BMC Genomics

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Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations

Richard Shippy, Timothy J Sendera*, Randall Lockner, Chockalingam Palaniappan, Tamma Kaysser-Kranich, George Watts and John Alsobrook

BMC Genomics 2004, 5:61 doi:10.1186/1471-2164-5-61

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Methodology article   Open Access

An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays

Erdem Arslan, Ian J Laurenzi BMC Bioinformatics 2009, 10:411 (10 December 2009)

Methodology article   Open Access Highly Accessed

Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis

Yongxin Chen, Jonathan AL Gelfond, Linda M McManus, Paula K Shireman BMC Genomics 2009, 10:407 (28 August 2009)

Research article   Open Access

Platform dependence of inference on gene-wise and gene-set involvement in human lung development

Rose Du, Kelan Tantisira, Vincent Carey, Soumyaroop Bhattacharya, Stephanie Metje, Alvin T Kho, Barbara J Klanderman, Roger Gaedigk, Ross Lazarus, Thomas J Mariani, J Steven Leeder, Scott T Weiss BMC Bioinformatics 2009, 10:189 (19 June 2009)

Methodology article   Open Access Highly Accessed

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes

Steven P Wilder, Pamela J Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, Dominique Gauguier BMC Genomics 2009, 10:63 (5 February 2009)

Proceedings   Open Access

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

Leming Shi, Wendell D Jones, Roderick V Jensen, Stephen C Harris, Roger G Perkins, Federico M Goodsaid, Lei Guo, Lisa J Croner, Cecilie Boysen, Hong Fang, Feng Qian, Shashi Amur, Wenjun Bao, Catalin C Barbacioru, Vincent Bertholet, Xiaoxi Cao, Tzu-Ming Chu, Patrick J Collins, Xiao-hui Fan, Felix W Frueh et al. BMC Bioinformatics 2008, 9(Suppl 9):S10 (12 August 2008)

Research article   Open Access Highly Accessed

Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors

LO Baumbusch, J Aarøe, FE Johansen, J Hicks, H Sun, L Bruhn, K Gunderson, B Naume, VN Kristensen, K Liestøl, A-L Børresen-Dale, OC Lingjærde BMC Genomics 2008, 9:379 (8 August 2008)

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Characterization of a newly developed chicken 44K Agilent microarray

Xianyao Li, Hsin-I Chiang, James Zhu, Scot E Dowd, Huaijun Zhou BMC Genomics 2008, 9:60 (31 January 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)

Research article   Open Access

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

Joseph C Lee, David Stiles, Jun Lu, Margaret C Cam BMC Genomics 2007, 8:284 (20 August 2007)

Research article   Open Access Highly Accessed

The utility of MAS5 expression summary and detection call algorithms

Stuart D Pepper, Emma K Saunders, Laura E Edwards, Claire L Wilson, Crispin J Miller BMC Bioinformatics 2007, 8:273 (30 July 2007)

Research   Open Access Highly Accessed

Cross platform microarray analysis for robust identification of differentially expressed genes

Roberta Bosotti, Giuseppe Locatelli, Sandra Healy, Emanuela Scacheri, Luca Sartori, Ciro Mercurio, Raffaele Calogero, Antonella Isacchi BMC Bioinformatics 2007, 8(Suppl 1):S5 (8 March 2007)

Methodology article   Open Access

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David DL Bowtell, Gordon K Smyth BMC Bioinformatics 2006, 7:511 (22 November 2006)

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Mining housekeeping genes with a Naive Bayes classifier

Luna De Ferrari, Stuart Aitken BMC Genomics 2006, 7:277 (30 October 2006)

Research article   Open Access

An analysis of intra array repeats: the good, the bad and the non informative

Yedid Elbez, Shlomit Farkash-Amar, Itamar Simon BMC Genomics 2006, 7:136 (5 June 2006)

Research article   Open Access Highly Accessed

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays

Yulei Wang, Catalin Barbacioru, Fiona Hyland, Wenming Xiao, Kathryn L Hunkapiller, Julie Blake, Frances Chan, Carolyn Gonzalez, Lu Zhang, Raymond R Samaha BMC Genomics 2006, 7:59 (21 March 2006)

Research article   Open Access Highly Accessed

Comparison of the latest commercial short and long oligonucleotide microarray technologies

Aurélien de Reyniès, Daniela Geromin, Jean-Michel Cayuela, Fabien Petel, Philippe Dessen, François Sigaux, David S Rickman BMC Genomics 2006, 7:51 (15 March 2006)

Primary research   Open Access Highly Accessed

Antineoplastic effects of the DNA methylation inhibitor hydralazine and the histone deacetylase inhibitor valproic acid in cancer cell lines

Alma Chavez-Blanco, Carlos Perez-Plasencia, Enrique Perez-Cardenas, Claudia Carrasco-Legleu, Edgar Rangel-Lopez, Blanca Segura-Pacheco, Lucia Taja-Chayeb, Catalina Trejo-Becerril, Aurora Gonzalez-Fierro, Myrna Candelaria, Gustavo Cabrera, Alfonso Duenas-Gonzalez Cancer Cell International 2006, 6:2 (31 January 2006)

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.

Research article   Open Access Highly Accessed

Comparison of normalization methods for CodeLink Bioarray data

Wei Wu, Nilesh Dave, George C Tseng, Thomas Richards, Eric P Xing, Naftali Kaminski BMC Bioinformatics 2005, 6:309 (28 December 2005)

Software   Open Access

Storing, linking, and mining microarray databases using SRS

Antoine Veldhoven, Don de Lange, Marcel Smid, Victor de Jager, Jan A Kors, Guido Jenster BMC Bioinformatics 2005, 6:192 (27 July 2005)

Proceedings   Open Access

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

Leming Shi, Weida Tong, Hong Fang, Uwe Scherf, Jing Han, Raj K Puri, Felix W Frueh, Federico M Goodsaid, Lei Guo, Zhenqiang Su, Tao Han, James C Fuscoe, Z Alex Xu, Tucker A Patterson, Huixiao Hong, Qian Xie, Roger G Perkins, James J Chen, Daniel A Casciano BMC Bioinformatics 2005, 6(Suppl 2):S12 (15 July 2005)

Methodology article   Open Access Highly Accessed

Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips

Fred van Ruissen, Jan M Ruijter, Gerben J Schaaf, Lida Asgharnegad, Danny A Zwijnenburg, Marcel Kool, Frank Baas BMC Genomics 2005, 6:91 (14 June 2005)