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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.
Research article
Unsupervised assessment of microarray data quality using a Gaussian mixture model
Howard BE, Sick B, Heber S
BMC Bioinformatics
2009,
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2009,
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2009,
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Similar gene expression profiles of sporadic,
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2009,
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Differential gene expression signatures for cell wall integrity found in chitin synthase II
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Rodríguez-Quiñones JF, Rodríguez-Medina JR
BMC Research Notes
2009,
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Systemic analysis of the response of
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Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity
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Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse
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MicroRNA and gene expression patterns in the differentiation of human embryonic stem cells
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Cbf
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2009,
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BMC Research Notes
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Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees
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BMC Bioinformatics
2009,
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Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis
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Transcriptome profiling of primary murine monocytes, lung macrophages and lung dendritic cells reveals a distinct expression of genes involved in cell trafficking
Zas
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Respiratory Research
2009,
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:2
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Development and application of versatile high density microarrays for genome-wide analysis of
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Bucca G, Laing E, Mersinias V, Allenby N, Hurd D, Holdstock J, Brenner V, Harrison M, Smith CP
Genome Biology
2009,
10
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Detailed transcriptome atlas of the pancreatic beta cell
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BMC Medical Genomics
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10
:22
(14 January 2009)
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Abstract
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BMC Genomics
2009,
10
:5
(6 January 2009)
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42.
Research article
Universal ligation-detection-reaction microarray applied for compost microbes
Hultman J, Ritari J, Romantschuk M, Paulin L, Auvinen P
BMC Microbiology
2008,
8
:237
(30 December 2008)
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43.
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The cancer translational research informatics platform
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BMC Medical Informatics and Decision Making
2008,
8
:60
(24 December 2008)
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Research article
Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3
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BMC Genomics
2008,
9
:601
(16 December 2008)
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Method
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Genome Biology
2008,
9
:R174
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Research article
Global transcriptional responses of
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BMC Microbiology
2008,
8
:209
(2 December 2008)
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Research article
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®
Exon 1.0 ST Affymetrix arrays
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BMC Genomics
2008,
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:571
(28 November 2008)
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48.
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Microarray-based gene set analysis: a comparison of current methods
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BMC Bioinformatics
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Numata K, Yoshida R, Nagasaki M, Saito A, Imoto S, Miyano S
BMC Bioinformatics
2008,
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:494
(26 November 2008)
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Abstract
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50.
Software
EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management
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BMC Bioinformatics
2008,
9
:493
(25 November 2008)
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Abstract
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51.
Research article
Discovery of DNA methylation markers in cervical cancer using relaxation ranking
Ongenaert M, Wisman GBA, Volders HH, Koning AJ, Zee AGJ, van Criekinge W, Schuuring E
BMC Medical Genomics
2008,
1
:57
(24 November 2008)
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Abstract
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52.
Methodology article
Identifying differential correlation in gene/pathway combinations
Braun R, Cope L, Parmigiani G
BMC Bioinformatics
2008,
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:488
(18 November 2008)
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Abstract
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53.
Research article
Transcriptional response of rat frontal cortex following acute
In Vivo
exposure to the pyrethroid insecticides permethrin and deltamethrin
Harrill JA, Li Z, Wright FA, Radio NM, Mundy WR, Tornero-Velez R, Crofton KM
BMC Genomics
2008,
9
:546
(18 November 2008)
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Abstract
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54.
Research article
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
Westholm JO, Xu F, Ronne H, Komorowski J
BMC Bioinformatics
2008,
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:484
(17 November 2008)
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Abstract
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55.
Methodology article
Gene set enrichment analysis for non-monotone association and multiple experimental categories
Lin R, Dai S, Irwin RD, Heinloth AN, Boorman GA, Li L
BMC Bioinformatics
2008,
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:481
(14 November 2008)
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56.
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A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data
Corradi L, Fato M, Porro I, Scaglione S, Torterolo L
BMC Bioinformatics
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Research article
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft
Magda D, Lecane P, Prescott J, Thiemann P, Ma X, Dranchak PK, Toleno DM, Ramaswamy K, Siegmund KD, Hacia JG
BMC Genomics
2008,
9
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(3 November 2008)
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61.
Research article
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
Luo W, Hankenson KD, Woolf PJ
BMC Bioinformatics
2008,
9
:467
(3 November 2008)
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[
1 comment
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62.
Software
minet
: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information
Meyer PE, Lafitte F, Bontempi G
BMC Bioinformatics
2008,
9
:461
(29 October 2008)
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63.
Research article
Genome-wide transcriptional analysis of super-embryogenic
Medicago truncatula
explant cultures
Imin N, Goffard N, Nizamidin M, Rolfe BG
BMC Plant Biology
2008,
8
:110
(27 October 2008)
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64.
Methodology article
Background correction using dinucleotide affinities improves the performance of GCRMA
Gharaibeh RZ, Fodor AA, Gibas CJ
BMC Bioinformatics
2008,
9
:452
(23 October 2008)
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65.
Research article
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age
Lee Y, Scheck AC, Cloughesy TF, Lai A, Dong J, Farooqi HK, Liau LM, Horvath S, Mischel PS, Nelson SF
BMC Medical Genomics
2008,
1
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(21 October 2008)
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66.
Software
CMA
a comprehensive Bioconductor package for supervised classification with high dimensional data
Slawski M, Daumer M, Boulesteix AL
BMC Bioinformatics
2008,
9
:439
(16 October 2008)
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67.
Software
easyExon
A Java-based GUI tool for processing and visualization of Affymetrix exon array data
Chang TY, Li YY, Jen CH, Yang TP, Lin CH, Hsu MT, Wang HW
BMC Bioinformatics
2008,
9
:432
(14 October 2008)
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68.
Research article
Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation
Asare AL, Kolchinsky SA, Gao Z, Wang R, Raddassi K, Bourcier K, Seyfert-Margolis V
BMC Genomics
2008,
9
:474
(10 October 2008)
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69.
Software
R/parallel
speeding up bioinformatics analysis with R
Vera G, Jansen RC, Suppi RL
BMC Bioinformatics
2008,
9
:390
(22 September 2008)
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70.
Research article
Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (
Triticum aestivum
L.) by using Wheat Genome Array
Qin D, Wu H, Peng H, Yao Y, Ni Z, Li Z, Zhou C, Sun Q
BMC Genomics
2008,
9
:432
(22 September 2008)
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71.
Research article
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,
1
:42
(21 September 2008)
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72.
Research article
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
Lange E, Tautenhahn R, Neumann S, Gröpl C
BMC Bioinformatics
2008,
9
:375
(15 September 2008)
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73.
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,
9
:R134
(10 September 2008)
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[
F1000 Biology
]
74.
Research article
Methodology capture: discriminating between the "best" and the rest of community practice
Eales JM, Pinney JW, Stevens RD, Robertson DL
BMC Bioinformatics
2008,
9
:359
(1 September 2008)
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75.
Research article
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,
9
:388
(18 August 2008)
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76.
Research article
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,
9
:381
(9 August 2008)
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[
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77.
Research article
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,
9
:376
(7 August 2008)
[
Abstract
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78.
Research article
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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Abstract
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PubMed
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79.
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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80.
Research article
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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PubMed
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81.
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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82.
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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83.
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
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(17 July 2008)
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84.
Research article
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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Abstract
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85.
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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[
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86.
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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87.
Research
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,
9
:R111
(9 July 2008)
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88.
Research
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,
9
:R108
(8 July 2008)
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89.
Research article
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,
9
:310
(30 June 2008)
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90.
Research
A weighted average difference method for detecting differentially expressed genes from microarray data
Kadota K, Nakai Y, Shimizu K
Algorithms for Molecular Biology
2008,
3
:8
(26 June 2008)
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91.
Research article
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,
9
:302
(25 June 2008)
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92.
Methodology article
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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93.
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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94.
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
(19 June 2008)
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95.
Research article
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,
9
:291
(17 June 2008)
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96.
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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PubMed
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97.
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,
7
:29
(9 June 2008)
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Abstract
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PubMed
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98.
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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99.
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
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(30 May 2008)
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100.
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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Abstract
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101.
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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102.
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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103.
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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104.
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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105.
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
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(19 May 2008)
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106.
Software
Automating dChip: toward reproducible sharing of microarray data analysis
Li C
BMC Bioinformatics
2008,
9
:231
(8 May 2008)
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107.
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
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108.
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
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109.
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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Cited on BioMed Central
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110.
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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111.
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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112.
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
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113.
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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114.
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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Cited on BioMed Central
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115.
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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116.
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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117.
Research
Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells
Mutarelli M, Cicatiello L, Ferraro L, Grober OMV, Ravo M, Facchiano AM, Angelini C, Weisz A
BMC Bioinformatics
2008,
9
(Suppl 2):S12
(26 March 2008)
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118.
Research article
Can subtle changes in gene expression be consistently detected with different microarray platforms?
Pedotti P, 't Hoen PAC, Vreugdenhil E, Schenk GJ, Vossen RHAM, Ariyurek Y, de Hollander M, Kuiper R, van Ommen GJB, den Dunnen JT, Boer JM, de Menezes RX
BMC Genomics
2008,
9
:124
(10 March 2008)
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119.
Methodology article
Empirical Bayes analysis of single nucleotide polymorphisms
Schwender H, Ickstadt K
BMC Bioinformatics
2008,
9
:144
(6 March 2008)
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120.
Research article
Transcriptional profiling of
Medicago truncatula
meristematic root cells
Holmes P, Goffard N, Weiller GF, Rolfe BG, Imin N
BMC Plant Biology
2008,
8
:21
(27 February 2008)
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121.
Methodology article
Exon level integration of proteomics and microarray data
Bitton DA, Okoniewski MJ, Connolly Y, Miller CJ
BMC Bioinformatics
2008,
9
:118
(25 February 2008)
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122.
Research article
Analysis of the retinal gene expression profile after hypoxic preconditioning identifies candidate genes for neuroprotection
Thiersch M, Raffelsberger W, Frigg R, Samardzija M, Wenzel A, Poch O, Grimm C
BMC Genomics
2008,
9
:73
(8 February 2008)
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123.
Research article
Transcriptomic dissection of tongue squamous cell carcinoma
Ye H, Yu T, Temam S, Ziober BL, Wang J, Schwartz JL, Mao L, Wong DT, Zhou X
BMC Genomics
2008,
9
:69
(6 February 2008)
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124.
Research article
Statistical issues in the analysis of Illumina data
Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S, Ritchie ME
BMC Bioinformatics
2008,
9
:85
(6 February 2008)
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125.
Methodology article
A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes
Carter B, Wu G, Woodward MJ, Anjum MF
BMC Genomics
2008,
9
:53
(29 January 2008)
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126.
Research article
Phosphatidylinositol 3-kinase signaling in proliferating cells maintains an anti-apoptotic transcriptional program mediated by inhibition of FOXO and non-canonical activation of NF
B transcription factors
Terragni J, Graham JR, Adams KW, Schaffer ME, Tullai JW, Cooper GM
BMC Cell Biology
2008,
9
:6
(28 January 2008)
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127.
Research article
Global mRNA expression analysis in myosin II deficient strains of
Saccharomyces cerevisiae
reveals an impairment of cell integrity functions
Rodríguez-Quiñones JF, Irizarry RA, Díaz-Blanco NL, Rivera-Molina FE, Gómez-Garzón D, Rodríguez-Medina JR
BMC Genomics
2008,
9
:34
(23 January 2008)
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128.
Research
Gene expression variation in African and European populations of
Drosophila melanogaster
Hutter S, Saminadin-Peter SS, Stephan W, Parsch J
Genome Biology
2008,
9
:R12
(21 January 2008)
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129.
Software
Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'
Kuhn A, Luthi-Carter R, Delorenzi M
BMC Bioinformatics
2008,
9
:26
(17 January 2008)
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130.
Research article
Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis
Jin H, Vacic V, Girke T, Lonardi S, Zhu JK
BMC Molecular Biology
2008,
9
:6
(14 January 2008)
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131.
Research article
Coordinated evolution of co-expressed gene clusters in the
Drosophila
transcriptome
Mezey JG, Nuzhdin SV, Ye F, Jones CD
BMC Evolutionary Biology
2008,
8
:2
(7 January 2008)
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132.
Research article
Evaluation of time profile reconstruction from complex two-color microarray designs
Fierro AC, Thuret R, Engelen K, Bernot G, Marchal K, Pollet N
BMC Bioinformatics
2008,
9
:1
(3 January 2008)
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133.
Research article
Profiling sex-biased gene expression during parthenogenetic reproduction in
Daphnia pulex
Eads BD, Colbourne JK, Bohuski E, Andrews J
BMC Genomics
2007,
8
:464
(18 December 2007)
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134.
Proceedings
Mapping of
trans
-acting regulatory factors from microarray data
McClintick JN, Liu Y, Edenberg HJ
BMC Proceedings
2007,
1
(Suppl 1):S155
(18 December 2007)
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135.
Proceedings
Effects on linkage analyses of different Affymetrix expression measures as quantitative trait phenotypes
Peralta JM, Almasy L
BMC Proceedings
2007,
1
(Suppl 1):S158
(18 December 2007)
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136.
Research article
Unravelling the molecular control of calvarial suture fusion in children with craniosynostosis
Coussens AK, Wilkinson CR, Hughes IP, Morris CP, van Daal A, Anderson PJ, Powell BC
BMC Genomics
2007,
8
:458
(12 December 2007)
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137.
Research article
Variable sexually dimorphic gene expression in laboratory strains of
Drosophila melanogaster
Baker DA, Meadows LA, Wang J, Dow JAT, Russell S
BMC Genomics
2007,
8
:454
(10 December 2007)
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138.
Research article
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
Casneuf T, Van de Peer Y, Huber W
BMC Bioinformatics
2007,
8
:461
(26 November 2007)
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139.
Research article
Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison
Pilati S, Perazzolli M, Malossini A, Cestaro A, Demattè L, Fontana P, Dal Ri A, Viola R, Velasco R, Moser C
BMC Genomics
2007,
8
:428
(22 November 2007)
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140.
Methodology article
Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana
Redestig H, Weicht D, Selbig J, Hannah MA
BMC Bioinformatics
2007,
8
:454
(18 November 2007)
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141.
Research article
Application of a correlation correction factor in a microarray cross-platform reproducibility study
Archer KJ, Dumur CI, Taylor GS, Chaplin MD, Guiseppi-Elie A, Grant G, Ferreira-Gonzalez A, Garrett CT
BMC Bioinformatics
2007,
8
:447
(15 November 2007)
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142.
Research article
Vascular microarray profiling in two models of hypertension identifies caveolin-1, Rgs2 and Rgs5 as antihypertensive targets
Grayson TH, Ohms SJ, Brackenbury TD, Meaney KR, Peng K, Pittelkow YE, Wilson SR, Sandow SL, Hill CE
BMC Genomics
2007,
8
:404
(7 November 2007)
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143.
Research article
Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets
Gormley M, Dampier W, Ertel A, Karacali B, Tozeren A
BMC Bioinformatics
2007,
8
:415
(26 October 2007)
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144.
Research article
Bioinformatic identification of novel putative photoreceptor specific
cis
-elements
Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM
BMC Bioinformatics
2007,
8
:407
(22 October 2007)
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145.
Research
Gene expression profiling of
Hfe
-/-
liver and duodenum in mouse strains with differing susceptibilities to iron loading: identification of transcriptional regulatory targets of Hfe and potential hemochromatosis modifiers
Coppin H, Darnaud V, Kautz L, Meynard D, Aubry M, Mosser J, Martinez M, Roth MP
Genome Biology
2007,
8
:R221
(18 October 2007)
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146.
Methodology article
Weighted analysis of general microarray experiments
Sjögren A, Kristiansson E, Rudemo M, Nerman O
BMC Bioinformatics
2007,
8
:387
(15 October 2007)
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147.
Research
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype
Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin SF, Dunning MJ, Barbosa-Morais NL, Teschendorff AE, Green AR, Ellis IO, Tavaré S, Caldas C, Miska EA
Genome Biology
2007,
8
:R214
(8 October 2007)
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148.
Research
Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia
Cohen J, Van Marter LJ, Sun Y, Allred E, Leviton A, Kohane IS
Genome Biology
2007,
8
:R210
(4 October 2007)
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149.
Review
Graphs in molecular biology
Huber W, Carey VJ, Long L, Falcon S, Gentleman R
BMC Bioinformatics
2007,
8
(Suppl 6):S8
(27 September 2007)
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150.
Research article
Microarray gene expression profiling of osteoarthritic bone suggests altered bone remodelling, WNT and transforming growth factor-
/bone morphogenic protein signalling
Hopwood B, Tsykin A, Findlay DM, Fazzalari NL
Arthritis Research & Therapy
2007,
9
:R100
(27 September 2007)
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151.
Methodology article
Linking microarray reporters with protein functions
Gaj S, van Erk A, van Haaften RIM, Evelo CTA
BMC Bioinformatics
2007,
8
:360
(26 September 2007)
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152.
Research
Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression
Beane J, Sebastiani P, Liu G, Brody JS, Lenburg ME, Spira A
Genome Biology
2007,
8
:R201
(25 September 2007)
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153.
Research article
Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes
Ellegren H, Hultin-Rosenberg L, Brunström B, Dencker L, Kultima K, Scholz B
BMC Biology
2007,
5
:40
(20 September 2007)
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154.
Research article
A framework for significance analysis of gene expression data using dimension reduction methods
Gidskehaug L, Anderssen E, Flatberg A, Alsberg BK
BMC Bioinformatics
2007,
8
:346
(18 September 2007)
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155.
Research article
Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina
Arvas M, Kivioja T, Mitchell A, Saloheimo M, Ussery D, Penttila M, Oliver S
BMC Genomics
2007,
8
:325
(17 September 2007)
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156.
Method
Identification of novel stem cell markers using gap analysis of gene expression data
Krzyzanowski PM, Andrade-Navarro MA
Genome Biology
2007,
8
:R193
(17 September 2007)
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157.
Research article
Aging impacts transcriptomes but not genomes of hormone-dependent breast cancers
Yau C, Fedele V, Roydasgupta R, Fridlyand J, Hubbard A, Gray JW, Chew K, Dairkee SH, Moore DH, Schittulli F, Tommasi S, Paradiso A, Albertson DG, Benz CC
Breast Cancer Research
2007,
9
:R59
(12 September 2007)
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158.
Software
PyCogent: a toolkit for making sense from sequence
Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA
Genome Biology
2007,
8
:R171
(21 August 2007)
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159.
Research article
Gene expression of transporters and phase I/II metabolic enzymes in murine small intestine during fasting
van den Bosch HM, Bünger M, de Groot PJ, van der Meijde J, Hooiveld GJEJ, Müller M
BMC Genomics
2007,
8
:267
(7 August 2007)
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160.
Research article
The utility of MAS5 expression summary and detection call algorithms
Pepper SD, Saunders EK, Edwards LE, Wilson CL, Miller CJ
BMC Bioinformatics
2007,
8
:273
(30 July 2007)
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161.
Research
Global analysis of patterns of gene expression during
Drosophila
embryogenesis
Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM
Genome Biology
2007,
8
:R145
(23 July 2007)
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162.
Research article
Whole genome expression profiling reveals a significant role for immune function in human abdominal aortic aneurysms
Lenk GM, Tromp G, Weinsheimer S, Gatalica Z, Berguer R, Kuivaniemi H
BMC Genomics
2007,
8
:237
(16 July 2007)
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163.
Methodology article
Post hoc
pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data
Hulshizer R, Blalock EM
BMC Bioinformatics
2007,
8
:240
(5 July 2007)
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164.
Methodology article
A transversal approach to predict gene product networks from ontology-based similarity
Chabalier J, Mosser J, Burgun A
BMC Bioinformatics
2007,
8
:235
(2 July 2007)
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165.
Research
Morphine effects on striatal transcriptome in mice
Korostynski M, Piechota M, Kaminska D, Solecki W, Przewlocki R
Genome Biology
2007,
8
:R128
(28 June 2007)
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166.
Software
Ringo
an R/Bioconductor package for analyzing ChIP-chip readouts
Toedling J, Sklyar O, Huber W
BMC Bioinformatics
2007,
8
:221
(26 June 2007)
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167.
Method
Correcting for sequence biases in present/absent calls
Schuster EF, Blanc E, Partridge L, Thornton JM
Genome Biology
2007,
8
:R125
(26 June 2007)
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168.
Research
Estimation and correction of non-specific binding in a large-scale spike-in experiment
Schuster EF, Blanc E, Partridge L, Thornton JM
Genome Biology
2007,
8
:R126
(26 June 2007)
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169.
Research article
Microarray analysis of gene expression induced by sexual contact in
Schistosoma mansoni
Waisberg M, Lobo FP, Cerqueira GC, Passos LKJ, Carvalho OS, Franco GR, El-Sayed NM
BMC Genomics
2007,
8
:181
(20 June 2007)
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170.
Research
Genetic background influences murine prostate gene expression: implications for cancer phenotypes
Bianchi-Frias D, Pritchard C, Mecham BH, Coleman IM, Nelson PS
Genome Biology
2007,
8
:R117
(18 June 2007)
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171.
Method
Celsius: a community resource for Affymetrix microarray data
Day A, Carlson MRJ, Dong J, O'Connor BD, Nelson SF
Genome Biology
2007,
8
:R112
(14 June 2007)
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172.
Research article
Genome-wide changes accompanying knockdown of fatty acid synthase in breast cancer
Knowles LM, Smith JW
BMC Genomics
2007,
8
:168
(12 June 2007)
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173.
Research article
Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression
Funari VA, Day A, Krakow D, Cohn ZA, Chen Z, Nelson SF, Cohn DH
BMC Genomics
2007,
8
:165
(12 June 2007)
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174.
Research article
Sensitive and robust gene expression changes in fish exposed to estrogen
a microarray approach
Gunnarsson L, Kristiansson E, Förlin L, Nerman O, Larsson DGJ
BMC Genomics
2007,
8
:149
(7 June 2007)
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175.
Research article
Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes
Warnat P, Oberthuer A, Fischer M, Westermann F, Eils R, Brors B
BMC Cancer
2007,
7
:89
(25 May 2007)
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176.
Research
Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray
Zhang X, De la Cruz O, Pinto JM, Nicolae D, Firestein S, Gilad Y
Genome Biology
2007,
8
:R86
(17 May 2007)
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177.
Software
An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
Okoniewski MJ, Yates T, Dibben S, Miller CJ
Genome Biology
2007,
8
:R79
(11 May 2007)
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178.
Research
Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study
Rustici G, van Bakel H, Lackner DH, Holstege FC, Wijmenga C, Bähler J, Brazma A
Genome Biology
2007,
8
:R73
(3 May 2007)
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179.
Research
Functional dissection of the
ash2
and
ash1
transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions
Beltran S, Angulo M, Pignatelli M, Serras F, Corominas M
Genome Biology
2007,
8
:R67
(28 April 2007)
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180.
Research
Molecular characterisation of the early response in pigs to experimental infection with
Actinobacillus pleuropneumoniae
using cDNA microarrays
Hedegaard J, Skovgaard K, Mortensen S, Sørensen P, Jensen TK, Hornshøj H, Bendixen C, Heegaard PMH
Acta Veterinaria Scandinavica
2007,
49
:11
(27 April 2007)
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181.
Methodology article
Supervised multivariate analysis of sequence groups to identify specificity determining residues
Wallace IM, Higgins DG
BMC Bioinformatics
2007,
8
:135
(23 April 2007)
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182.
Research
Global analyses of mRNA translational control during early
Drosophila
embryogenesis
Qin X, Ahn S, Speed TP, Rubin GM
Genome Biology
2007,
8
:R63
(22 April 2007)
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183.
Research article
Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent
Gaile DP, Miecznikowski JC
BMC Genomics
2007,
8
:105
(19 April 2007)
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184.
Methodology article
A full Bayesian hierarchical mixture model for the variance of gene differential expression
Manda SOM, Walls RE, Gilthorpe MS
BMC Bioinformatics
2007,
8
:124
(17 April 2007)
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185.
Research article
Identification of a robust gene signature that predicts breast cancer outcome in independent data sets
Korkola JE, Blaveri E, DeVries S, Moore DH, Hwang ES, Chen YY, Estep ALH, Chew KL, Jensen RH, Waldman FM
BMC Cancer
2007,
7
:61
(11 April 2007)
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186.
Methodology article
Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays
Hess A, Iyer H
BMC Genomics
2007,
8
:96
(9 April 2007)
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187.
Research
Integration of
Arabidopsis thaliana
stress-related transcript profiles, promoter structures, and cell-specific expression
Ma S, Bohnert HJ
Genome Biology
2007,
8
:R49
(4 April 2007)
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[
F1000 Biology
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188.
Methodology article
Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
Lu J, Lee JC, Salit ML, Cam MC
BMC Bioinformatics
2007,
8
:108
(29 March 2007)
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189.
Research article
Gene function in early mouse embryonic stem cell differentiation
Sene KH, Porter CJ, Palidwor G, Perez-Iratxeta C, Muro EM, Campbell PA, Rudnicki MA, Andrade-Navarro MA
BMC Genomics
2007,
8
:85
(29 March 2007)
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190.
Research article
Gene expression profiling of aging reveals activation of a p53-mediated transcriptional program
Edwards MG, Anderson RM, Yuan M, Kendziorski CM, Weindruch R, Prolla TA
BMC Genomics
2007,
8
:80
(23 March 2007)
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191.
Research article
A comparative genomics approach to identifying the plasticity transcriptome
Pfenning AR, Schwartz R, Barth AL
BMC Neuroscience
2007,
8
:20
(13 March 2007)
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192.
Research
Cross platform microarray analysis for robust identification of differentially expressed genes
Bosotti R, Locatelli G, Healy S, Scacheri E, Sartori L, Mercurio C, Calogero R, Isacchi A
BMC Bioinformatics
2007,
8
(Suppl 1):S5
(8 March 2007)
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193.
Research
A Grid-based solution for management and analysis of microarrays in distributed experiments
Porro I, Torterolo L, Corradi L, Fato M, Papadimitropoulos A, Scaglione S, Schenone A, Viti F
BMC Bioinformatics
2007,
8
(Suppl 1):S7
(8 March 2007)
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194.
Research article
Intercenter reliability and validity of the rhesus macaque GeneChip
Duan F, Spindel ER, Li YH, Norgren RB
BMC Genomics
2007,
8
:61
(28 February 2007)
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195.
Research article
Normalization of low-density microarray using external spike-in controls: analysis of macrophage cell lines expression profile
Fardin P, Moretti S, Biasotti B, Ricciardi A, Bonassi S, Varesio L
BMC Genomics
2007,
8
:17
(17 January 2007)
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196.
Research article
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
Stalteri MA, Harrison AP
BMC Bioinformatics
2007,
8
:13
(15 January 2007)
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197.
Method
Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes
Oshlack A, Emslie D, Corcoran LM, Smyth GK
Genome Biology
2007,
8
:R2
(4 January 2007)
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198.
Research article
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Sartor MA, Tomlinson CR, Wesselkamper SC, Sivaganesan S, Leikauf GD, Medvedovic M
BMC Bioinformatics
2006,
7
:538
(19 December 2006)
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199.
Software
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments
Usadel B, Nagel A, Steinhauser D, Gibon Y, Bläsing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M
BMC Bioinformatics
2006,
7
:535
(18 December 2006)
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200.
Research article
Effect of infliximab on mRNA expression profiles in synovial tissue of rheumatoid arthritis patients
Lindberg J, af Klint E, Catrina AI, Nilsson P, Klareskog L, Ulfgren AK, Lundeberg J
Arthritis Research & Therapy
2006,
8
:R179
(29 November 2006)
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201.
Research article
Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria
Lovegrove FE, Peña-Castillo L, Mohammad N, Liles WC, Hughes TR, Kain KC
BMC Genomics
2006,
7
:295
(22 November 2006)
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202.
Software
CoXpress: differential co-expression in gene expression data
Watson M
BMC Bioinformatics
2006,
7
:509
(20 November 2006)
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203.
Method
ProCAT: a data analysis approach for protein microarrays
Zhu X, Gerstein M, Snyder M
Genome Biology
2006,
7
:R110
(16 November 2006)
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204.
Methodology
The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data
Woody OZ, Nadon R
Source Code for Biology and Medicine
2006,
1
:6
(8 November 2006)
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205.
Research
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics
Vandepoele K, Casneuf T, Van de Peer Y
Genome Biology
2006,
7
:R103
(7 November 2006)
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206.
Research
Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
Ertel A, Verghese A, Byers SW, Ochs M, Tozeren A
Molecular Cancer
2006,
5
:55
(2 November 2006)
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207.
Software
Goulphar: rapid access and expertise for standard two-color microarray normalization methods
Lemoine S, Combes F, Servant N, Le Crom S
BMC Bioinformatics
2006,
7
:467
(23 October 2006)
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Abstract
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208.
Methodology article
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database
Katz S, Irizarry RA, Lin X, Tripputi M, Porter MW
BMC Bioinformatics
2006,
7
:464
(23 October 2006)
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209.
Research article
Gene expression signatures of morphologically normal breast tissue identify basal-like tumors
Finak G, Sadekova S, Pepin F, Hallett M, Meterissian S, Halwani F, Khetani K, Souleimanova M, Zabolotny B, Omeroglu A, Park M
Breast Cancer Research
2006,
8
:R58
(20 October 2006)
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210.
Research article
Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma
Diboun I, Wernisch L, Orengo CA, Koltzenburg M
BMC Genomics
2006,
7
:252
(9 October 2006)
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211.
Methodology article
Analysis with respect to instrumental variables for the exploration of microarray data structures
Baty F, Facompré M, Wiegand J, Schwager J, Brutsche MH
BMC Bioinformatics
2006,
7
:422
(29 September 2006)
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