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year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-208

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year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-13

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pages: 305
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-305

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pages: 238
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-238

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year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-99

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year: 2003
volume: 4
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year: 2005
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ee: http://dx.doi.org/10.1186/1471-2105-6-220

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year: 2006
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ee: http://dx.doi.org/10.1186/1471-2105-7-235

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year: 2004
volume: 5
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pages: 152
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volume: 6
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year: 2003
volume: 4
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ee: http://dx.doi.org/10.1186/1471-2105-4-45

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year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-32

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year: 2006
volume: 7
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/e/Eddy:Sean_R=.html
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volume: 5
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pages: 4
year: 2006
volume: 7
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pages: 99
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-99

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pages: 95
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-95

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year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-58

GaoFB04
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pages: 31
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volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-31

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year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-209

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year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-153

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pages: 186
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-186

LeePWGSTK06
type: Article
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pages: 170
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-170

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pages: 23
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-23

TruongI02
type: Article
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year: 2002
volume: 3
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-3-1

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type: Article
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pages: 142
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-142

TeelingWLBG04
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author: Bauer:Margarete.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Gl=ouml=ckner:Frank_Oliver.html
title: TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.
pages: 163
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-163

ConlonSL06
type: Article
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pages: 247
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-247

LarionovKM05
type: Article
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author: Krause:Andreas.html
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pages: 62
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-62

QiYB05
type: Article
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pages: 288
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-288

MailundSPMMS05
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Schierup:Mikkel_H=.html
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pages: 252
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-252

ZhangJFW06
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/j/Jackson:George_W=.html
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pages: 117
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-117

MorrisonBHG05
type: Article
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pages: 233
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-233

LevenstienYO03
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/o/Ott:J=uuml=rg.html
title: Statistical significance for hierarchical clustering in genetic association and microarray expression studies.
pages: 62
year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-62

GreenK04
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Green:Michelle_L=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Karp:Peter_D=.html
title: A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases.
pages: 76
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-76

McClurgPWS06
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last modified date: 2006-05-18
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/p/Pletcher:Mathew_T=.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Su:Andrew_I=.html
title: Comparative analysis of haplotype association mapping algorithms.
pages: 61
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-61

WuXMMB05
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/x/Xing:Eric_P=.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Bissell:Mina_J=.html
title: k-NN classification.
pages: 191
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-191

Konishi04a
type: Article
last modified date: 2006-05-17
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title: Correction: Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment.
pages: 82
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-82

YangY06
type: Article
last modified date: 2006-05-18
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/y/Yang:James_J=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/y/Yang:Mark_C=_K=.html
title: An improved procedure for gene selection from microarray experiments using false discovery rate criterion.
pages: 15
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-15

Hennequet-AntierCPDHRRR05
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/h/Hennequet=Antier:Christelle.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Chiapello:H=eacute=l=egrave=ne.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Robin:St=eacute=phane.html
title: AnovArray: a set of SAS macros for the analysis of variance of gene expression data.
pages: 150
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-150

DepledgeD05
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/d/Depledge:Daniel_P=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/d/Dalby:Andrew_R=.html
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pages: 182
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BarreraBTWZ04
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ChooTR05
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MailundBFPP06
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WegnerK05
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NeuhauserBJ05
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pages: 35
year: 2005
volume: 6
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BreitlingAH04
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title: Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments.
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volume: 5
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MillenaarOMZVP06
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Rosenberg05
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ElefsiniotiBSH04
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KimDTRSGMCR05
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SunZ04
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pages: 112
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ArcherDR04
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pages: 60
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BrodieSRTU04
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title: Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments.
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Carmona-SaezPTCP06
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CannonY03
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title: OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies.
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BagosLH05
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SinhaSUGS04
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title: Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila.
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BilkeBS03
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KumarLGRLL04
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pages: 176
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LassmannS05
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TrisslRMSKPFL05
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SamTGGLM06
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title: ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification.
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CastroTGR05
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GuoZ06
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title: ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes.
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WasmuthB04
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SeguritanR01
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DeanR05
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ChenS04
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AlakoVBJVRPJ05
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MartinBB04
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title: GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.
pages: 178
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NeuwaldL04
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title: Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model.
pages: 157
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CummingsS04
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title: rpoBMycobacterium tuberculosis.
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SchwarzMKESSD05
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SonnhammerH05
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HiggsWS06
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JoachimiakWM06
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Crowe05
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Thornton-WellsMH06
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ErnstB06
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LuZGB04
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TiroshB05
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DowdZROP05
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KonigSOSSZRE06
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Mangalam02
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title: grepfor DNA.
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PriceAA06
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title: OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments.
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volume: 7
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LinLLC05
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CherkasovSBJ04
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volume: 5
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volume: 7
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BetelH02
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KellySM04
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volume: 7
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volume: 7
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HedgesS03
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volume: 6
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LuLFDB04
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YePSB05
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DenoeudV04
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PicardRLVD05
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volume: 6
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HoltH04
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volume: 4
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pages: 195
year: 2004
volume: 5
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ShegogueZ05
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pages: 113
year: 2005
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pages: 235
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year: 2006
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pages: 36
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VencioKGP06
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pages: 86
year: 2006
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ee: http://dx.doi.org/10.1186/1471-2105-7-86

YangPLF06
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pages: 233
year: 2006
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ee: http://dx.doi.org/10.1186/1471-2105-7-233

WolskiLJR05
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pages: 203
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BiR06
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Rogan:Peter_K=.html
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pages: 76
year: 2006
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-76

CoteJAH06
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ee: http://dx.doi.org/10.1186/1471-2105-7-97

LemaE05
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pages: 226
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-226

LeiD05
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pages: 291
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ee: http://dx.doi.org/10.1186/1471-2105-6-291

JainCOL05
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pages: 187
year: 2005
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-187

FoissacS05
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pages: 25
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-25

TressCTV06
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pages: 213
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PanSCGMHDZ03
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title: Arabidopsis.
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Thierry-Mieg06
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pages: 28
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-28

BrunHG04
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title: Clustering proteins from interaction networks for the prediction of cellular functions.
pages: 95
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-95

LarsenK03
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title: EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance.
pages: 21
year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-21

MagnussonCKEOJ05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/j/Jensen:Jens_L=.html
title: Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis.
pages: 311
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-311

InaokaFK06
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title: C. elegansgermline.
pages: 112
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-112

OliverBSAH04
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/o/Oliver:Diane_E=.html
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title: Tools for loading MEDLINE into a local relational database.
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year: 2004
volume: 5
journal name: BMC Bioinformatics
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DozmorovKTC04
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pages: 53
year: 2004
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journal name: BMC Bioinformatics
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GiriAG04
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pages: 127
year: 2004
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volume: 6
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DowellE04
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pages: 186
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NilssonRLU04
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ee: http://dx.doi.org/10.1186/1471-2105-5-87

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year: 2004
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ee: http://dx.doi.org/10.1186/1471-2105-5-51

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pages: 74
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pages: 202
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volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-202

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year: 2005
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year: 2004
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volume: 5
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volume: 7
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year: 2005
volume: 6
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year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-294

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pages: 94
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-94

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pages: 148
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ee: http://dx.doi.org/10.1186/1471-2105-5-148

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pages: 175
year: 2004
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ee: http://dx.doi.org/10.1186/1471-2105-5-175

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pages: 72
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-72

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type: Article
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year: 2004
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ee: http://dx.doi.org/10.1186/1471-2105-5-139

ShahPBA03
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year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-20

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pages: 112
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ee: http://dx.doi.org/10.1186/1471-2105-6-112

SchubertTJE05
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title: CGH-Profiler: Data mining based on genomic aberration profiles.
pages: 188
year: 2005
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-188

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title: Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.
pages: 24
year: 2004
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ee: http://dx.doi.org/10.1186/1471-2105-5-24

NothB05
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pages: 307
year: 2005
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ee: http://dx.doi.org/10.1186/1471-2105-6-307

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title: Evaluating concentration estimation errors in ELISA microarray experiments.
pages: 17
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-17

SnyderFDSH06
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title: Domain-based small molecule binding site annotation.
pages: 152
year: 2006
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ee: http://dx.doi.org/10.1186/1471-2105-7-152

Radivoyevitch04
type: Article
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pages: 190
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-190

DaubSSK04
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author: Selbig:Joachim.html
author: Kloska:Sebastian.html
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pages: 118
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-118

ChanK05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Kibler:Dennis_F=.html
title: Using hexamers to predict cis-regulatory motifs in Drosophila.
pages: 262
year: 2005
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-262

RenekerS05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Shyu:Chi=Ren.html
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pages: 111
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-111

BatyBPCB05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Bihl:Michel_P=.html
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pages: 239
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volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-239

ThygesenZ06
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title: Modeling Sage data with a truncated gamma-Poisson model.
pages: 157
year: 2006
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-157

Lyons-WeilerPBG04
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Becich:Michael_J=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Godfrey:Tony_E=.html
title: Tests for finding complex patterns of differential expression in cancers: towards individualized medicine.
pages: 110
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volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-110

CatalanoLTGSD06
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author: Licciulli:Flavio.html
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author: Grillo:Giorgio.html
author: Saccone:Cecilia.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/d/D=Elia:Domenica.html
title: MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.
pages: 36
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-36

CummingsM04
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/Myers:Daniel_S=.html
title: Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA.
pages: 132
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-132

Sanchez-PulidoRWMV04
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title: SPOC: A widely distributed domain associated with cancer, apoptosis and transcription.
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RuzanovJ06
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AnisimovS04
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TuckKK06
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CoinBD04
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FurlanelloSMJ03
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SperisenP05
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GollOCF06
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BehrsinBLSW06
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ColbourneSG05
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CristobalZFRE01
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GellyCG05
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SteffenG05
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CroceLC06
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BerrarBD06
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GramadaB06
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BadididLB03
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WangHXMS05
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ChenM06
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ZhaoLS05
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KaplanFFL04
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Galibert:Marie=Dominique.html
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Bateman02
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MarinescuKR05
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LuCCHDS05
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HamadyPKS06
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LottMSLF06
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title: Simplifying gene trees for easier comprehension.
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McNuttTCCFMHCG05
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LuTK05
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title: Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach.
pages: 165
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VogelHPS05
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title: Chromosomal clustering of a human transcriptome reveals regulatory background.
pages: 230
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ee: http://dx.doi.org/10.1186/1471-2105-6-230

BrinkworthMK06
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title: Protein kinases associated with the yeast phosphoproteome.
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Chen05
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title: Identification of significant periodic genes in microarray gene expression data.
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WangLCWMZd05
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title: Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries.
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AuburnRFMMR06
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title: SimArray: a user-friendly and user-configurable microarray design tool.
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CarterEMKS05
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title: Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements.
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ChakrabartiBAS04
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/a/Anand:Prem_A=.html
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title: Improvement of alignment accuracy utilizing sequentially conserved motifs.
pages: 167
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ReesDMBS04
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title: GeneXplorer: an interactive web application for microarray data visualization and analysis.
pages: 141
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ArgravesJBA05
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title: ArrayQuest: a web resource for the analysis of DNA microarray data.
pages: 287
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ee: http://dx.doi.org/10.1186/1471-2105-6-287

MoglichWMGK05
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/M=ouml=glich:Andreas.html
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title: A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles.
pages: 91
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volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-91

TsaiWCLHHSH06
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/h/Hsu:Wen=Lian.html
title: Various criteria in the evaluation of biomedical named entity recognition.
pages: 92
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ee: http://dx.doi.org/10.1186/1471-2105-7-92

Altaf-Ul-AminSMKK06
type: Article
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author: Shinbo:Yoko.html
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title: Development and implementation of an algorithm for detection of protein complexes in large interaction networks.
pages: 207
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-207

FengCWSS04
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Cronin:Christopher_J=.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Schafer:William_R=.html
title: C. elegansbehavior.
pages: 115
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-115

NoeK04
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/n/No=eacute=:Laurent.html
author: Kucherov:Gregory.html
title: Improved hit criteria for DNA local alignment.
pages: 149
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-149

BradleyB06
type: Article
last modified date: 2006-05-18
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Benner:Steven_A=.html
title: Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins.
pages: 89
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-89

CoraCPSC04
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Cor=agrave=:Davide.html
author: Cunto:Ferdinando Di.html
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title: Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs.
pages: 57
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-57

HongC03
type: Article
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author: Hong:Yan.html
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title: A format for databasing and comparison of AFLP fingerprint profiles.
pages: 7
year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-7

JonssonCZB06
type: Article
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title: Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis.
pages: 2
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-2

Holmes05
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title: Accelerated probabilistic inference of RNA structure evolution.
pages: 73
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-73

JinSALD06
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title: Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs.
pages: 114
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-114

JunkerKS06
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title: VANTED: A system for advanced data analysis and visualization in the context of biological networks.
pages: 109
year: 2006
volume: 7
journal name: BMC Bioinformatics
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NimgaonkarSBHKBK03
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title: Reproducibility of gene expression across generations of Affymetrix microarrays.
pages: 27
year: 2003
volume: 4
journal name: BMC Bioinformatics
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LiuS05
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author: Liu:Jiajian.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Stormo:Gary_D=.html
title: Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein.
pages: 176
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-176

MotsingerLMR06
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title: GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease.
pages: 39
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-39

RitchieWPHM03
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title: Optimizationof neural network architecture using genetic programming improvesdetection and modeling of gene-gene interactions in studies of humandiseases.
pages: 28
year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-28

SgourakisBPH05
type: Article
last modified date: 2006-05-17
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title: A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models.
pages: 104
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-104

ShakhnovichHCLDS03
type: Article
last modified date: 2006-05-16
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Shakhnovich:Boris_E=.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Shakhnovich:Eugene_I=.html
title: ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations.
pages: 34
year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-34

MartinBP06
type: Article
last modified date: 2006-05-18
author: Martin:Patrick.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Boulukos:Kim_E=.html
author: Pognonec:Philippe.html
title: REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance.
pages: 98
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-98

LottazS05
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pages: 211
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-211

ZhuQ05
type: Article
last modified date: 2006-05-17
author: Zhu:Dongxiao.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/q/Qin:Zhaohui_S=.html
title: Structural comparison of metabolic networks in selected single cell organisms.
pages: 8
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-8

BarsnesME06
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last modified date: 2006-05-18
author: Barsnes:Harald.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/Mikalsen:Svein=Ole.html
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title: MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences.
pages: 42
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-42

RomeroNDOJ04
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Romero:Lisa_C=.html
author: Nguyen:Thanh Vinh.html
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author: Ogunjumo:Oluwasanmi.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/j/James:Anthony_A=.html
title: MB2Plasmodiumspecies has a unique combination of S1 and GTP-binding domains.
pages: 83
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-83

Page05
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/p/Page:Roderic_D=_M=.html
title: A Taxonomic Search Engine: Federating taxonomic databases using web services.
pages: 48
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-48

AggarwalWMM03
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Worthey:E=_A=.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/Myler:Peter_J=.html
title: Leishmaniagenome project.
pages: 23
year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-23

SheddenCKGMCGGFTH05
type: Article
last modified date: 2006-05-17
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author: Hanash:Samir.html
title: Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data.
pages: 26
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-26

HuW06
type: Article
last modified date: 2006-05-18
author: Hu:Zihua.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Willsky:Gail_R=.html
title: t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies.
pages: 12
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-12

KurowskiSFDB03
type: Article
last modified date: 2006-05-16
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Kurowski:Michal_A=.html
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author: Debski:Janusz.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Bujnicki:Janusz_M=.html
title: S-adenosylmethionine to three crystal structures.
pages: 9
year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-9

MiddendorfZAHKLWCW04
type: Article
last modified date: 2006-05-17
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title: Discriminative topological features reveal biological network mechanisms.
pages: 181
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-181

PavelkaPVCSGR04
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author: Capozzoli:Monica.html
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author: Granucci:Francesca.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Ricciardi=Castagnoli:Paola.html
title: A power law global error model for the identification of differentially expressed genes in microarray data.
pages: 203
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-203

DiemandS04
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/d/Diemand:Alexander_V=.html
author: Scheib:Holger.html
title: MolTalk - a programming library for protein structures and structure analysis.
pages: 39
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-39

MichalskyDGP05
type: Article
last modified date: 2006-05-17
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author: Dunkel:Mathias.html
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title: SuperLigands - a database of ligand structures derived from the Protein Data Bank.
pages: 122
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-122

LiQGLXHSSHL06
type: Article
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title: In silicodiscovery of human natural antisense transcripts.
pages: 18
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-18

Bollback06
type: Article
last modified date: 2006-05-18
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Bollback:Jonathan_P=.html
title: SIMMAP: Stochastic character mapping of discrete traits on phylogenies.
pages: 88
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-88

Murray-RustMR05a
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/Murray=Rust:Peter.html
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title: Communication and re-use of chemical information in bioscience.
pages: 180
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-180

NeverovANFGM05
type: Article
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title: Alternative splicing and protein function.
pages: 266
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-266

Lamparter06
type: Article
last modified date: 2006-05-18
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title: A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions.
pages: 141
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-141

ReederG04
type: Article
last modified date: 2006-05-17
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title: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
pages: 104
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-104

MajorosS04
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/Majoros:William_H=.html
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title: An empirical analysis of training protocols for probabilistic gene finders.
pages: 206
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-206

PanditBGBAS04
type: Article
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title: SUPFAM: A database of sequence superfamilies of protein domains.
pages: 28
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-28

SeilerMPW06
type: Article
last modified date: 2006-05-18
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author: Mehrle:Alexander.html
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title: The 3of5 web application for complex and comprehensive pattern matching in protein sequences.
pages: 144
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-144

LoraineH02
type: Article
last modified date: 2006-05-16
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/l/Loraine:Ann_E=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/h/Helt:Gregg_A=.html
title: Visualizing the genome: techniques for presenting human genome data and annotations.
pages: 19
year: 2002
volume: 3
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-3-19

StewartWL01
type: Article
last modified date: 2006-05-16
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Stewart:Jeffrey_J=.html
author: Watts:Perry.html
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title: An algorithm for mapping positively selected members of quasispecies-type viruses.
pages: 1
year: 2001
volume: 2
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-2-1

HuangK04
type: Article
last modified date: 2006-05-17
author: Huang:Yanlin.html
author: Kowalski:David.html
title: PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability.
pages: 134
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-134

AdieAEPP05
type: Article
last modified date: 2006-05-17
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/a/Adie:Euan_A=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/a/Adams:Richard_R=.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/p/Pickard:Ben_S=.html
title: Speeding disease gene discovery by sequence based candidate prioritization.
pages: 55
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-55

SemeiksRBM06
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GhaiHC04
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BermanDKMODPDB04
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ZakharkinKMCBSPAP05
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GiesegCMMRK02
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HudekB05
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DunnDS05
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ChungAANM06
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SpitzerLCSF06
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title: A comparison of RNA folding measures.
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volume: 6
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ThibertBR05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Bredesen:Dale_E=.html
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title: Improved prediction of critical residues for protein function based on network and phylogenetic analyses.
pages: 213
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-213

KimLB06
type: Article
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author: Lee:Jae Won.html
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pages: 134
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-134

YangCLL06
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title: A stable gene selection in microarray data analysis.
pages: 228
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volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-228

HermidaSDDP06
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title: MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation.
pages: 190
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volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-190

RacunasSF06
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/f/Fedoroff:Nina_V=.html
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pages: 196
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volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-196

Mower05
type: Article
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title: PREP-Mt: predictive RNA editor for plant mitochondrial genes.
pages: 96
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volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-96

PengRVDO06
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/d/Dunker:A=_Keith.html
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title: Length-dependent prediction of protein intrinsic disorder.
pages: 208
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-208

StevensD05
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title: Combining Affymetrix microarray results.
pages: 57
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-57

LuPOK06
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Krawetz:Stephen_A=.html
title: K-SPMM: a database of murine spermatogenic promoters modules & motifs.
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year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-238

DesaiE04
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ee: http://dx.doi.org/10.1186/1471-2105-5-182

KanhereB05
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volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-1

Broberg05
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pages: 199
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-199

SalgadoSGPPMKC06
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ee: http://dx.doi.org/10.1186/1471-2105-7-5

VulloWP06
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pages: 180
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ZhangSU04
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author: Sheng:Huitao.html
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VeldhovenLSJKJ05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Kors:Jan_A=.html
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pages: 192
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-192

KaskiNOVTC03
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pages: 48
year: 2003
volume: 4
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ee: http://dx.doi.org/10.1186/1471-2105-4-48

BerreraMF03
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title: Amino acid empirical contact energy definitions for fold recognition in the space of contact maps.
pages: 8
year: 2003
volume: 4
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ee: http://dx.doi.org/10.1186/1471-2105-4-8

AnwarNT06
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title: Identification of consensus RNA secondary structures using suffix arrays.
pages: 244
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-244

HauboldPMW05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/M=ouml=ller:Friedrich.html
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title: Genome comparison without alignment using shortest unique substrings.
pages: 123
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ee: http://dx.doi.org/10.1186/1471-2105-6-123

MissirlisMBODLH05
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pages: 145
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-145

ZhuPSD04
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title: Asynchronous adaptive time step in quantitative cellular automata modeling.
pages: 85
year: 2004
volume: 5
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BylesjoESSJAT05
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title: MASQOT: a method for cDNA microarray spot quality control.
pages: 250
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-250

LuttekeL04
type: Article
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title: pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files.
pages: 69
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-69

OhlsonE05
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author: Ohlson:Tomas.html
author: Elofsson:Arne.html
title: ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins.
pages: 253
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volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-253

AnderssonIG06
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title: Bayesian detection of periodic mRNA time profiles without use of training examples.
pages: 63
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-63

KillionSI03
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title: The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD).
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year: 2003
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LiangSWQJPC06
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author: Sun:Feng.html
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title: MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools.
pages: 115
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ee: http://dx.doi.org/10.1186/1471-2105-7-115

KarpievitchA06
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title: mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.
pages: 139
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ee: http://dx.doi.org/10.1186/1471-2105-7-139

SchwartzK06
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Schwartz:Jean=Marc.html
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title: Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis.
pages: 186
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ee: http://dx.doi.org/10.1186/1471-2105-7-186

KustraSZ06
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author: Shioda:Romy.html
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title: A factor analysis model for functional genomics.
pages: 216
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ee: http://dx.doi.org/10.1186/1471-2105-7-216

PopescuY05
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pages: 217
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ee: http://dx.doi.org/10.1186/1471-2105-6-217

MajorNMRSSWAKKW06
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title: AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.
pages: 192
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volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-192

DumontierH02
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/h/Hogue:Christopher_W=_V=.html
title: NBLAST: a cluster variant of BLAST for NxN comparisons.
pages: 13
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KatajamaaO05
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title: Processing methods for differential analysis of LC/MS profile data.
pages: 179
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-179

NovikovB05
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pages: 293
year: 2005
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ee: http://dx.doi.org/10.1186/1471-2105-6-293

SharmaSSR04
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Sharma:Vineet_K=.html
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title: ArrayD: A general purpose software for Microarray design.
pages: 142
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-142

YugiNKKT05
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author: Kitayama:Tomoya.html
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title: A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks.
pages: 299
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ee: http://dx.doi.org/10.1186/1471-2105-6-299

BigelowWWH04
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title: CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting.
pages: 27
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-27

LiuG06
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Graber:Joel_H=.html
title: Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation.
pages: 77
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ee: http://dx.doi.org/10.1186/1471-2105-7-77

BonizzoniRP05
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title: ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.
pages: 244
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-244

RivaK04
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Kohane:Isaac_S=.html
title: A SNP-centric database for the investigation of the human genome.
pages: 33
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-33

XiaMW05
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title: WebArray: an online platform for microarray data analysis.
pages: 306
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journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-306

KimPBBSA06
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/a/Allison:David_B=.html
title: A proposed metric for assessing the measurement quality of individual microarrays.
pages: 35
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ee: http://dx.doi.org/10.1186/1471-2105-7-35

LiuKM05
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title: An Entropy-based gene selection method for cancer classification using microarray data.
pages: 76
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-76

NilssonKRL05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/l/Larsson:Karl=Henrik.html
title: Approaching the taxonomic affiliation of unidentified sequences in public databases - an example from the mycorrhizal fungi.
pages: 178
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volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-178

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volume: 4
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year: 2004
volume: 5
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CannoneSSCDDFLMMPSYG02
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volume: 5
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Cockerill04
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SmolkinG03
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volume: 5
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GadkarGD05
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year: 2005
volume: 6
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HughesHL04
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year: 2004
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FerreAZH05
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SwartHS04
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volume: 5
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KadotaFRAA05
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ShabalinaSO06
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volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-65

GreerMBH06
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pages: 149
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-149

RobinsonGMH02
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year: 2002
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journal name: BMC Bioinformatics
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SalisSK06
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year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-93

LiRJLXGZWDLLZW06
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year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-26

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type: Article
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pages: 155
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-155

VarmaS04
type: Article
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pages: 126
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-126

QiaoW04
type: Article
last modified date: 2006-05-17
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Weigel:Ronald_M=.html
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pages: 102
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-102

YiHCHS06
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pages: 30
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-30

MaglieryR05
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title: Sequence variation in ligand binding sites in proteins.
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year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-240

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type: Article
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pages: 97
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-97

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year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-205

HuMWD04
type: Article
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pages: 17
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-17

BendtsenNWPB05
type: Article
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year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-167

Holmes04
type: Article
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title: A probabilistic model for the evolution of RNA structure.
pages: 166
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-166

EmberlyRS03
type: Article
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author: Rajewsky:Nikolaus.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Siggia:Eric_D=.html
title: Conservation of regulatory elements between two species of Drosophila.
pages: 57
year: 2003
volume: 4
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-4-57

SvenssonMTGV05
type: Article
last modified date: 2006-05-17
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pages: 177
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-177

LambertLFG05
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volume: 6
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Perez-IratxetaA05
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WagnerNPKDASW04
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volume: 5
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KosinskiFB05
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year: 2005
volume: 6
journal name: BMC Bioinformatics
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MacCarthyPS05
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volume: 6
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PehkonenWT05
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volume: 6
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RossnesEL05
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volume: 6
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ZeebergQNSCKRSBBEHWCSNW05
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year: 2005
volume: 6
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LettHP04
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volume: 5
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HamahashiOK05
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year: 2005
volume: 6
journal name: BMC Bioinformatics
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StankeSMW06
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volume: 7
journal name: BMC Bioinformatics
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ChangMFGS06
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volume: 7
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FirthB06
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year: 2006
volume: 7
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RaskoMR05
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year: 2005
volume: 6
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StuartB04
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pages: 204
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ee: http://dx.doi.org/10.1186/1471-2105-5-204

ChenMWJCGWA04
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pages: 191
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volume: 5
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Sharma-OatesQW05
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title: TmaDB: a repository for tissue microarray data.
pages: 218
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-218

VencioBPP04
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year: 2004
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GibbsAG05
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title: Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences.
pages: 90
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-90

KimHK06
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title: Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae.
pages: 165
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-165

CaiLXZ01
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title: Support Vector Machines for predicting protein structural class.
pages: 3
year: 2001
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ee: http://dx.doi.org/10.1186/1471-2105-2-3

OffmanNGF04
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pages: 41
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-41

DohertyCM06
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pages: 151
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volume: 7
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SharabianiSLV05
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title: Dynamic covariation between gene expression and proteome characteristics.
pages: 215
year: 2005
volume: 6
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FiddyCXDM06
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title: An integrated system for genetic analysis.
pages: 210
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-210

BiroB04
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title: Frequent occurrence of recognition Site-like sequences in the restriction endonucleases.
pages: 30
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-30

Townsend04
type: Article
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title: Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays.
pages: 54
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-54

SnipenRNAZA06
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title: Detection of divergent genes in microbial aCGH experiments.
pages: 181
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-181

GoedeMSP06
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title: SuperMimic - Fitting peptide mimetics into protein structures.
pages: 11
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-11

BuiSDSNS06
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title: Predicting population coverage of T-cell epitope-based diagnostics and vaccines.
pages: 153
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-153

ReimersW05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Weinstein:John_N=.html
title: Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases.
pages: 166
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-166

MorelandGBZB05
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title: The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.
pages: 21
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-21

ViaH04
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author: Via:Allegra.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/h/Helmer=Citterich:Manuela.html
title: A structural study for the optimisation of functional motifs encoded in protein sequences.
pages: 50
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-50

KothapalliYMJ02
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/y/Yoder:Sean_J=.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/j/Jr:Thomas_P=_Loughran.html
title: Microarray results: how accurate are they?
pages: 22
year: 2002
volume: 3
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ee: http://dx.doi.org/10.1186/1471-2105-3-22

SunB06
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title: Choosing the best heuristic for seeded alignment of DNA sequences.
pages: 133
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-133

LeeSMRCYSHCSS06
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Scheuermann:Richard_H=.html
title: Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation.
pages: 237
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-237

BisogninBD04
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author: Bortoluzzi:Stefania.html
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title: Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma.
pages: 68
year: 2004
volume: 5
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-5-68

RuanZ05
type: Article
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author: Ruan:Jianhua.html
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title: CAGER: classification analysis of gene expression regulation using multiple information sources.
pages: 114
year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-114

ChenERLU05
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title: CGHPRO - A comprehensive data analysis tool for array CGH.
pages: 85
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-85

KoziolF05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Koziol:James_A=.html
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title: A note on generalized Genome Scan Meta-Analysis statistics.
pages: 32
year: 2005
volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-32

TingYTRP06
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title: Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.
pages: 25
year: 2006
volume: 7
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-7-25

XiaoFGKY04
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author: Frisina:Robert.html
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title: Multivariate search for differentially expressed gene combinations.
pages: 164
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-164

PatiVHGM06
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volume: 7
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year: 2005
volume: 6
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volume: 6
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pages: 121
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volume: 5
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volume: 6
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BurgerDYB04
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pages: 184
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-184

YamadaKG06
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volume: 7
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year: 2005
volume: 6
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PetriFM04
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year: 2004
volume: 5
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DrabkinHHB05
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year: 2005
volume: 6
journal name: BMC Bioinformatics
ee: http://dx.doi.org/10.1186/1471-2105-6-29

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pages: 116
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volume: 6
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DawsonRM05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Rodriguez:Raymond_L=.html
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pages: 195
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volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-195

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pages: 194
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-194

ParkYKLLS03
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pages: 33
year: 2003
volume: 4
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ee: http://dx.doi.org/10.1186/1471-2105-4-33

DienerHKWBOD05
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pages: 147
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volume: 6
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ee: http://dx.doi.org/10.1186/1471-2105-6-147

KeiblerB03
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Brent:Michael_R=.html
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pages: 50
year: 2003
volume: 4
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ee: http://dx.doi.org/10.1186/1471-2105-4-50

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author: Chen:Jun.html
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pages: 81
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-81

WangZSA06
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year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-116

Konishi04
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pages: 5
year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-5

BizzaroM03
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pages: 22
year: 2003
volume: 4
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ee: http://dx.doi.org/10.1186/1471-2105-4-22

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pages: 113
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-113

HsingBSC04
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Bellenson:Joel_L=.html
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title: Modeling of cell signaling pathways in macrophages by semantic networks.
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year: 2004
volume: 5
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ee: http://dx.doi.org/10.1186/1471-2105-5-156

TeelingG06
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Gl=ouml=ckner:Frank_Oliver.html
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pages: 66
year: 2006
volume: 7
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ee: http://dx.doi.org/10.1186/1471-2105-7-66

XuKB06
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title: The Use of Functional Domains to Improve Transmembrane Protein Topology Prediction.
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year: 2006
volume: 4
journal name: J. Bioinformatics and Computational Biology
number: 1
ee: http://dx.doi.org/10.1142/S0219720006001722

NgT04
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title: Discovering Protein-protein Interactions.
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year: 2004
volume: 1
journal name: J. Bioinformatics and Computational Biology
number: 4
ee: http://dx.doi.org/10.1142/S0219720004000600

LinTC05
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author: Tegos:Theodore.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Chen:Zhi=Zhong.html
title: Heuristic Search in Constrained Bipartite Matching with Applications to Protein Nmr Backbone Resonance Assignment.
pages: 1331-1350
year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 6
ee: http://dx.doi.org/10.1142/S0219720005001570

TakahashiMML03
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author: Matsuda:Fumihiko.html
author: Margetic:Nino.html
author: Lathrop:Mark.html
title: Automated Identification of Single Nucleotide Polymorphismsfrom Sequencing Data.
pages: 253-266
year: 2003
volume: 1
journal name: J. Bioinformatics and Computational Biology
number: 2
ee: http://dx.doi.org/10.1142/S021972000300006X

CuiJW05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/j/Jernigan:Robert_L=.html
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title: Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints.
pages: 1315-1330
year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 6
ee: http://dx.doi.org/10.1142/S0219720005001582

VulloF03
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year: 2003
volume: 1
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number: 2
ee: http://dx.doi.org/10.1142/S0219720003000149

WangL05
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author: Wang:Yi.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/l/Li:Kuo=Bin.html
title: Multiple Sequence Alignment Using an Exhaustive and Greedy Algorithm.
pages: 243-256
year: 2005
volume: 3
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number: 2
ee: http://dx.doi.org/10.1142/S021972000500103X

WuZK05
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title: Dynamic Model-based Clustering for Time-course Gene Expression Data.
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year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 4
ee: http://dx.doi.org/10.1142/S0219720005001314

X05
type: Article
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title: Foreword.
pages: 530-550
year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 3
ee: http://dx.doi.org/10.1142/S0219720005001260

KimmelS05
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author: Shamir:Ron.html
title: The Incomplete Perfect Phylogeny Haplotype Problem.
pages: 359-384
year: 2005
volume: 3
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number: 2
ee: http://dx.doi.org/10.1142/S0219720005001090

WongCATKT04
type: Article
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author: Wong:Kee Yew.html
author: Chuan:Yin Choy.html
author: Aggarwal:Amit.html
author: Tham:Lawrence.html
author: Kong:Wai Ming.html
author: Tan:Patrick.html
title: Identifying Patterns of Dna for Tumor Diagnosis Using Capillary Electrophoresis-amplified Fragment Length Polymorphism (ce-aflp) Screening.
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year: 2004
volume: 2
journal name: J. Bioinformatics and Computational Biology
number: 3
ee: http://dx.doi.org/10.1142/S0219720004000740

El-MabroukRDLL05
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/e/El=Mabrouk:Nadia.html
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title: Approximate Matching of Structured Motifs in Dna Sequences.
pages: 317-342
year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 2
ee: http://dx.doi.org/10.1142/S0219720005001065

WuD03
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author: Wu:Xiwei.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/d/Dewey:T=_Gregory.html
title: Cluster Analysis of Dynamic Parameters of Gene Expression.
pages: 447-458
year: 2003
volume: 1
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number: 3
ee: http://dx.doi.org/10.1142/S0219720003000307

Guenoche04
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Gu=eacute=noche:Alain.html
title: Supersequences of Masks for Oligo-chips.
pages: 459-470
year: 2004
volume: 2
journal name: J. Bioinformatics and Computational Biology
number: 3
ee: http://dx.doi.org/10.1142/S0219720004000685

ChanCCL05
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Chan:Shih=Huang.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Chen:Li=Ju.html
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title: An Ancova Approach to Normalize Microarray Data, and its Performance to Existing Methods.
pages: 257-268
year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 2
ee: http://dx.doi.org/10.1142/S0219720005001041

RantanenGKJ05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Rantanen:Ville=Veikko.html
author: Gyllenberg:Mats.html
author: Koski:Timo.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/j/Johnson:Mark_S=.html
title: a PrioriContact Preferences in Molecular Recognition.
pages: 861-890
year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 4
ee: http://dx.doi.org/10.1142/S0219720005001417

LiangSB04
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/l/Liang:S=.html
author: Samanta:Manoj Pratim.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Biegel:B=_A=.html
title: Cwinnower Algorithm for Finding Fuzzy Dna Motifs.
pages: 47-60
year: 2004
volume: 2
journal name: J. Bioinformatics and Computational Biology
number: 1
ee: http://dx.doi.org/10.1142/S0219720004000466

GilDG05
type: Article
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author: Dessimoz:Christophe.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Gonnet:Gaston_H=.html
title: A Dimensionless Fit Measure for Phylogenetic Distance Trees.
pages: 1429-1440
year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 6
ee: http://dx.doi.org/10.1142/S0219720005001636

X04
type: Article
last modified date: 2006-05-19
title: Foreword.
pages: 3-20
year: 2004
volume: 2
journal name: J. Bioinformatics and Computational Biology
number: 1
ee: http://dx.doi.org/10.1142/S0219720004000636

LoraineHCS03
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title: Exploring Alternative Transcript Structure in the Humangenome Using Blocks and Interpro.
pages: 289-306
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ShehadiAUWMIO05
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year: 2005
volume: 3
journal name: J. Bioinformatics and Computational Biology
number: 1
ee: http://dx.doi.org/10.1142/S0219720005000916

YuanCRB05
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author: Chen:Guanjie.html
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title: A Statistical Framework for Haplotype Block Inference.
pages: 1021-1038
year: 2005
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PalopoliT04
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pages: 471-496
year: 2004
volume: 2
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number: 3
ee: http://dx.doi.org/10.1142/S0219720004000697

MukherjeeR05
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last modified date: 2006-05-19
author: Mukherjee:Sach.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Roberts:Stephen_J=.html
title: A Theoretical Analysis of the Selection of Differentially Expressed Genes.
pages: 627-644
year: 2005
volume: 3
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number: 3
ee: http://dx.doi.org/10.1142/S0219720005001211

JinTF05
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pages: 915-928
year: 2005
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number: 4
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Xu05a
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title: Erratum: Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics.
pages: 771
year: 2005
volume: 3
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number: 3
ee: http://dx.doi.org/10.1142/S0219720005001284

Rahmann03
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title: Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach.
pages: 343-362
year: 2003
volume: 1
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number: 2
ee: http://dx.doi.org/10.1142/S0219720003000125

ZhuYHA04
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title: Robustness, Stability and Efficiency of Phage lambda Genetic Switch: Dynamical Structure Analysis.
pages: 785-818
year: 2004
volume: 2
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number: 4
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BreitlingH05
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last modified date: 2006-05-19
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title: Rank-based Methods as a Non-parametric Alternative of the T-statistic for the Analysis of Biological Microarray Data.
pages: 1171-1190
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volume: 3
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number: 5
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TamadaBIKKM05
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title: Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models.
pages: 1295-1314
year: 2005
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number: 6
ee: http://dx.doi.org/10.1142/S0219720005001569

MeintjesR05
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title: Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type-1.
pages: 157-168
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volume: 3
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number: 1
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BandyopadhyayBM05
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title: Active Site Driven Ligand Design: an Evolutionary Approach.
pages: 1053-1070
year: 2005
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YamadaM04
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author: Morishita:Shinichi.html
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pages: 21-46
year: 2004
volume: 2
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number: 1
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GuoP05
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title: Using Weighted Permutation Scores to Detect Differential Gene Expression with Microarray Data.
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volume: 3
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AhrenO04
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last modified date: 2006-05-19
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title: Robustness of Metabolic Map Reconstruction.
pages: 589-593
year: 2004
volume: 2
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number: 3
ee: http://dx.doi.org/10.1142/S021972000400079X

GusfieldEL04
type: Article
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author: Eddhu:Satish.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/l/Langley:Charles_H=.html
title: Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination.
pages: 173-214
year: 2004
volume: 2
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RamseyOB05a
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OhtaniSSOM04
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title: Development of Image Processing Program for Yeast Cell Morphology.
pages: 695-710
year: 2004
volume: 1
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CamogluKS04
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title: Index-based Similarity Search for Protein Structure Databases.
pages: 99-126
year: 2004
volume: 2
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OlmanXX03
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title: Cubic: Identification of Regulatory Binding Sites through Data Clustering.
pages: 21-40
year: 2003
volume: 1
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BourqueS04
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title: Improving Gene Network Inference by Comparing Expression Time-series across Species, Developmental Stages or Tissues.
pages: 765-784
year: 2004
volume: 2
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GohK05
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last modified date: 2006-05-19
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Kasabov:Nikola_K=.html
title: An Integrated Feature Selection and Classification Method to Select Minimum Number of Variables on the Case Study of Gene Expression Data.
pages: 1107-1136
year: 2005
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LiuCBX05
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author: Chen:Dechang.html
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title: Clustering Gene Expression Data with Kernel Principal Components.
pages: 303-316
year: 2005
volume: 3
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ThamHC03
type: Article
last modified date: 2006-05-19
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Chin:W=_C=.html
title: Predicting Risk of Coronary Artery Disease from Dna Microarray-based Genotyping Using Neural Networks and Other Statistical Analysis Tool.
pages: 521-540
year: 2003
volume: 1
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LiuWFXB03
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author: Wang:Yuhong.html
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title: An Interactive Tool for Extracting Exons and Snp from Genomic Sequence: Isolation of Hcn1 and Hcn3 Ion Channel Genes.
pages: 433-446
year: 2003
volume: 1
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RamseyOB05
type: Article
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author: Orrell:David.html
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title: Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks.
pages: 415-436
year: 2005
volume: 3
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BoydPRWB05
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title: Pops: a Computational Tool for Modeling and Predicting Protease Specificity.
pages: 551-586
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ImotoKGATKM03
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author: Kim:SunYong.html
author: Goto:Takao.html
author: Aburatani:Sachiyo.html
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title: Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network.
pages: 231-252
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volume: 1
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number: 2
ee: http://dx.doi.org/10.1142/S0219720003000071

Ozery-FlatoS03
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title: Two Notes on Genome Rearrangement.
pages: 71-94
year: 2003
volume: 1
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number: 1
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XiaoP05
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title: Gene Function Prediction by a Combined Analysis of Gene Expression Data and Protein-protein Interaction Data.
pages: 1371-1390
year: 2005
volume: 3
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number: 6
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LinXCJWX03
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author: Xu:Dong.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Chen:Zhi=Zhong.html
author: Jiang:Tao.html
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title: Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering.
pages: 387-410
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volume: 1
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GopalRSI05
type: Article
last modified date: 2006-05-19
author: Gopal:Kreshna.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Romo:Tod_D=.html
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title: Determining Relevant Features to Recognize Electron Density Patterns in X-ray Protein Crystallography.
pages: 645-676
year: 2005
volume: 3
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JiangZ05
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title: Protein Folding on the Hexagonal Lattice in the Hp Model.
pages: 19-34
year: 2005
volume: 3
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SaraiSSGK05
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author: Siebers:Jorg.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/g/Gromiha:M=_Michael.html
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title: Integration of Bioinformatics and Computational Biology to Understand Protein-dna Recognition Mechanism.
pages: 169-183
year: 2005
volume: 3
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number: 1
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ImotoSAKTKM03
type: Article
last modified date: 2006-05-22
author: Imoto:Seiya.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Savoie:Christopher_J=.html
author: Aburatani:Sachiyo.html
author: Kim:SunYong.html
author: Tashiro:Kousuke.html
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title: Use of Gene Networks for Identifying and Validating Drug Targets.
pages: 459-474
year: 2003
volume: 1
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number: 3
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ChangHOZ05
type: Article
last modified date: 2006-05-22
author: Chang:Jeong Ho.html
author: Hwang:Kyu Baek.html
author: Oh:Sok June.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/z/Zhang:Byoung=Tak.html
title: Bayesian Network Learning with Feature Abstraction for Gene-drug Dependency Analysis.
pages: 61-78
year: 2005
volume: 3
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YeJL04
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title: Pairwise Protein Structure Alignment Based on an Orientation-independent Backbone Representation.
pages: 699-718
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volume: 2
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WeiA03
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author: Wei:Liping.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/a/Altman:Russ_B=.html
title: Recognizing Complex, Asymmetric Functional Sites in Protein Structures Using a Bayesian Scoring Function.
pages: 119-138
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volume: 1
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Yu04
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title: Ruleminer: a Knowledge System for Supporting High-throughput Protein Function Annotations.
pages: 595-618
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MatsunoIOFM06
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/i/Inouye:Shin=Ichi_T=.html
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title: A New Regulatory Interaction Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals.
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XuLKX03
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title: Raptor: Optimal Protein Threading by Linear Programming.
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HeHJS06
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title: Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets.
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year: 2006
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MakiTAWAEUAKO04
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author: Takahashi:Yoriko.html
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title: voyagene.
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Brusic03
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title: From Immunoinformatics to Immunomics.
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InoueNHNSYA04
type: Article
last modified date: 2006-06-01
author: Inoue:Masato.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/n/Nishimura:Shin=ichi.html
author: Hori:Gen.html
author: Nakahara:Hiroyuki.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/a/Amari:Shun=ichi.html
title: Improved Parameter Estimation for Variance-stabilizing Transformation of Gene-expression Microarray Data.
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volume: 2
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ImotoHGTKM04
type: Article
last modified date: 2006-05-19
author: Imoto:Seiya.html
author: Higuchi:Tomoyuki.html
author: Goto:Takao.html
author: Tashiro:Kousuke.html
author: Kuhara:Satoru.html
author: Miyano:Satoru.html
title: Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks.
pages: 77-98
year: 2004
volume: 2
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Krivan04
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last modified date: 2006-05-19
author: Krivan:William.html
title: Searching for Transcription Factor Binding Site Clusters: How True Are True Positives?
pages: 413-416
year: 2004
volume: 2
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ChangHCCLL05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/c/Chang:Chang=Heng.html
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title: Shannon Information in Complete Genomes.
pages: 587-608
year: 2005
volume: 3
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ee: http://dx.doi.org/10.1142/S0219720005001181

HardyR04
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author: Hardy:Simon.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Robillard:Pierre_N=.html
title: Modeling and Simulation of Molecular Biology Systems Using Petri Nets: Modeling Goals of Various Approaches.
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year: 2004
volume: 2
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ee: http://dx.doi.org/10.1142/S0219720004000764

LiMKT04
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title: Patternhunter Ii: Highly Sensitive and Fast Homology Search.
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year: 2004
volume: 2
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number: 3
ee: http://dx.doi.org/10.1142/S0219720004000661

ZhangWZWC05
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title: Exploring Protein's Optimal Hp Configurations by Self-organizing Mapping.
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volume: 3
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number: 2
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KonagurthuWS04
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title: Progressive Multiple Alignment Using Sequence Triplet Optimizations and Three-residue Exchange Costs.
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year: 2004
volume: 2
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number: 4
ee: http://dx.doi.org/10.1142/S0219720004000831

LongacreSL05
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title: Linear Independence of Pairwise Comparisons of Dna Microarray Data.
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year: 2005
volume: 3
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ee: http://dx.doi.org/10.1142/S0219720005001600

X03a
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pages: 205-230
year: 2003
volume: 1
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number: 2
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Wang04
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title: Reconstructing Genetic Networks from Time Ordered Gene Expression Data Using Bayesian Method with Global Search Algorithm.
pages: 441-458
year: 2004
volume: 2
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number: 3
ee: http://dx.doi.org/10.1142/S0219720004000673

KimP04
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title: Bioie: Retargetable Information Extraction and Ontological Annotation of Biological Interactions from the Literature.
pages: 551-568
year: 2004
volume: 2
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number: 3
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LiuML06
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title: Prima: Peptide Robust Identification from Ms/ms Spectra.
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ee: http://dx.doi.org/10.1142/S0219720006001746

BahadurTSA05
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title: Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach.
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year: 2005
volume: 3
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ee: http://dx.doi.org/10.1142/S0219720005000904

CieliebakEW05
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title: Complexity and Approximability of Double Digest.
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year: 2005
volume: 3
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ee: http://dx.doi.org/10.1142/S0219720005001016

LacroixRE04
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title: Techniques for Optimization of Queries on Integrated Biological Resources.
pages: 375-412
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number: 2
ee: http://dx.doi.org/10.1142/S0219720004000648

PaiSWCCFL06
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title: Unique Peptide Identification of Rnasea Superfamily Sequences Based on Reinforced Merging Algorithms.
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PhamSH05
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title: Support Vector Machines for Prediction and Analysis of Beta and Gamma-turns in Proteins.
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volume: 3
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number: 2
ee: http://dx.doi.org/10.1142/S0219720005001089

YeCLWLZ05
type: Article
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author: Chen:Huajun.html
author: Liu:Ting.html
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title: A Wavelet Approach for the Analysis of Folding Trajectory of Protein Trp-cage.
pages: 1351-1370
year: 2005
volume: 3
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number: 6
ee: http://dx.doi.org/10.1142/S0219720005001594

Michelson03
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title: Assessing the Impact of Predictive Biosimulation on Drug Discovery and Development.
pages: 169-178
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number: 1
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ChanKC05
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title: A Hybrid Genetic Algorithm and Expectation Maximization Method for Global Gene Trajectory Clustering.
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year: 2005
volume: 3
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TanabeW04
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title: Generation of a Large Gene/protein Lexicon by Morphological Pattern Analysis.
pages: 611-626
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volume: 1
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number: 4
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KaminumaHYNMT05
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title: in SilicoPhenotypic Screening Method of Mutants Based on Statistical Modeling of Genetically Mixed Samples.
pages: 1281-1294
year: 2005
volume: 3
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number: 6
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MaCC05
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/m/Ma:Patrick_C=_H=.html
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pages: 281-302
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ee: http://dx.doi.org/10.1142/S0219720005001053

RiazYL05
type: Article
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author: Yi 0003:Wang.html
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title: A Tabu Search Algorithm for Post-processing Multiple Sequence Alignment.
pages: 145-156
year: 2005
volume: 3
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number: 1
ee: http://dx.doi.org/10.1142/S0219720005000928

KearneyT03
type: Article
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title: Bioinformatics Meets Proteomics - Bridging the Gap between Massspectrometry Data Analysis and Cell Biology.
pages: 183-200
year: 2003
volume: 1
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number: 1
ee: http://dx.doi.org/10.1142/S021972000300023X

LiuZZ04
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title: Prediction of Protein Secondary Structure Based on Residue Pairs.
pages: 343-352
year: 2004
volume: 2
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number: 2
ee: http://dx.doi.org/10.1142/S0219720004000594

ZhouCTZ05
type: Article
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author: Chen:Luonan.html
author: Tang:Yun.html
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title: Aligning Multiple Protein Structures by Deterministic Annealing.
pages: 837-860
year: 2005
volume: 3
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number: 4
ee: http://dx.doi.org/10.1142/S0219720005001351

SahinalpEGBFE04
type: Article
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year: 2004
volume: 2
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number: 4
ee: http://dx.doi.org/10.1142/S0219720004000788

WanTL04
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title: Histogram-based Scoring Schemes for Protein Nmr Resonance Assignment.
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year: 2004
volume: 2
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number: 4
ee: http://dx.doi.org/10.1142/S0219720004000843

DukkaTSHA06
type: Article
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title: Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms.
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year: 2006
volume: 4
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number: 1
ee: http://dx.doi.org/10.1142/S0219720006001680

Thorvaldsen05
type: Article
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title: A Tutorial on Markov Models Based on Mendel's Classical Experiments.
pages: 1441-1460
year: 2005
volume: 3
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number: 6
ee: http://dx.doi.org/10.1142/S021972000500165X

WangZ05
type: Article
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author: Zhang:Kaizhong.html
title: Multiple Rna Structure Alignment.
pages: 609-626
year: 2005
volume: 3
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number: 3
ee: http://dx.doi.org/10.1142/S0219720005001296

BackofenW04
type: Article
last modified date: 2006-05-19
author: Backofen:Rolf.html
author: Will:Sebastian.html
title: Local Sequence-structure Motifs in Rna.
pages: 681-698
year: 2004
volume: 2
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number: 4
ee: http://dx.doi.org/10.1142/S0219720004000818

StuartB03
type: Article
last modified date: 2006-05-19
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Stuart:Gary_W=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Berry:Michael_W=.html
title: A Comprehensive Whole Genome Bacterial Phylogeny Using Correlated Peptide Motifs Defined in a High Dimensional Vector Space.
pages: 475-494
year: 2003
volume: 1
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number: 3
ee: http://dx.doi.org/10.1142/S0219720003000265

PapadimitriouL04
type: Article
last modified date: 2006-05-19
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/l/Likothanassis:Spiridon_D=.html
title: Kernel-based Self-organized Maps Trained with Supervised Bias for Gene Expression Data Analysis.
pages: 647-680
year: 2004
volume: 1
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number: 4
ee: http://dx.doi.org/10.1142/S021972000400034X

Wang05
type: Article
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wang:Lu=Yong.html
title: Covariation Analysis of Local Amino Acid Sequences in Recurrent Protein Local Structures.
pages: 1391-1410
year: 2005
volume: 3
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number: 6
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LiZ05
type: Article
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author: Zhou:Yaoqi.html
title: Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function.
pages: 1151-1170
year: 2005
volume: 3
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number: 5
ee: http://dx.doi.org/10.1142/S0219720005001430

BianchettiTLPP05
type: Article
last modified date: 2006-05-19
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author: Thompson:Julie Dawn.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/p/Plewniak:Fr=eacute=d=eacute=ric.html
author: Poch:Olivier.html
title: Valid: Validation of Protein Sequence Quality Based on Multiple Alignment Data.
pages: 929-948
year: 2005
volume: 3
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number: 4
ee: http://dx.doi.org/10.1142/S0219720005001326

YangB04
type: Article
last modified date: 2006-05-19
author: Yang:Zheng Rong.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/b/Berry:Emily_A=.html
title: Reduced Bio-basis Function Neural Networks for Protease Cleavage Site Prediction.
pages: 511-532
year: 2004
volume: 2
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number: 3
ee: http://dx.doi.org/10.1142/S0219720004000715

ErramiGD03
type: Article
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author: Errami:Mounir.html
author: Geourjon:Christophe.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/d/Del=eacute=age:Gilbert.html
title: Conservation of Amino Acids into Multiple Alignments Involved in Pairwise Interactions in Three-dimensional Protein Structures.
pages: 505-520
year: 2003
volume: 1
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number: 3
ee: http://dx.doi.org/10.1142/S0219720003000228

WangD05
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author: Dong:Liang.html
title: Randomized Algorithms for Motif Detection.
pages: 1039-1052
year: 2005
volume: 3
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number: 5
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AittokallioKNNWL03
type: Article
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author: Kurki:Markus.html
author: Nevalainen:Olli.html
author: Nikula:Tuomas.html
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author: Lahesmaa:Riitta.html
title: Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments.
pages: 541-586
year: 2003
volume: 1
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number: 3
ee: http://dx.doi.org/10.1142/S0219720003000319

HaworthFW06
type: Article
last modified date: 2006-05-19
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/h/Haworth:Naomi_L=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/f/Feng:Lina_L=.html
author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wouters:Merridee_A=.html
title: High Torsional Energy Disulfides: Relationship between Cross-strand Disulfides and Right-handed Staples.
pages: 155-168
year: 2006
volume: 4
journal name: J. Bioinformatics and Computational Biology
number: 1
ee: http://dx.doi.org/10.1142/S0219720006001734

Kitamura-AbeIWTT04
type: Article
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author: Tsutsumi:Akihiro.html
author: Tomita:Masaru.html
title: Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas.
pages: 309-332
year: 2004
volume: 2
journal name: J. Bioinformatics and Computational Biology
number: 2
ee: http://dx.doi.org/10.1142/S0219720004000570

NiijimaK05
type: Article
last modified date: 2006-05-19
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author: Kuhara:Satoru.html
title: Multiclass Molecular Cancer Classification by Kernel Subspace Methods with Effective Kernel Parameter Selection.
pages: 1071-1088
year: 2005
volume: 3
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number: 5
ee: http://dx.doi.org/10.1142/S0219720005001491

DaiTZLSWY04
type: Article
last modified date: 2006-05-19
author: Dai:Heng.html
author: Tian:Bin.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wan:Jackson_S=.html
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title: Dynamic Integration of Gene Annotation and its Application to Microarray Analysis.
pages: 627-646
year: 2004
volume: 1
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number: 4
ee: http://dx.doi.org/10.1142/S0219720004000387

PodowskiCGAH05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/h/Hayes:William_S=.html
title: Suregene, a Scalable System for Automated Term Disambiguation of Gene and Protein Names.
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GrossmanKHL04
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year: 2004
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KaminumaHTNGKMT05
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pages: 401-414
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GaleJW05
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year: 2005
volume: 3
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KaurR03
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title: Bteval: a Server for Evaluation of beta-turn Prediction Methods.
pages: 495-504
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volume: 1
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FutschikC05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/f/Futschik:Matthias_E=.html
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title: Noise-robust Soft Clustering of Gene Expression Time-course Data.
pages: 965-988
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ChouPB05
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title: Systematic Variation Normalization in Microarray Data to Get Gene Expression Comparison Unbiased.
pages: 225-242
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volume: 3
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X06
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title: Editorial.
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volume: 4
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ee: http://dx.doi.org/10.1142/S0219720006001679

LiuA05
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title: Computational Identification of Transcription Factors Involved in Early Cellular Response to a Stimulus.
pages: 949-964
year: 2005
volume: 3
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number: 4
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Chen05
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title: Guest Editor's Introduction: Advanced Techniques for Bioinformatics.
pages: 99-102
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volume: 3
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KimGM04
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title: Binding Matrix: a Novel Approach for Binding Site Recognition.
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volume: 2
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KhanAM05
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title: Genome Wide Identification of Dna Binding Motifs of Nodd-factor in Sinorhizobium Meliloti and Mesorhizobium Loti.
pages: 773-802
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volume: 3
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SoukupL04
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/l/Lee:Jae_K=.html
title: Developing Optimal Prediction Models for Cancer Classification Using Gene Expression Data.
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volume: 1
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XingWJK04
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Addario-BerryCHLPW04
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title: Ancestral Maximum Likelihood of Evolutionary Trees Is Hard.
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OgasawaraM03
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title: A Fast and Sensitive Algorithm for Aligning Ests to the Human Genome.
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CamogluCSW05
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title: Decision Tree Based Information Integration for Automated Protein Classification.
pages: 717-742
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volume: 3
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number: 3
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KrebsB04
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title: Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data.
pages: 61-76
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volume: 2
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MukherjeeM05
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pages: 491-526
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ChinnasamySM05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/s/Sung:Wing=Kin.html
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title: Protein Structure and Fold Prediction Using Tree-augmented Naïve Bayesian Classifier.
pages: 803-820
year: 2005
volume: 3
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LeongPSW05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/p/Preparata:Franco_P=.html
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title: Adaptive Control of Hybridization Noise in Dna Sequencing-by-hybridization.
pages: 79-98
year: 2005
volume: 3
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number: 1
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ZhangKSAB05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/k/Khan:Asif_M=.html
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title: Neural Models for Predicting Viral Vaccine Targets.
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Capobianco05
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title: Mining Time-dependent Gene Features.
pages: 1191-1206
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volume: 3
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FridmanRVHPX05
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author: Razumovskaya:Jane.html
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title: The Probability Distribution for a Random Match between an Experimental-theoretical Spectral Pair in Tandem Mass Spectrometry.
pages: 455-476
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GerasimovaG05
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title: Evolution of the Nadr Regulon in Enterobacteriaceae.
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LeungC06
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title: Algorithms for Challenging Motif Problems.
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Xu05
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title: Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics.
pages: 477-490
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LiJ03
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title: Efficient Inference of Haplotypes from Genotypes on a Pedigree.
pages: 41-70
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LiuSLLMM05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/l/Liu:Tie=Fei.html
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title: Effective Algorithms for Tag Snp Selection.
pages: 1089-1106
year: 2005
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BrownLM04
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title: A Tutorial of Recent Developments in the Seeding of Local Alignment.
pages: 819-842
year: 2004
volume: 2
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LiuW03
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title: Data Mining Tools for Biological Sequences.
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volume: 1
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ReijmersMBKTV05
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title: Integrated Statistical Analysis of Cdna Microarray and Nir Spectroscopic Data Applied to a Hemp Dataset.
pages: 891-914
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volume: 3
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OuyangZWS04
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title: Multivariate Entropy Distance Method for Prokaryotic Gene Identification.
pages: 353-374
year: 2004
volume: 2
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number: 2
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HuangD06
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last modified date: 2006-05-19
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title: Direct Prediction of T-cell Epitopes Using Support Vector Machines with Novel Sequence Encoding Schemes.
pages: 93-108
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ReddyK05
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/r/Reddy:Boojala_V=_B=.html
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title: A Quantitative Analysis of Interfacial Amino Acid Conservation in Protein-protein Hetero Complexes.
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NovikovB05
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title: A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments.
pages: 1411-1428
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volume: 3
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BrejovaBV04
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title: Optimal Spaced Seeds for Homologous Coding Regions.
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PengVRBDO05
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author: Vucetic:Slobodan.html
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author: http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/d/Dunker:A=_Keith.html
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title: Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information.
pages: 35-60
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volume: 3
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LopesS04
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title: Dissecting the Human Spliceosome through Bioinformatics and Proteomics Approaches.
pages: 743-750
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volume: 1
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HayashiKSIKKT04
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title: Protein Classification Using Comparative Molecular Interaction Profile Analysis System.
pages: 497-510
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volume: 2
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title: Preface.
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HanMZ05
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title: de NovoSequencing Error.
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PalakalSMRR03
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title: Identification of Biological Relationships from Text Documentsusing Efficient Computational Methods.
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MaoD05
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title: Discovery of Highly Differentiative Gene Groups from Microarray Gene Expression Data Using the Gene Club Approach.
pages: 1263-1280
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CanW04
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title: Protein Structure Alignment and Fast Similarity Search Using Local Shape Signatures.
pages: 215-239
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Zheng04
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last modified date: 2006-05-19
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title: Clustering of Amino Acids for Protein Secondary Structure Prediction.
pages: 333-342
year: 2004
volume: 2
journal name: J. Bioinformatics and Computational Biology
number: 2
ee: http://dx.doi.org/10.1142/S0219720004000582