TY  - JOUR
A1  - Franz F. Roos
A1  - Riko Jacob
A1  - Jonas Grossmann
A1  - Bernd Fischer
A1  - Joachim M. Buhmann
A1  - Wilhelm Gruissem
A1  - Sacha Baginsky
A1  - Peter Widmayer
T1  - PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra
JO  - Bioinformatics
Y1  - 2007
SP  - 3016
EP  - 3023
VL  - 23
IS  - 22
UR  - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/22/3016?etoc
ER  - 

TY  - JOUR
A1  - He QY
A1  - He QZ
A1  - Deng XC
A1  - Yao L
A1  - Meng E
A1  - Liu ZH
A1  - Liang SP
T1  - ATDB: a uni-database platform for animal toxins
JO  - Nucleic Acids Res
Y1  - 2007/10/11
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1093/nar/gkm832
ER  - 

TY  - JOUR
A1  - Heazlewood JL
A1  - Durek P
A1  - Hummel J
A1  - Selbig J
A1  - Weckwerth W
A1  - Walther D
A1  - Schulze WX
T1  - PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
JO  - Nucleic Acids Res
Y1  - 2007/11/4
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1093/nar/gkm812
ER  - 

TY  - JOUR
A1  - Fenyo D
A1  - Beavis RC
T1  - Informatics development: Challenges and solutions for MALDI mass spectrometry
JO  - Mass Spectrom Rev
Y1  - 2008
SP  - 1
EP  - 19
VL  - 27
IS  - 1
UR  - http://dx.doi.org/10.1002/mas.20152
ER  - 

TY  - JOUR
A1  - Gendler K
A1  - Paulsen T
A1  - Napoli C
T1  - ChromDB: The Chromatin Database
JO  - Nucleic Acids Res
Y1  - 2007/10/16
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1093/nar/gkm768
ER  - 

TY  - JOUR
A1  - Bodenmiller B
A1  - Malmstrom J
A1  - Gerrits B
A1  - Campbell D
A1  - Lam H
A1  - Schmidt A
A1  - Rinner O
A1  - Mueller LN
A1  - Shannon PT
A1  - Pedrioli PG
A1  - Panse C
A1  - Lee HK
A1  - Schlapbach R
A1  - Aebersold R
T1  - PhosphoPep-a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17940529&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Cline MS
A1  - Smoot M
A1  - Cerami E
A1  - Kuchinsky A
A1  - Landys N
A1  - Workman C
A1  - Christmas R
A1  - Avila-Campilo I
A1  - Creech M
A1  - Gross B
A1  - Hanspers K
A1  - Isserlin R
A1  - Kelley R
A1  - Killcoyne S
A1  - Lotia S
A1  - Maere S
A1  - Morris J
A1  - Ono K
A1  - Pavlovic V
A1  - Pico AR
A1  - Vailaya A
A1  - Wang PL
A1  - Adler A
A1  - Conklin BR,
T1  - Integration of biological networks and gene expression data using Cytoscape
JO  - Nat Protoc
Y1  - 2007
SP  - 2366
EP  - 82
VL  - 2
IS  - 10
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17947979&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Su C
A1  - Peregrin-Alvarez JM
A1  - Butland G
A1  - Phanse S
A1  - Fong V
A1  - Emili A
A1  - Parkinson J
T1  - Bacteriome.org an integrated protein interaction database for E. coli
JO  - Nucleic Acids Res
Y1  - 2007/10/16
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://dx.doi.org/10.1093/nar/gkm807
ER  - 

TY  - JOUR
A1  - McLaughlin WA
A1  - Chen K
A1  - Hou T
A1  - Wang W
T1  - On the detection of functionally coherent groups of protein domains with an extension to protein annotation
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17937820&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Wu X
A1  - Tseng CW
A1  - Edwards N
T1  - HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models
JO  - J Comput Biol
Y1  - 2007
SP  - 1025
EP  - 43
VL  - 14
IS  - 8
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17985986&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Andrew Smith
A1  - Kei Cheung
A1  - Michael Krauthammer
A1  - Martin Schultz
A1  - Mark Gerstein
T1  - Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics
JO  - Bioinformatics
Y1  - 2007
SP  - 3073
EP  - 3079
VL  - 23
IS  - 22
UR  - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/22/3073?etoc
ER  - 

TY  - JOUR
A1  - Kall L
A1  - Canterbury JD
A1  - Weston J
A1  - Noble WS
A1  - Maccoss MJ
T1  - Semi-supervised learning for peptide identification from shotgun proteomics datasets
JO  - Nat Methods
Y1  - 2007
SP  - 923
EP  - 5
VL  - 4
IS  - 11
UR  - http://dx.doi.org/10.1038/nmeth1113
ER  - 

TY  - JOUR
A1  - Jiyang Zhang
A1  - Jianqi Li
A1  - Hongwei Xie
A1  - Yunping Zhu
A1  - Fuchu He
T1  - A new strategy to filter out false positive identifications of peptides in SEQUEST database search results
JO  - PROTEOMICS
Y1  - 2007
SP  - 4036
EP  - 4044
VL  - 7
IS  - 22
UR  - http://dx.doi.org/10.1002/pmic.200600929
ER  - 

TY  - JOUR
A1  - Huhne R
A1  - Koch FT
A1  - Suhnel J
T1  - A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules
JO  - Brief Funct Genomic Proteomic
Y1  - 2007
SP  - 220
EP  - 39
VL  - 6
IS  - 3
UR  - http://dx.doi.org/10.1093/bfgp/elm020
ER  - 

TY  - JOUR
A1  - Waters M
A1  - Stasiewicz S
A1  - Merrick BA
A1  - Tomer K
A1  - Bushel P
A1  - Paules R
A1  - Stegman N
A1  - Nehls G
A1  - Yost KJ
A1  - Johnson CH
A1  - Gustafson SF
A1  - Xirasagar S
A1  - Xiao N
A1  - Huang CC
A1  - Boyer P
A1  - Chan DD
A1  - Pan Q
A1  - Gong H
A1  - Taylor J
A1  - Choi D
A1  - Rashid A
A1  - Ahmed A
A1  - Howle R
A1  - Selkirk J
A1  - Tennant R
A1  - Fos
T1  - CEBS Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data
JO  - Nucleic Acids Res
Y1  - 2007/10/25
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17962311&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Alves P
A1  - Arnold RJ
A1  - Novotny MV
A1  - Radivojac P
A1  - Reilly JP
A1  - Tang H
T1  - Advancement in protein inference from shotgun proteomics using peptide detectability
JO  - Pac Symp Biocomput
Y1  - 2007
SP  - 409
EP  - 20
VL  - 12
IS  - 
UR  - http://psb.stanford.edu/psb-online/proceedings/psb07/abstracts/2007_p409.html
ER  - 

TY  - JOUR
A1  - Dodds ED
A1  - Clowers BH
A1  - Hagerman PJ
A1  - Lebrilla CB
T1  - Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting
JO  - Anal Biochem
Y1  - 2008
SP  - 156
EP  - 66
VL  - 372
IS  - 2
UR  - http://dx.doi.org/10.1016/j.ab.2007.10.009
ER  - 

TY  - JOUR
A1  - Alves G
A1  - Ogurtsov AY
A1  - Wu WW
A1  - Wang G
A1  - Shen RF
A1  - Yu YK
T1  - Calibrating E-values for MS2 database search methods
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17983478&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Han X
T1  - Cancer molecular pattern discovery by subspace consensus kernel classification
JO  - Comput Syst Bioinformatics Conf
Y1  - 2007
SP  - 55
EP  - 65
VL  - 6
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17951812&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Alves G
A1  - Ogurtsov AY
A1  - Yu YK
T1  - RAId DbS: Peptide Identification using Database Searches with Realistic Statistics
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17961253&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Song Z
A1  - Chen L
A1  - Zhang C
A1  - Xu D
T1  - Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification
JO  - Conf Proc IEEE Eng Med Biol Soc
Y1  - 2006
SP  - 4556
EP  - 4559
VL  - 1
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17946250&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Kerrien S
A1  - Orchard S
A1  - Montecchi-Palazzi L
A1  - Aranda B
A1  - Quinn AF
A1  - Vinod N
A1  - Bader GD
A1  - Xenarios I
A1  - Wojcik J
A1  - Sherman D
A1  - Tyers M
A1  - Salama JJ
A1  - Moore S
A1  - Ceol A
A1  - Chatr-Aryamontri A
A1  - Oesterheld M
A1  - Stumpflen V
A1  - Salwinski L
A1  - Nerothin J
A1  - Cerami E
A1  - Cusick ME
A1  - Vidal M
A1  - G
T1  - Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions
JO  - 
Y1  - 
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17925023&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Mano S
A1  - Miwa T
A1  - Nishikawa SI
A1  - Mimura T
A1  - Nishimura M
T1  - The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research
JO  - Nucleic Acids Res
Y1  - 2007/10/11
SP  - 
EP  - 
VL  - 
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17932059&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Ning K
A1  - Leong HW
T1  - Algorithm for Peptide sequencing by tandem mass spectrometry based on better preprocessing and anti-symmetric computational model
JO  - Comput Syst Bioinformatics Conf
Y1  - 2007
SP  - 19
EP  - 30
VL  - 6
IS  - 
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17951809&dopt=Abstract
ER  - 

TY  - JOUR
A1  - Jonas Grossmann
A1  - Bernd Fischer
A1  - Katja Baerenfaller
A1  - Judith Owiti
A1  - Joachim M. Buhmann
A1  - Wilhelm Gruissem
A1  - Sacha Baginsky
T1  - A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments
JO  - PROTEOMICS
Y1  - 2007
SP  - 4245
EP  - 4254
VL  - 7
IS  - 23
UR  - http://dx.doi.org/10.1002/pmic.200700474
ER  -