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Bioconductor: open software development for computational biology and bioinformatics.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J
Genome Biol
2004,
5
:R80
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1.
Software
R/parallel
speeding up bioinformatics analysis with R
Vera G, Jansen RC, Suppi RL
BMC Bioinformatics
2008,
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(22 September 2008)
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Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using Wheat Genome Array
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BMC Genomics
2008,
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The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets
improving meta-analysis and prediction of prognosis
Sims AH, Smethurst GJ, Hey Y, Okoniewski MJ, Pepper SD, Howell A, Miller CJ, Clarke RB
BMC Medical Genomics
2008,
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Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
Lange E, Tautenhahn R, Neumann S, Groepl C
BMC Bioinformatics
2008,
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(15 September 2008)
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Research
Conserved chromosomal clustering of genes governed by chromatin regulators in
Drosophila
Blanco E, Pignatelli M, Beltran S, Punset A, Pérez-Lluch S, Serras F, Guigó R, Corominas M
Genome Biology
2008,
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Methodology capture: discriminating between the "best" and the rest of community practice
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BMC Bioinformatics
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Dynamic RNA profiling in
Plasmodium falciparum
synchronized blood stages exposed to lethal doses of artesunate
Natalang O, Bischoff E, Deplaine G, Proux C, Dillies MA, Sismeiro O, Guigon G, Bonnefoy S, Patarapotikul J, Mercereau-Puijalon O, Coppée JY, David PH
BMC Genomics
2008,
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8.
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Characterization of hemizygous deletions in
Citrus
using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome
Ríos G, Naranjo MA, Iglesias DJ, Ruiz-Rivero O, Geraud M, Usach A, Talón M
BMC Genomics
2008,
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Novel functional view of the crocidolite asbestos-treated A549 human lung epithelial transcriptome reveals an intricate network of pathways with opposing functions
Hevel JM, Olson-Buelow LC, Ganesan B, Stevens JR, Hardman JP, Aust AE
BMC Genomics
2008,
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Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines
Cody NAL, Zietarska M, Filali-Mouhim A, Provencher DM, Mes-Masson AM, Tonin PN
BMC Medical Genomics
2008,
1
:34
(7 August 2008)
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11.
Research article
Transcriptional responses of
Arabidopsis thaliana
plants to As (V) stress
Abercrombie JM, Halfhill MD, Ranjan P, Rao MR, Saxton AM, Yuan JS, Stewart CN
BMC Plant Biology
2008,
8
:87
(6 August 2008)
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12.
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Gene expression profiles in liver of pigs with extreme high and low levels of androstenone
Moe M, Lien S, Bendixen C, Hedegaard J, Hornshøj H, Berget I, Meuwissen THE, Grindflek E
BMC Veterinary Research
2008,
4
:29
(6 August 2008)
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13.
Software
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
Chu VT, Gottardo R, Raftery AE, Bumgarner RE, Yeung KY
Genome Biology
2008,
9
:R118
(24 July 2008)
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14.
Research article
Structural conservation versus functional divergence of maternally expressed microRNAs in the
Dlk1/Gtl2
imprinting region
Kircher M, Bock C, Paulsen M
BMC Genomics
2008,
9
:346
(23 July 2008)
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15.
Methodology
Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles
Ma Q, Chirn GW, Szustakowski JD, Bakhtiarova A, Kosinski PA, Kemp D, Nirmala N
BioData Mining
2008,
1
:4
(17 July 2008)
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16.
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Genes responsive to both oxidant stress and loss of estrogen receptor function identify a poor prognosis group of estrogen receptor positive primary breast cancers
Yau C, Benz CC
Breast Cancer Research
2008,
10
:R61
(17 July 2008)
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17.
Methodology article
MAID : An effect size based model for microarray data integration across laboratories and platforms
Borozan I, Chen L, Paeper B, Heathcote JE, Edwards AM, Katze M, Zhang Z, McGilvray ID
BMC Bioinformatics
2008,
9
:305
(10 July 2008)
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18.
Method
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in
Arabidopsis thaliana
Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Schölkopf B, Rätsch G, Weigel D
Genome Biology
2008,
9
:R112
(9 July 2008)
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19.
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Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors
Lukas TJ, Miao H, Chen L, Riordan SM, Li W, Crabb AM, Wise A, Du P, Lin SM, Hernandez MR
Genome Biology
2008,
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:R111
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20.
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Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers
Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS
Genome Biology
2008,
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Meta-Analysis Approach identifies Candidate Genes and associated Molecular Networks for Type-2 Diabetes Mellitus
Rasche A, Al-Hasani H, Herwig R
BMC Genomics
2008,
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A weighted average difference method for detecting differentially expressed genes from microarray data
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Algorithms for Molecular Biology
2008,
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23.
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Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells
Maouche S, Poirier O, Godefroy T, Olaso R, Gut I, Collet JP, Montalescot G, Cambien F
BMC Genomics
2008,
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:302
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24.
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Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease
Jelier R, 't Hoen PAC, Sterrenburg E, den Dunnen JT, van Ommen GJB, Kors JA, Mons B
BMC Bioinformatics
2008,
9
:291
(24 June 2008)
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25.
Research article
The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages
Koumandou VL, Natesan SKA, Sergeenko T, Field MC
BMC Genomics
2008,
9
:298
(23 June 2008)
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26.
Research article
Predicting transcriptional regulatory interactions with artificial neural networks applied to
E. coli
multidrug resistance efflux pumps
Veiga DFT, Vicente FFR, Nicolás MF, Vasconcelos ATR
BMC Microbiology
2008,
8
:101
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27.
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Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in
Dictyostelium
Sillo A, Bloomfield G, Balest A, Balbo A, Pergolizzi B, Peracino B, Skelton J, Ivens A, Bozzaro S
BMC Genomics
2008,
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:291
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28.
Research article
Gene-expression of metastasized versus non-metastasized primary head and neck squamous cell carcinomas: A pathway-based analysis
Hensen EF, De Herdt MJ, Goeman JJ, Oosting J, Smit VTHBM, Cornelisse CJ, de Jong RJB
BMC Cancer
2008,
8
:168
(10 June 2008)
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29.
Methodology
Integrating open-source technologies to build low-cost information systems for improved access to public health data
Yi Q, Hoskins RE, Hillringhouse EA, Sorensen SS, Oberle MW, Fuller SS, Wallace JC
International Journal of Health Geographics
2008,
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:29
(9 June 2008)
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30.
Research
Regulation of xylose metabolism in recombinant
Saccharomyces cerevisiae
Salusjärvi L, Kankainen M, Soliymani R, Pitkänen JP, Penttilä M, Ruohonen L
Microbial Cell Factories
2008,
7
:18
(4 June 2008)
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31.
Research article
Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
Tomazou EM, Rakyan VK, Lefebvre G, Andrews R, Ellis P, Jackson DK, Langford C, Francis MD, Bäckdahl L, Miretti M, Coggill P, Ottaviani D, Sheer D, Murrell A, Beck S
BMC Medical Genomics
2008,
1
:19
(30 May 2008)
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32.
Methodology
Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice
Edwards JD, Janda J, Sweeney MT, Gaikwad AB, Liu B, Leung H, Galbraith DW
Plant Methods
2008,
4
:13
(29 May 2008)
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33.
Research
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses
Stokes TH, Torrance JT, Li H, Wang MD
BMC Bioinformatics
2008,
9
(Suppl 6):S18
(28 May 2008)
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34.
Research article
Global expression profiling in leaves of free-growing aspen
Sjödin A, Wissel K, Bylesjö M, Trygg J, Jansson S
BMC Plant Biology
2008,
8
:61
(23 May 2008)
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35.
Research
Gene expression profiling of human prostate cancer stem cells reveals a pro-inflammatory phenotype and the importance of extracellular matrix interactions
Birnie R, Bryce SD, Roome C, Dussupt V, Droop A, Lang SH, Berry PA, Hyde CF, Lewis JL, Stower MJ, Maitland NJ, Collins AT
Genome Biology
2008,
9
:R83
(20 May 2008)
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36.
Research
Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus
Magnaporthe oryzae
Oh Y, Donofrio N, Pan H, Coughlan S, Brown DE, Meng S, Mitchell T, Dean RA
Genome Biology
2008,
9
:R85
(20 May 2008)
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Abstract
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37.
Research article
Pro-neural transcription factors as cancer markers
Vias M, Massie CE, East P, Scott H, Warren A, Zhou Z, Nikitin AY, Neal DE, Mills IG
BMC Medical Genomics
2008,
1
:17
(19 May 2008)
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Abstract
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38.
Software
Automating dChip: toward reproducible sharing of microarray data analysis
Li C
BMC Bioinformatics
2008,
9
:231
(8 May 2008)
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Abstract
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39.
Research article
Performance of a 70-mer oligonucleotide microarray for genotyping of
Campylobacter jejuni
Rodin S, Andersson AF, Wirta V, Eriksson L, Ljungström M, Björkholm B, Lindmark H, Engstrand L
BMC Microbiology
2008,
8
:73
(8 May 2008)
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Abstract
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40.
Database
RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina
Kalathur RKR, Gagniere N, Berthommier G, Poidevin L, Raffelsberger W, Ripp R, Léveillard T, Poch O
BMC Genomics
2008,
9
:208
(5 May 2008)
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Abstract
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41.
Research article
Overexpression of
Scg5
increases enzymatic activity of PCSK2 and is inversely correlated with body weight in congenic mice
Farber CR, Chitwood J, Lee SN, Verdugo RA, Islas-Trejo A, Rincon G, Lindberg I, Medrano JF
BMC Genetics
2008,
9
:34
(25 April 2008)
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42.
Methodology article
Conserved co-expression for candidate disease gene prioritization
Oti M, van Reeuwijk J, Huynen MA, Brunner HG
BMC Bioinformatics
2008,
9
:208
(23 April 2008)
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Abstract
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43.
Research article
Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening
Bagnaresi P, Moschella A, Beretta O, Vitulli F, Ranalli P, Perata P
BMC Genomics
2008,
9
:176
(16 April 2008)
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44.
Research article
Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis
Blenk S, Engelmann JC, Pinkert S, Weniger M, Schultz J, Rosenwald A, Müller-Hermelink HK, Müller T, Dandekar T
BMC Cancer
2008,
8
:106
(16 April 2008)
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45.
Research article
Transcriptional regulation by Poly(ADP-ribose) polymerase-1 during T cell activation
Saenz L, Lozano JJ, Valdor R, Baroja-Mazo A, Ramirez P, Parrilla P, Aparicio P, Sumoy L, Yélamos J
BMC Genomics
2008,
9
:171
(16 April 2008)
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46.
Methodology article
A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays
Ge H, Cheng C, Li LM
BMC Bioinformatics
2008,
9
:194
(14 April 2008)
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Abstract
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47.
Method
Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays
Lin S, Carvalho B, Cutler DJ, Arking DE, Chakravarti A, Irizarry RA
Genome Biology
2008,
9
:R63
(3 April 2008)
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1 comment
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48.
Research article
A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
Pearson RD
BMC Bioinformatics
2008,
9
:164
(26 March 2008)
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49.
Research
