - JOUR A1 - Dihui Lu A1 - Richard Z. Liu A1 - Victoria Izumi A1 - David Fenstermacher A1 - Eric B. Haura A1 - John Koomen A1 - Steven A. Eschrich T1 - IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry JO - Bioinformatics Y1 - 2008 SP - 2801 EP - 2802 VL - 24 IS - 23 UR - http://dx.doi.org/10.1093/bioinformatics/btn511 ER - TY - JOUR A1 - Benjamin Mann A1 - Milan Madera A1 - Quanhu Sheng A1 - Haixu Tang A1 - Yehia Mechref A1 - Milos V. Novotny T1 - ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics JO - Rapid Communications in Mass Spectrometry Y1 - 2008 SP - 3823 EP - 3834 VL - 22 IS - 23 UR - http://dx.doi.org/10.1002/rcm.3781 ER - TY - JOUR A1 - Lustgarten JL A1 - Gopalakrishnan V A1 - Grover H A1 - Visweswaran S T1 - Improving classification performance with discretization on biomedical datasets JO - AMIA Annu Symp Proc Y1 - 2008 SP - 445 EP - 9 VL - IS - UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=18999186&dopt=Abstract ER - TY - JOUR A1 - Yi-Wei Yang A1 - Shao-Min Bian A1 - Yuan Yao A1 - Jin-Yuan Liu T1 - Comparative Proteomic Analysis Provides New Insights into the Fiber Elongating Process in Cotton JO - JOURNAL OF PROTEOME RESEARCH Y1 - 2008 SP - 4623 EP - 4637 VL - 7 IS - 11 UR - http://dx.doi.org/10.1021/pr800550q ER - TY - JOUR A1 - Craig E. Jones A1 - Julian Schwerdt A1 - Tessa Arwen Bretag A1 - Ute Baumann A1 - Alfred L. Brown T1 - GOSLING: a rule-based protein annotator using BLAST and GO JO - Bioinformatics Y1 - 2008 SP - 2628 EP - 2629 VL - 24 IS - 22 UR - http://dx.doi.org/10.1093/bioinformatics/btn486 ER - TY - JOUR A1 - Maraziotis IA A1 - Dimitrakopoulou K A1 - Bezerianos A T1 - An in silico method for detecting overlapping functional modules from biological networks JO - Y1 - SP - EP - VL - IS - UR - http://dx.doi.org/10.1186/1752-0509-2-93 ER - TY - JOUR A1 - Ta-tsen Soong A1 - Kazimierz O. Wrzeszczynski A1 - Burkhard Rost T1 - Physical protein-protein interactions predicted from microarrays JO - Bioinformatics Y1 - 2008 SP - 2608 EP - 2614 VL - 24 IS - 22 UR - http://dx.doi.org/10.1093/bioinformatics/btn498 ER - TY - JOUR A1 - John T. Prince and Edward M. Marcotte T1 - mspire: mass spectrometry proteomics in Ruby JO - Bioinformatics Y1 - 2008 SP - 2796 EP - 2797 VL - 24 IS - 23 UR - http://dx.doi.org/10.1093/bioinformatics/btn513 ER - TY - JOUR A1 - Hakan Viklund A1 - Andreas Bernsel A1 - Marcin Skwark A1 - Arne Elofsson T1 - SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology JO - Bioinformatics Y1 - 2008 SP - 2928 EP - 2929 VL - 24 IS - 24 UR - http://dx.doi.org/10.1093/bioinformatics/btn550 ER - TY - JOUR A1 - Khalid Belhajjame A1 - Andrew R. Jones A1 - Norman W. Paton T1 - A toolkit for capturing and sharing FuGE experiments JO - Bioinformatics Y1 - 2008 SP - 2647 EP - 2649 VL - 24 IS - 22 UR - http://dx.doi.org/10.1093/bioinformatics/btn496 ER -