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%T Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics
%0 Journal Article
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%J Nucl Acids Res
%P D762-6
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%N Database issue
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%A Cox J
%A Mann M
%T MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
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%J Nat Biotechnol
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%U http://dx.doi.org/10.1038/nbt.1511

%A Hong-Bin Shen
%A Dong-Liang Yi
%A Li-Xiu Yao
%A Jie Yang
%A Kuo-Chen Chou
%T Knowledge-based computational intelligence development for predicting protein secondary structures from sequences
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%J Expert Review of Proteomics
%P 653-662
%V 5
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%U http://dx.doi.org/10.1586/14789450.5.5.653 

%A Richard S. P. Horler
%A Andrew Butcher
%A Nikitas Papangelopoulos
%A Peter D. Ashton
%A Gavin H. Thomas
%T EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations
%0 Journal Article
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%J Bioinformatics
%P 163-166
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%A Min-Seok Kwon
%A Hyoung-Joo Lee
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%A Sang Yun Cho
%A Young-Ki Paik
%T IntelliMS: A platform to efficiently manage and visualize tandem mass spectral data
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%J PROTEOMICS
%P 4910-4913
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%U http://dx.doi.org/10.1002/pmic.200800296

%A Ma Y
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%T An integrative genomic and proteomic approach to chemosensitivity prediction
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%J Int J Oncol
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%A Ganesan Pugalenthi
%A Ke Tang
%A P. N. Suganthan
%A Saikat Chakrabarti
%T Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble
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%J Bioinformatics
%P 204-210
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%T Discovery and revision of Arabidopsis genes by proteogenomics
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%J Proc Natl Acad Sci U S A
%P 21034-8
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%U http://dx.doi.org/10.1073/pnas.0811066106

%A Aleksandr Barinov
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%A Amal Hammani
%A Pierre Nicolas
%A Philippe Langella
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%A Emmanuelle Maguin
%A Maarten van de Guchte
%T Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria
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%J PROTEOMICS
%P 61-73
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%U http://dx.doi.org/10.1002/pmic.200800195

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%T A sparse PLS for variable selection when integrating omics data
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%A Davies
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%T Alignment-Independent Techniques for Protein Classification
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%J Current Proteomics
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%A Robert D. Finn
%A Peter J. Sims
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%A Andreas Biegert
%A Johannes Soding
%T Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors
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%J Bioinformatics
%P 159-162
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%T Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach
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%A Hao Zhang
%A Claus Lundegaard
%A Morten Nielsen
%T Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods
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%J Bioinformatics
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%A Seth Carbon
%A Amelia Ireland
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%A Brad Marshall
%A Suzanna Lewis
%A the AmiGO Hub
%A the Web Presence Working Group
%T AmiGO: online access to ontology and annotation data
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%J Bioinformatics
%P 288-289
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%A Peter J.; Li
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%T Application of Network Theory in Understanding and Predicting Protein Structure and Function
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%T The protein structure initiative structural genomics knowledgebase
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%A Shinji; Yunokawa
%A Harunobu
%T Amino Acid Sequence Database Suitable for the Protein and Proteome Analysis
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%T NetPhosBac - A predictor for Ser/Thr phosphorylation sites in bacterial proteins
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%T Improving peptide identification using an empirical peptide retention time database
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%T An Extended Markov Blanket Approach to Proteomic Biomarker Detection from High-Resolution Mass Spectrometry Data
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%A Search of Tandem Mass Spectra
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%T Combining multiple positive training sets to generate confidence scores for protein-protein interactions
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%T A linear-time algorithm for predicting functional annotations from ppi networks
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%A Sach Mukherjee
%A Steven Pelech
%A Richard M. Neve
%A Wen-Lin Kuo
%A Safiyyah Ziyad
%A Paul T. Spellman
%A Joe W. Gray
%A Terence P. Speed
%T Sparse combinatorial inference with an application in cancer biology
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%J Bioinformatics
%P 265-271
%V 25
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%U http://dx.doi.org/10.1093/bioinformatics/btn611

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%A Jonathan W Arthur
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%T Information management for proteomics: a perspective
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%T Genome and proteome annotation: organization, interpretation and integration
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%8 Nov 11, 2008

%A Nguyen TP
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%T An integrative domain-based approach to predicting protein-protein interactions
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%A Iain Melvin
%A Jason Weston
%A Christina Leslie
%A William Stafford Noble
%T RANKPROP: a web server for protein remote homology detection
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%J Bioinformatics
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%A Sacha A. F. T. van Hijum
%A Oscar P. Kuipers
%T MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
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%J Bioinformatics
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%A Francesca Diella
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%A Katja Luck
%A Claudia Chica
%A Chenna Ramu
%A Claus Nerlov
%A Toby J. Gibson
%T KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
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%T Breast Cancer Diagnosis from Proteomic Mass Spectrometry Data: A Comparative Evaluation
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%A Michel Zivy
%T A method based on bead flows for spot detection on 2-D gel images
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%T Computational Analysis and Experimental Validation of Gene Predictions in Toxoplasma gondii
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%A Ladenson J
%A Turk J
%T Algorithms for automatic processing of data from mass spectrometric analyses of lipids
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%8 Dec 25, 2008

%A Christine Hoogland
%A Daniel Walther
%A Patricia M. Palagi
%A Gérard Bouchet
%A Khaled Mostaguir
%A Xavier Robin
%A Ron D. Appel
%A Frédérique Lisacek
%T A suite of tools to analyse and publish 2-DE data
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%J PROTEOMICS
%P 4907-4909
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%N 23-24
%U http://dx.doi.org/10.1002/pmic.200800301

%A Nie L
%A Wu G
%A Zhang W
%T Statistical Application and Challenges in Global Gel-Free Proteomic Analysis by Mass Spectrometry
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%J Crit Rev Biotechnol
%P 297-307
%V 28
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%U http://dx.doi.org/10.1080/07388550802543158

%A Hu ZZ
%A Huang H
%A Cheema A
%A Jung M
%A Dritschilo A
%A Wu CH
%T Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data
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%J J Proteomics Bioinform
%P 47-60
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%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19088860&dopt=Abstract