BMC Bioinformatics

official impact factor 3.03

Open Access

Correlation test to assess low-level processing of high-density oligonucleotide microarray data

Alexander Ploner*, Lance D Miller, Per Hall, Jonas Bergh and Yudi Pawitan

BMC Bioinformatics 2005, 6:80 doi:10.1186/1471-2105-6-80

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Research article   Open Access

Expression signatures of TP53 mutations in serous ovarian cancers

Marcus Q Bernardini, Tsukasa Baba, Paula S Lee, Jason C Barnett, Gregory P Sfakianos, Angeles Secord, Susan K Murphy, Edwin Iversen, Jeffrey R Marks, Andrew Berchuck BMC Cancer 2010, 10:237 (26 May 2010)

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)

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 Highly Accessed

Normalization of oligonucleotide arrays based on the least-variant set of genes

Stefano Calza, Davide Valentini, Yudi Pawitan BMC Bioinformatics 2008, 9:140 (5 March 2008)

Research article   Open Access

Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues

Tatiana Popova, Detlev Mennerich, Andreas Weith, Karsten Quast BMC Genomics 2008, 9:91 (25 February 2008)

Methodology article   Open Access Highly Accessed

A new method for class prediction based on signed-rank algorithms applied to Affymetrix® microarray experiments

Thierry Rème, Dirk Hose, John De Vos, Aurélien Vassal, Pierre-Olivier Poulain, Véronique Pantesco, Hartmut Goldschmidt, Bernard Klein BMC Bioinformatics 2008, 9:16 (11 January 2008)

Research   Open Access

Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis?

Lev Klebanov, Linlin Chen, Andrei Yakovlev Biology Direct 2007, 2:28 (7 November 2007)

Research article   Open Access

Genome-wide changes accompanying knockdown of fatty acid synthase in breast cancer

Lynn M Knowles, Jeffrey W Smith BMC Genomics 2007, 8:168 (12 June 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)

Methodology article   Open Access

Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme

Li-Jen Su, Ching-Wei Chang, Yu-Chung Wu, Kuang-Chi Chen, Chien-Ju Lin, Shu-Ching Liang, Chi-Hung Lin, Jacqueline Whang-Peng, Shih-Lan Hsu, Chen-Hsin Chen, Chi-Ying F Huang BMC Genomics 2007, 8:140 (1 June 2007)

Research article   Open Access

Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients

Stefano Calza, Per Hall, Gert Auer, Judith Bjöhle, Sigrid Klaar, Ulrike Kronenwett, Edison T Liu, Lance Miller, Alexander Ploner, Johanna Smeds, Jonas Bergh, Yudi Pawitan Breast Cancer Research 2006, 8:R34 (17 July 2006)

Methodology article   Open Access

Correction of scaling mismatches in oligonucleotide microarray data

Martino Barenco, Jaroslav Stark, Daniel Brewer, Daniela Tomescu, Robin Callard, Michael Hubank BMC Bioinformatics 2006, 7:251 (9 May 2006)

Research article   Open Access Highly Accessed

Evaluation of methods for oligonucleotide array data via quantitative real-time PCR

Li-Xuan Qin, Richard P Beyer, Francesca N Hudson, Nancy J Linford, Daryl E Morris, Kathleen F Kerr BMC Bioinformatics 2006, 7:23 (17 January 2006)

Research article   Open Access Highly Accessed

Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts

Yudi Pawitan, Judith Bjöhle, Lukas Amler, Anna-Lena Borg, Suzanne Egyhazi, Per Hall, Xia Han, Lars Holmberg, Fei Huang, Sigrid Klaar, Edison T Liu, Lance Miller, Hans Nordgren, Alexander Ploner, Kerstin Sandelin, Peter M Shaw, Johanna Smeds, Lambert Skoog, Sara Wedrén, Jonas Bergh Breast Cancer Research 2005, 7:R953-R964 (3 October 2005)