%A Navratil V
%A de Chassey B
%A Meyniel L
%A Delmotte S
%A Gautier C
%A Andre P
%A Lotteau V
%A Rabourdin-Combe C
%T VirHostNet: a knowledge base for the management and the analysis of virus-host interaction networks
%0 Journal Article
%D 2008 Nov 4
%J Nucleic Acids Res
%P -
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%8 2008 Nov 4

%A Elmer A. Ferna;ndez
%A Maria R. Girotti
%A Juan A. Lopez del Olmo
%A Andrea S. Llera
%A Osvaldo L. Podhajcer
%A Rodolfo J. C. Cantet
%A Monica Balzarini
%T Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2706-2712
%V 24
%N 23
%U http://dx.doi.org/10.1093/bioinformatics/btn508

%A Ying Ding
%A Hyungwon Choi
%A Alexey I. Nesvizhskii
%T Adaptive Discriminant Function Analysis and Reranking of MS/MS Database Search Results for Improved Peptide Identification in Shotgun Proteomics
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4878-4889
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800484x

%A Marcel P. Stoop
%A Robert-Jan A. N. Lamers
%A Peter C. Burgers
%A Peter A. E. Sillevis Smitt
%A Rogier Q. Hintzen
%A Theo M. Luider
%T The Rate of False Positive Sequence Matches of Peptides Profiled by MALDI MS and Identified by MS/MS
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4841-4847
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800489a

%A Francesco Sirocco and Silvio C. E. Tosatto
%T TESE: generating specific protein structure test set ensembles
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2632-2633
%V 24
%N 22
%U http://dx.doi.org/10.1093/bioinformatics/btn488

%A Michael Heymann
%A David Paramelle
%A Gilles Subra
%A Eric Forest
%A Jean Martinez
%A Christophe Geourjon
%A Gilbert Deleage
%T MSX-3D: a tool to validate 3D protein models using mass spectrometry
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2782-2783
%V 24
%N 23
%U http://dx.doi.org/10.1093/bioinformatics/btn510

%A Thanh Hai Dang
%A Koenraad Van Leemput
%A Alain Verschoren
%A Kris Laukens
%T Prediction of kinase-specific phosphorylation sites using conditional random fields
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2857-2864
%V 24
%N 24
%U http://dx.doi.org/10.1093/bioinformatics/btn546

%A Ahmad Y
%A Boisvert FM
%A Gregor P
%A Cobley A
%A Lamond AI
%T NOPdb: Nucleolar Proteome Database--2008 update
%0 Journal Article
%D 2008 Nov 4
%J Nucleic Acids Res
%P -
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%N 
%U http://dx.doi.org/10.1093/nar/gkn804
%8 2008 Nov 4

%A Montazery-Kordy H
%A Miran-Baygi MH
%A Moradi MH
%T A data-mining approach to biomarker identification from protein profiles discrete stationary wavelet transform
%0 Journal Article
%D 2008
%J J Zhejiang Univ Sci B
%P 863-70
%V 9
%N 11
%U http://dx.doi.org/10.1631/jzus.B0820163

%A Eizadora T. Yu
%A Arie Hawkins
%A Irwin D. Kuntz
%A Larry A. Rahn
%A Andrew Rothfuss
%A Kenneth Sale
%A Malin M. Young
%A Christine L. Yang
%A Carmen M. Pancerella
%A Daniele Fabris
%T The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and Their Assemblies Using Mass Spectrometry-Based Approaches
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4848-4857
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800443f

%A Troshin PV
%A Morris C
%A Prince SM
%A Papiz MZ
%T Laboratory information management system for membrane protein structure initiative - from gene to crystal
%0 Journal Article
%D 2008
%J Mol Membr Biol
%P 639-52
%V 25
%N 8
%U http://dx.doi.org/10.1080/09687680802511766

%A Prasad TS
%A Goel R
%A Kandasamy K
%A Keerthikumar S
%A Kumar S
%A Mathivanan S
%A Telikicherla D
%A Raju R
%A Shafreen B
%A Venugopal A
%A Balakrishnan L
%A Marimuthu A
%A Banerjee S
%A Somanathan DS
%A Sebastian A
%A Rani S
%A Ray S
%A Kishore CJ
%A Kanth S
%A Ahmed M
%A Kashyap MK
%A Mohmood R
%T Human Protein Reference Database--2009 update
%0 Journal Article
%D 2008 Nov 6
%J Nucleic Acids Res
%P -
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%8 2008 Nov 6

%A Croning MD
%A Marshall MC
%A McLaren P
%A Armstrong JD
%A Grant SG
%T G2Cdb: the Genes to Cognition database
%0 Journal Article
%D 2008 Nov 4
%J Nucleic Acids Res
%P -
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%U http://dx.doi.org/10.1093/nar/gkn700
%8 2008 Nov 4

%A Katie Cottingham
%T Proteomics researchers now agree on some aspects of data sharing
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4612-4612
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800781d

%A Manually Validating Selected Results
%T Peptizer, a Tool for Assessing False Positive Peptide Identifications and
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 2364-2372
%V 7
%N 12
%U http://www.mcponline.org/cgi/content/abstract/7/12/2364?etoc

%A Corey E. Bakalarski
%A Joshua E. Elias
%A Judit Villén
%A Wilhelm Haas
%A Scott A. Gerber
%A Patrick A. Everley
%A Steven P. Gygi
%T The Impact of Peptide Abundance and Dynamic Range on Stable-Isotope-Based Quantitative Proteomic Analyses
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4756-4765
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800333e

%A Minyue Ma
%A Xuejiang Guo
%A Fuqiang Wang
%A Chun Zhao
%A Zichuan Liu
%A Zhonghua Shi
%A Yufeng Wang
%A Ping Zhang
%A Kemei Zhang
%A Ningling Wang
%A Min Lin
%A Zuomin Zhou
%A Jiayin Liu
%A Qingzhang Li
%A Liu Wang
%A Ran Huo
%A Jiahao Sha
%A Qi Zhou
%T Protein Expression Profile of the Mouse Metaphase-II Oocyte
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4821-4830
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800392s

%A Seesandra V. Rajagopala
%A Johannes Goll
%A N.D. Deve Gowda
%A Kumar C. Sunil
%A Bjorn Titz
%A Arnab Mukherjee
%A Sharmila S. Mary
%A Naresh Raviswaran
%A Chetan S. Poojari
%A Srinivas Ramachandra
%A Svetlana Shtivelband
%A Stephen M. Blazie
%A Julia Hofmann
%A Peter Uetz
%T MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2622-2627
%V 24
%N 22
%U http://dx.doi.org/10.1093/bioinformatics/btn481

%A Li SJ
%A Peng M
%A Li H
%A Liu BS
%A Wang C
%A Wu JR
%A Li YX
%A Zeng R
%T Sys-BodyFluid: a systematical database for human body fluid proteome research
%0 Journal Article
%D 2008 Oct 31
%J Nucleic Acids Res
%P -
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%U http://dx.doi.org/10.1093/nar/gkn849
%8 2008 Oct 31

%A Jayson A. Falkner
%A Jarret W. Falkner
%A Anastasia K. Yocum
%A Philip C. Andrews
%T A Spectral Clustering Approach to MS/MS Identification of Post-Translational Modifications
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4614-4622
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800226w

%A Gabriele Cavallaro
%A Leonardo Decaria
%A Antonio Rosato
%T Genome-Based Analysis of Heme Biosynthesis and Uptake in Prokaryotic Systems
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4946-4954
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr8004309

%A Aleksey V. Tolmachev
%A Matthew E. Monroe
%A Samuel O. Purvine
%A Ronald J. Moore
%A Navdeep Jaitly
%A Joshua N. Adkins
%A Gordon A. Anderson
%A Richard D. Smith
%T Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS Instruments
%0 Journal Article
%D 2008
%J ANALYTICAL CHEMISTRY
%P 8514-8525
%V 80
%N 22
%U http://dx.doi.org/10.1021/ac801376g

%A Daniel B. Martin
%A Ted Holzman
%A Damon May
%A Amelia Peterson
%A Ashley Eastham
%A Jimmy Eng
%A Martin McIntosh
%T MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments
%0 Journal Article
%D 2008
%J Mol Cell Proteomics
%P 2270-2278
%V 7
%N 11
%U http://www.mcponline.org/cgi/content/abstract/7/11/2270?etoc

%A Simon Rogers
%A Mark Girolami
%A Walter Kolch
%A Katrina M. Waters
%A Tao Liu
%A Brian Thrall
%A H. Steven Wiley
%T Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2894-2900
%V 24
%N 24
%U http://dx.doi.org/10.1093/bioinformatics/btn553

%A Bhasi A
%A Philip P
%A Manikandan V
%A Senapathy P
%T ExDom: an integrated database for comparative analysis of the structures of protein domains in eukaryotes
%0 Journal Article
%D 2008 Nov 4
%J Nucleic Acids Res
%P -
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%U http://dx.doi.org/10.1093/nar/gkn746
%8 2008 Nov 4

%A Quanhu Sheng
%A Yehia Mechref
%A Yixue Li
%A Milos V. Novotny
%A Haixu Tang
%T A computational approach to characterizing bond linkages of glycan isomers using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry
%0 Journal Article
%D 2008
%J Rapid Communications in Mass Spectrometry
%P 3561-3569
%V 22
%N 22
%U http://dx.doi.org/10.1002/rcm.3765

%A Kelli G. Kline
%A Barbara Frewen
%A Michael R. Bristow
%A Michael J. MacCoss
%A Christine C. Wu
%T High Quality Catalog of Proteotypic Peptides from Human Heart
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 5055-5061
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800239e

%A Llewellyn R
%A Eisenberg DS
%T Annotating proteins with generalized functional linkages
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%J Proc Natl Acad Sci U S A
%P 17700-5
%V 105
%N 46
%U http://dx.doi.org/10.1073/pnas.0809583105

%A Gu J
%A Hilser VJ
%T Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome
%0 Journal Article
%D 2008
%J Structure
%P 1627-37
%V 16
%N 11
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19000815&dopt=Abstract

%A Melanie Osl
%A Stephan Dreiseitl
%A Bernhard Pfeifer
%A Klaus Weinberger
%A Helmut Klocker
%A Georg Bartsch
%A Georg Schafer
%A Bernhard Tilg
%A Armin Graber
%A Christian Baumgartner
%T A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2908-2914
%V 24
%N 24
%U http://dx.doi.org/10.1093/bioinformatics/btn506

%A Shiyong Liu
%A Ying Gao
%A Ilya A. Vakser
%T DOCKGROUND protein-protein docking decoy set
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2634-2635
%V 24
%N 22
%U http://dx.doi.org/10.1093/bioinformatics/btn497

%A Sheila J. Barton
%A John C. Whittaker
%T Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors
%0 Journal Article
%D 2009
%J Mass Spectrometry Reviews
%P 177-187
%V 28
%N 1
%U http://dx.doi.org/10.1002/mas.20188

%A Lustgarten JL
%A Visweswaran S
%A Grover H
%A Kimmel CP
%A Ryberg HL
%A Bowser RP
%A Gopalakrishnan V
%A Hogan W
%T Using a novel resource to decrease proteomic biomarker identification time
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%A Alves G
%A Ogurtsov AY
%A Yu YK
%T RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration
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%A Daehee Hwang
%A Ning Zhang
%A Hookeun Lee
%A Eugene Yi
%A Hui Zhang
%A Inyoul Y. Lee
%A Leroy Hood
%A Ruedi Aebersold
%T MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2641-2642
%V 24
%N 22
%U http://dx.doi.org/10.1093/bioinformatics/btn491

%A Cruz-Monteagudo M
%A Munteanu CR
%A Borges F
%A Cordeiro MN
%A Uriarte E
%A González-Díaz H
%T Quantitative Proteome-Property Relationships (QPPRs). Part 1: Finding biomarkers of organic drugs with mean Markov connectivity indices of spiral networks of blood mass spectra
%0 Journal Article
%D 2008
%J Bioorg Med Chem
%P 9684-93
%V 16
%N 22
%U http://dx.doi.org/10.1016/j.bmc.2008.10.004

%A Dihui Lu
%A Richard Z. Liu
%A Victoria Izumi
%A David Fenstermacher
%A Eric B. Haura
%A John Koomen
%A Steven A. Eschrich
%T IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2801-2802
%V 24
%N 23
%U http://dx.doi.org/10.1093/bioinformatics/btn511

%A Benjamin Mann
%A Milan Madera
%A Quanhu Sheng
%A Haixu Tang
%A Yehia Mechref
%A Milos V. Novotny
%T ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics
%0 Journal Article
%D 2008
%J Rapid Communications in Mass Spectrometry
%P 3823-3834
%V 22
%N 23
%U http://dx.doi.org/10.1002/rcm.3781

%A Lustgarten JL
%A Gopalakrishnan V
%A Grover H
%A Visweswaran S
%T Improving classification performance with discretization on biomedical datasets
%0 Journal Article
%D 2008
%J AMIA Annu Symp Proc
%P 445-9
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%A Yi-Wei Yang
%A Shao-Min Bian
%A Yuan Yao
%A Jin-Yuan Liu
%T Comparative Proteomic Analysis Provides New Insights into the Fiber Elongating Process in Cotton
%0 Journal Article
%D 2008
%J JOURNAL OF PROTEOME RESEARCH
%P 4623-4637
%V 7
%N 11
%U http://dx.doi.org/10.1021/pr800550q

%A Craig E. Jones
%A Julian Schwerdt
%A Tessa Arwen Bretag
%A Ute Baumann
%A Alfred L. Brown
%T GOSLING: a rule-based protein annotator using BLAST and GO
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2628-2629
%V 24
%N 22
%U http://dx.doi.org/10.1093/bioinformatics/btn486

%A Maraziotis IA
%A Dimitrakopoulou K
%A Bezerianos A
%T An in silico method for detecting overlapping functional modules from biological networks
%0 Journal Article
%D 
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%U http://dx.doi.org/10.1186/1752-0509-2-93

%A Ta-tsen Soong
%A Kazimierz O. Wrzeszczynski
%A Burkhard Rost
%T Physical protein-protein interactions predicted from microarrays
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2608-2614
%V 24
%N 22
%U http://dx.doi.org/10.1093/bioinformatics/btn498

%A John T. Prince and Edward M. Marcotte
%T mspire: mass spectrometry proteomics in Ruby
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2796-2797
%V 24
%N 23
%U http://dx.doi.org/10.1093/bioinformatics/btn513

%A Hakan Viklund
%A Andreas Bernsel
%A Marcin Skwark
%A Arne Elofsson
%T SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2928-2929
%V 24
%N 24
%U http://dx.doi.org/10.1093/bioinformatics/btn550

%A Khalid Belhajjame
%A Andrew R. Jones
%A Norman W. Paton
%T A toolkit for capturing and sharing FuGE experiments
%0 Journal Article
%D 2008
%J Bioinformatics
%P 2647-2649
%V 24
%N 22
%U http://dx.doi.org/10.1093/bioinformatics/btn496