Genome Biology

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Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays

Hong-Ying Wang, Renae L Malek, Anne E Kwitek, Andrew S Greene, Truong V Luu, Babak Behbahani, Bryan Frank, John Quackenbush and Norman H Lee*

Genome Biology 2003, 4:R5 doi:10.1186/gb-2003-4-1-r5

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Research article   Open Access

Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses

Zheng Wang, Anthony P Malanoski, Baochuan Lin, Carolyn Kidd, Nina C Long, Kate M Blaney, Dzung C Thach, Clark Tibbetts, David A Stenger BMC Genomics 2008, 9:577 (1 December 2008)

Short Report   Open Access

Advanced spot quality analysis in two-colour microarray experiments

Mikalai Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar, Evelyne Friederich BMC Research Notes 2008, 1:80 (17 September 2008)

This article is part of a collection on Microarray normalization...

Research   Open Access Highly Accessed

Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila

Enrique Blanco, Miguel Pignatelli, Sergi Beltran, Adrià Punset, Silvia Pérez-Lluch, Florenci Serras, Roderic Guigó, Montserrat Corominas Genome Biology 2008, 9:R134 (10 September 2008)

Transcriptional analysis of chromatin regulator mutants in Drosophila melanogaster identified clusters of functionally related genes conserved in other insect species.

Methodology article   Open Access

MAID : An effect size based model for microarray data integration across laboratories and platforms

Ivan Borozan, Limin Chen, Bryan Paeper, Jenny E Heathcote, Aled M Edwards, Michael Katze, Zhaolei Zhang, Ian D McGilvray BMC Bioinformatics 2008, 9:305 (10 July 2008)

Research article   Open Access

Transcriptomic analysis of the dialogue between Pseudorabies virus and porcine epithelial cells during infection

Laurence Flori, Claire Rogel-Gaillard, Marielle Cochet, Gaetan Lemonnier, Karine Hugot, Patrick Chardon, Stéphane Robin, François Lefèvre BMC Genomics 2008, 9:123 (10 March 2008)

Methodology article   Open Access

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton

Jean Muller, André Mehlen, Guillaume Vetter, Mikalai Yatskou, Arnaud Muller, Frédéric Chalmel, Olivier Poch, Evelyne Friederich, Laurent Vallar BMC Genomics 2007, 8:294 (29 August 2007)

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Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions

Sergi Beltran, Mireia Angulo, Miguel Pignatelli, Florenci Serras, Montserrat Corominas Genome Biology 2007, 8:R67 (28 April 2007)

Analysis of the gene expression profiles of wing imaginal discs from ash2 and ash1 mutants shows that they are highly similar, supporting a model in which they act together to maintain stable states of transcription.

Methodology article   Open Access Highly Accessed

Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis

Nils E Magnusson, Alessandra K Cardozo, Mogens Kruhøffer, Decio L Eizirik, Torben F Ørntoft, Jens L Jensen BMC Bioinformatics 2005, 6:311 (29 December 2005)

A freely available microarray chip of 574 apoptosis-responsive genes in rat pancreatic beta cells has been developed and validated, and may ultimately offer insights into the unbalanced regulation of beta-cell apoptosis in diabetes.

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Three microarray platforms: an analysis of their concordance in profiling gene expression

David Petersen, GVR Chandramouli, Joel Geoghegan, Joanne Hilburn, Jonathon Paarlberg, Chang Kim, David Munroe, Lisa Gangi, Jing Han, Raj Puri, Lou Staudt, John Weinstein, J Carl Barrett, Jeffrey Green, Ernest S Kawasaki BMC Genomics 2005, 6:63 (5 May 2005)

Research article   Open Access

Secondary structure in the target as a confounding factor in synthetic oligomer microarray design

Vladyslava G Ratushna, Jennifer W Weller, Cynthia J Gibas BMC Genomics 2005, 6:31 (8 March 2005)

Methodology article   Open Access Highly Accessed

A robust method for the amplification of RNA in the sense orientation

Nicholas F Marko, Bryan Frank, John Quackenbush, Norman H Lee BMC Genomics 2005, 6:27 (1 March 2005)

Methodology article   Open Access Highly Accessed

Evaluation of sense-strand mRNA amplification by comparative quantitative PCR

Loyal A Goff, Jessica Bowers, Jaime Schwalm, Kevin Howerton, Robert C Getts, Ronald P Hart BMC Genomics 2004, 5:76 (6 October 2004)

Methodology article   Open Access

Immobilized probe and glass surface chemistry as variables in microarray fabrication

Martin J Hessner, Lisa Meyer, Jennifer Tackes, Sanaa Muheisen, Xujing Wang BMC Genomics 2004, 5:53 (4 August 2004)

Research article   Open Access

Improving signal intensities for genes with low-expression on oligonucleotide microarrays

Latha Ramdas, David E Cogdell, Jack Y Jia, Ellen E Taylor, Valerie R Dunmire, Limei Hu, Stanley R Hamilton, Wei Zhang BMC Genomics 2004, 5:35 (14 June 2004)

Increasing the length of micoarray oligonucleotide probes to 70 nucleotides has a significant benefit in the detection of low-expressing genes, while high-expressing gene signals are increased to a lesser degree.

Research   Open Access

Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis

Elodie Ghedin, Anne Pumfery, Cynthia de la Fuente, Karen Yao, Naomi Miller, Vincent Lacoste, John Quackenbush, Steven Jacobson, Fatah Kashanchi Retrovirology 2004, 1:10 (25 May 2004)