BMC Bioinformatics

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Probe set algorithms: is there a rational best bet?

Jinwook Seo and Eric P Hoffman*

BMC Bioinformatics 2006, 7:395 doi:10.1186/1471-2105-7-395

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BioMed Central: 14 citations

Methodology article   Open Access Highly Accessed

Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements

Jakub Mieczkowski, Magdalena E Tyburczy, Michal Dabrowski, Piotr Pokarowski BMC Bioinformatics 2010, 11:104 (24 February 2010)

Research article   Open Access Highly Accessed

Prioritizing genes for follow-up from genome wide association studies using information on gene expression in tissues relevant for type 2 diabetes mellitus

Hemang Parikh, Valeriya Lyssenko, Leif C Groop BMC Medical Genomics 2009, 2:72 (31 December 2009)

Methodology article   Open Access

A white-box approach to microarray probe response characterization: the BaFL pipeline

Kevin J Thompson, Hrishikesh Deshmukh, Jeffrey L Solka, Jennifer W Weller BMC Bioinformatics 2009, 10:449 (29 December 2009)

Research article   Open Access Highly Accessed

Novel transcriptional profile in wrist muscles from cerebral palsy patients

Lucas R Smith, Eva Pontén, Yvette Hedström, Samuel R Ward, Henry G Chambers, Shankar Subramaniam, Richard L Lieber BMC Medical Genomics 2009, 2:44 (14 July 2009)

Research   Open Access

Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations

Reija Autio, Sami Kilpinen, Matti Saarela, Olli Kallioniemi, Sampsa Hautaniemi, Jaakko Astola BMC Bioinformatics 2009, 10(Suppl 1):S24 (30 January 2009)

Research article   Open Access Highly Accessed

Infection and genotype remodel the entire soybean transcriptome

Lecong Zhou, Santiago X Mideros, Lei Bao, Regina Hanlon, Felipe D Arredondo, Sucheta Tripathy, Konstantinos Krampis, Adam Jerauld, Clive Evans, Steven K St Martin, MA Saghai Maroof, Ina Hoeschele, Anne E Dorrance, Brett M Tyler BMC Genomics 2009, 10:49 (26 January 2009)

Infection of soybean by the fungal pathogen Phytophthora causes low-amplitude gene-expression changes affecting 97-99% of the genome, as detected using 648 soybean GeneChips including 72 biological replicates to produce unprecedented statistical sensitivity.

Method   Open Access Highly Accessed

Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues

Sami Kilpinen, Reija Autio, Kalle Ojala, Kristiina Iljin, Elmar Bucher, Henri Sara, Tommi Pisto, Matti Saarela, Rolf I Skotheim, Mari Björkman, John-Patrick Mpindi, Saija Haapa-Paananen, Paula Vainio, Henrik Edgren, Maija Wolf, Jaakko Astola, Matthias Nees, Sampsa Hautaniemi, Olli Kallioniemi Genome Biology 2008, 9:R139 (19 September 2008)

A method for the comparison of mRNA expression levels of most human genes across gene expression array experiments, and a database of the results, are presented.

Research article   Open Access

Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle

Siriluck Ponsuksili, Elisabeth Jonas, Eduard Murani, Chirawath Phatsara, Tiranun Srikanchai, Christina Walz, Manfred Schwerin, Karl Schellander, Klaus Wimmers BMC Genomics 2008, 9:367 (31 July 2008)

Research article   Open Access Highly Accessed

Methods for evaluating gene expression from Affymetrix microarray datasets

Ning Jiang, Lindsey J Leach, Xiaohua Hu, Elena Potokina, Tianye Jia, Arnis Druka, Robbie Waugh, Michael J Kearsey, Zewei W Luo BMC Bioinformatics 2008, 9:284 (17 June 2008)

Comparison of the most commonly used statistical methods for assessing differential gene expression from Affymetrix microarrays on a high-quality dataset shows that PDNN is the best performer, clearly superior to the standard Affymetrix MAS5.0 method.

Research   Open Access

ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses

Todd H Stokes, JT Torrance, Henry Li, May D Wang BMC Bioinformatics 2008, 9(Suppl 6):S18 (28 May 2008)

Research article   Open Access

Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection

Neil S Graham, Martin R Broadley, John P Hammond, Philip J White, Sean T May BMC Genomics 2007, 8:344 (1 October 2007)

Research article   Open Access

Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips

Andrew P Harrison, Caroline E Johnston, Christine A Orengo BMC Bioinformatics 2007, 8:195 (11 June 2007)

Research article   Open Access

Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine

Dorothy E Grice, Ilkka Reenilä, Pekka T Männistö, Andrew I Brooks, George G Smith, Greg T Golden, Joseph D Buxbaum, Wade H Berrettini BMC Genomics 2007, 8:76 (16 March 2007)

Research   Open Access

Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling

Adrian Liston, Kristine Hardy, Yvonne Pittelkow, Susan R Wilson, Lydia E Makaroff, Aude M Fahrer, Christopher C Goodnow Genome Biology 2007, 8:R12 (21 January 2007)

A transcription profiling study, together with genetic linkage data, provides a molecular map of the T-cell negative selection response in vivo.