TY  - JOUR
A1  - Maruyama Y
A1  - Wakamatsu A
A1  - Kawamura Y
A1  - Kimura K
A1  - Yamamoto J
A1  - Nishikawa T
A1  - Kisu Y
A1  - Sugano S
A1  - Goshima N
A1  - Isogai T
A1  - Nomura N
T1  - Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics
JO  - Nucl Acids Res
Y1  - 2009
SP  - D762
EP  - 6
VL  - 37
IS  - Database issue
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19073703&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Cox J
A1  - Mann M
T1  - MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
JO  - Nat Biotechnol
Y1  - 2008
SP  - 1367
EP  - 72
VL  - 26
IS  - 12
UR  - http://dx.doi.org/10.1038/nbt.1511
ER  - 

TY  - JOUR
A1  - Hong-Bin Shen
A1  - Dong-Liang Yi
A1  - Li-Xiu Yao
A1  - Jie Yang
A1  - Kuo-Chen Chou
T1  - Knowledge-based computational intelligence development for predicting protein secondary structures from sequences
JO  - Expert Review of Proteomics
Y1  - 2008
SP  - 653
EP  - 662
VL  - 5
IS  - 5
UR  - http://dx.doi.org/10.1586/14789450.5.5.653 
ER  - 

TY  - JOUR
A1  - Richard S. P. Horler
A1  - Andrew Butcher
A1  - Nikitas Papangelopoulos
A1  - Peter D. Ashton
A1  - Gavin H. Thomas
T1  - EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations
JO  - Bioinformatics
Y1  - 2009
SP  - 163
EP  - 166
VL  - 25
IS  - 2
UR  - http://dx.doi.org/10.1093/bioinformatics/btn596
ER  - 

TY  - JOUR
A1  - Min-Seok Kwon
A1  - Hyoung-Joo Lee
A1  - Seul-Ki Jeong
A1  - Eun-Young Lee
A1  - Sang Yun Cho
A1  - Young-Ki Paik
T1  - IntelliMS: A platform to efficiently manage and visualize tandem mass spectral data
JO  - PROTEOMICS
Y1  - 2008
SP  - 4910
EP  - 4913
VL  - 8
IS  - 23-24
UR  - http://dx.doi.org/10.1002/pmic.200800296
ER  - 

TY  - JOUR
A1  - Ma Y
A1  - Ding Z
A1  - Qian Y
A1  - Wan YW
A1  - Tosun K
A1  - Shi X
A1  - Castranova V
A1  - Harner EJ
A1  - Guo NL
T1  - An integrative genomic and proteomic approach to chemosensitivity prediction
JO  - Int J Oncol
Y1  - 2009
SP  - 107
EP  - 15
VL  - 34
IS  - 1
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19082483&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Ganesan Pugalenthi
A1  - Ke Tang
A1  - P. N. Suganthan
A1  - Saikat Chakrabarti
T1  - Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble
JO  - Bioinformatics
Y1  - 2009
SP  - 204
EP  - 210
VL  - 25
IS  - 2
UR  - http://dx.doi.org/10.1093/bioinformatics/btn618
ER  - 

TY  - JOUR
A1  - Castellana NE
A1  - Payne SH
A1  - Shen Z
A1  - Stanke M
A1  - Bafna V
A1  - Briggs SP
T1  - Discovery and revision of Arabidopsis genes by proteogenomics
JO  - Proc Natl Acad Sci U S A
Y1  - 2008
SP  - 21034
EP  - 8
VL  - 105
IS  - 52
UR  - http://dx.doi.org/10.1073/pnas.0811066106
ER  - 

TY  - JOUR
A1  - Aleksandr Barinov
A1  - Valentin Loux
A1  - Amal Hammani
A1  - Pierre Nicolas
A1  - Philippe Langella
A1  - Dusko Ehrlich
A1  - Emmanuelle Maguin
A1  - Maarten van de Guchte
T1  - Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria
JO  - PROTEOMICS
Y1  - 2009
SP  - 61
EP  - 73
VL  - 9
IS  - 1
UR  - http://dx.doi.org/10.1002/pmic.200800195
ER  - 

TY  - JOUR
A1  - Lê Cao KA
A1  - Rossouw D
A1  - Robert-Granié C
A1  - Besse P
T1  - A sparse PLS for variable selection when integrating omics data
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19049491&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Davies
A1  - Matthew N.; Secker
A1  - Andrew; Freitas
A1  - Alex A.; Timmis
A1  - Jon; Clark
A1  - Edward; Flower
A1  - Darren R
T1  - Alignment-Independent Techniques for Protein Classification
JO  - Current Proteomics
Y1  - 2008
SP  - 217
EP  - 223
VL  - 5
IS  - 4
UR  - http://www.ingentaconnect.com/content/ben/cp/2008/00000005/00000004/art00002 
ER  - 

TY  - JOUR
A1  - Alex Bateman
A1  - Robert D. Finn
A1  - Peter J. Sims
A1  - Therese Wiedmer
A1  - Andreas Biegert
A1  - Johannes Soding
T1  - Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors
JO  - Bioinformatics
Y1  - 2009
SP  - 159
EP  - 162
VL  - 25
IS  - 2
UR  - http://dx.doi.org/10.1093/bioinformatics/btn595
ER  - 

TY  - JOUR
A1  - Rodriguez-Ortega MJ
A1  - Luque I
A1  - Tarradas C
A1  - Barcena JA
T1  - Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19061494&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Hao Zhang
A1  - Claus Lundegaard
A1  - Morten Nielsen
T1  - Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods
JO  - Bioinformatics
Y1  - 2009
SP  - 83
EP  - 89
VL  - 25
IS  - 1
UR  - http://dx.doi.org/10.1093/bioinformatics/btn579
ER  - 

TY  - JOUR
A1  - Seth Carbon
A1  - Amelia Ireland
A1  - Christopher J. Mungall
A1  - ShengQiang Shu
A1  - Brad Marshall
A1  - Suzanna Lewis
A1  - the AmiGO Hub
A1  - the Web Presence Working Group
T1  - AmiGO: online access to ontology and annotation data
JO  - Bioinformatics
Y1  - 2009
SP  - 288
EP  - 289
VL  - 25
IS  - 2
UR  - http://dx.doi.org/10.1093/bioinformatics/btn615
ER  - 

TY  - JOUR
A1  - Galan
A1  - Jhenny F.; Gao
A1  - Jun; Pabuwal
A1  - Vagmita; Meek
A1  - Peter J.; Li
A1  - Zhijun
T1  - Application of Network Theory in Understanding and Predicting Protein Structure and Function
JO  - Current Proteomics
Y1  - 2008
SP  - 181
EP  - 190
VL  - 5
IS  - 3
UR  - http://www.ingentaconnect.com/content/ben/cp/2008/00000005/00000003/art00005 
ER  - 

TY  - JOUR
A1  - Berman HM
A1  - Westbrook JD
A1  - Gabanyi MJ
A1  - Tao W
A1  - Shah R
A1  - Kouranov A
A1  - Schwede T
A1  - Arnold K
A1  - Kiefer F
A1  - Bordoli L
A1  - Kopp J
A1  - Podvinec M
A1  - Adams PD
A1  - Carter LG
A1  - Minor W
A1  - Nair R
A1  - Baer JL
T1  - The protein structure initiative structural genomics knowledgebase
JO  - Nucl Acids Res
Y1  - 2009
SP  - D365
EP  - 8
VL  - 37
IS  - Database issue
UR  - http://dx.doi.org/10.1093/nar/gkn790
ER  - 

TY  - JOUR
A1  - Kawakami
A1  - Takao; Ozaki
A1  - Junko; Kondo
A1  - Kazuhiro; Sato
A1  - Shinji; Yunokawa
A1  - Harunobu
T1  - Amino Acid Sequence Database Suitable for the Protein and Proteome Analysis
JO  - Current Proteomics
Y1  - 2008
SP  - 267
EP  - 275
VL  - 5
IS  - 4
UR  - http://www.ingentaconnect.com/content/ben/cp/2008/00000005/00000004/art00005 
ER  - 

TY  - JOUR
A1  - Martin Lee Miller
A1  - Boumediene Soufi
A1  - Carsten Jers
A1  - Nikolaj Blom
A1  - Boris Macek
A1  - Ivan Mijakovic
T1  - NetPhosBac - A predictor for Ser/Thr phosphorylation sites in bacterial proteins
JO  - PROTEOMICS
Y1  - 2009
SP  - 116
EP  - 125
VL  - 9
IS  - 1
UR  - http://dx.doi.org/10.1002/pmic.200800285
ER  - 

TY  - JOUR
A1  - Sun W
A1  - Zhang L
A1  - Yang R
A1  - Shao C
A1  - Zhang Z
A1  - Gao Y
T1  - Improving peptide identification using an empirical peptide retention time database
JO  - Rapid Commun Mass Spectrom
Y1  - 2008
SP  - 109
EP  - 118
VL  - 23
IS  - 1
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19065623&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Oh J
A1  - Gurnani P
A1  - Schorge J
A1  - Rosenblatt K
A1  - Gao J
T1  - An Extended Markov Blanket Approach to Proteomic Biomarker Detection from High-Resolution Mass Spectrometry Data
JO  - IEEE Trans Inf Technol Biomed
Y1  - 2008/12/31
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1109/TITB.2008.2007909
ER  - 

TY  - JOUR
A1  - Search of Tandem Mass Spectra
T1  - Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database
JO  - Mol Cell Proteomics
Y1  - 2009
SP  - 53
EP  - 69
VL  - 8
IS  - 1
UR  - http://www.mcponline.org/cgi/content/abstract/8/1/53?etoc
ER  - 

TY  - JOUR
A1  - Jingkai Yu and Russell L. Finley
A1  - Jr
T1  - Combining multiple positive training sets to generate confidence scores for protein-protein interactions
JO  - Bioinformatics
Y1  - 2009
SP  - 105
EP  - 111
VL  - 25
IS  - 1
UR  - http://dx.doi.org/10.1093/bioinformatics/btn597
ER  - 

TY  - JOUR
A1  - Wu Y
A1  - Lonardi S
T1  - A linear-time algorithm for predicting functional annotations from ppi networks
JO  - J Bioinform Comput Biol
Y1  - 2008
SP  - 1049
EP  - 65
VL  - 6
IS  - 6
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19090017&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Sach Mukherjee
A1  - Steven Pelech
A1  - Richard M. Neve
A1  - Wen-Lin Kuo
A1  - Safiyyah Ziyad
A1  - Paul T. Spellman
A1  - Joe W. Gray
A1  - Terence P. Speed
T1  - Sparse combinatorial inference with an application in cancer biology
JO  - Bioinformatics
Y1  - 2009
SP  - 265
EP  - 271
VL  - 25
IS  - 2
UR  - http://dx.doi.org/10.1093/bioinformatics/btn611
ER  - 

TY  - JOUR
A1  - Marc R Wilkins
A1  - Jonathan W Arthur
A1  - F Keith Junius
A1  - Mathew J Harrison,
T1  - Information management for proteomics: a perspective
JO  - Expert Review of Proteomics
Y1  - 2008
SP  - 663
EP  - 678
VL  - 5
IS  - 5
UR  - http://dx.doi.org/10.1586/14789450.5.5.663
ER  - 

TY  - JOUR
A1  - Reeves GA
A1  - Talavera D
A1  - Thornton JM
T1  - Genome and proteome annotation: organization, interpretation and integration
JO  - J R Soc Interface
Y1  - 2008/11/11
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19019817&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Nguyen TP
A1  - Ho TB
T1  - An integrative domain-based approach to predicting protein-protein interactions
JO  - J Bioinform Comput Biol
Y1  - 2008
SP  - 1115
EP  - 32
VL  - 6
IS  - 6
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19090020&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Iain Melvin
A1  - Jason Weston
A1  - Christina Leslie
A1  - William Stafford Noble
T1  - RANKPROP: a web server for protein remote homology detection
JO  - Bioinformatics
Y1  - 2009
SP  - 121
EP  - 122
VL  - 25
IS  - 1
UR  - http://dx.doi.org/10.1093/bioinformatics/btn567
ER  - 

TY  - JOUR
A1  - Rutger W. W. Brouwer
A1  - Sacha A. F. T. van Hijum
A1  - Oscar P. Kuipers
T1  - MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
JO  - Bioinformatics
Y1  - 2009
SP  - 139
EP  - 140
VL  - 25
IS  - 1
UR  - http://dx.doi.org/10.1093/bioinformatics/btn588
ER  - 

TY  - JOUR
A1  - Francesca Diella
A1  - Sophie Chabanis
A1  - Katja Luck
A1  - Claudia Chica
A1  - Chenna Ramu
A1  - Claus Nerlov
A1  - Toby J. Gibson
T1  - KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
JO  - Bioinformatics
Y1  - 2009
SP  - 1
EP  - 5
VL  - 25
IS  - 1
UR  - http://dx.doi.org/10.1093/bioinformatics/btn594
ER  - 

TY  - JOUR
A1  - Hand DJ
T1  - Breast Cancer Diagnosis from Proteomic Mass Spectrometry Data: A Comparative Evaluation
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19120032&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Olivier Langella
A1  - Michel Zivy
T1  - A method based on bead flows for spot detection on 2-D gel images
JO  - PROTEOMICS
Y1  - 2008
SP  - 4914
EP  - 4918
VL  - 8
IS  - 23-24
UR  - http://dx.doi.org/10.1002/pmic.200800644
ER  - 

TY  - JOUR
A1  - Dybas JM
A1  - Madrid-Aliste CJ
A1  - Che FY
A1  - Nieves E
A1  - Rykunov D
A1  - Angeletti RH
A1  - Weiss LM
A1  - Kim K
A1  - Fiser A
T1  - Computational Analysis and Experimental Validation of Gene Predictions in Toxoplasma gondii
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19065262&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Song H
A1  - Ladenson J
A1  - Turk J
T1  - Algorithms for automatic processing of data from mass spectrometric analyses of lipids
JO  - J Chromatogr B Analyt Technol Biomed Life Sci
Y1  - 2008/12/25
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19131280&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Christine Hoogland
A1  - Daniel Walther
A1  - Patricia M. Palagi
A1  - Gérard Bouchet
A1  - Khaled Mostaguir
A1  - Xavier Robin
A1  - Ron D. Appel
A1  - Frédérique Lisacek
T1  - A suite of tools to analyse and publish 2-DE data
JO  - PROTEOMICS
Y1  - 2008
SP  - 4907
EP  - 4909
VL  - 8
IS  - 23-24
UR  - http://dx.doi.org/10.1002/pmic.200800301
ER  - 

TY  - JOUR
A1  - Nie L
A1  - Wu G
A1  - Zhang W
T1  - Statistical Application and Challenges in Global Gel-Free Proteomic Analysis by Mass Spectrometry
JO  - Crit Rev Biotechnol
Y1  - 2008
SP  - 297
EP  - 307
VL  - 28
IS  - 4
UR  - http://dx.doi.org/10.1080/07388550802543158
ER  - 

TY  - JOUR
A1  - Hu ZZ
A1  - Huang H
A1  - Cheema A
A1  - Jung M
A1  - Dritschilo A
A1  - Wu CH
T1  - Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data
JO  - J Proteomics Bioinform
Y1  - 2008
SP  - 47
EP  - 60
VL  - 1
IS  - 2
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19088860&dopt=Abstract
ER  -