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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 and Olli Kallioniemi*

Genome Biology 2008, 9:R139 doi:10.1186/gb-2008-9-9-r139

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Research article   Open Access

Maximizing biomarker discovery by minimizing gene signatures

Chang Chang, Junwei Wang, Chen Zhao, Jennifer Fostel, Weida Tong, Pierre R Bushel, Youping Deng, Lajos Pusztai, W Fraser Symmans, Tieliu Shi BMC Genomics 2011, 12(Suppl 5):S6 (23 December 2011)

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Research article   Open Access

Identification of proprotein convertase substrates using genome-wide expression correlation analysis

Hannu Turpeinen, Sampo Kukkurainen, Kati Pulkkinen, Timo Kauppila, Kalle Ojala, Vesa P Hytönen, Marko Pesu BMC Genomics 2011, 12:618 (20 December 2011)

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Classification of unknown primary tumors with a data-driven method based on a large microarray reference database

Kalle A Ojala, Sami K Kilpinen, Olli P Kallioniemi Genome Medicine 2011, 3:63 (17 October 2011)

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wAGEP is a scalable, adaptable method that can be used to accurately classify cancers of unknown primary origin by aligning microarray profiles against a microarray reference database.

Research article   Open Access

Expression cartography of human tissues using self organizing maps

Henry Wirth, Markus Löffler, Martin von Bergen, Hans Binder BMC Bioinformatics 2011, 12:306 (27 July 2011)

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Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas

Guro E Lind, Stine A Danielsen, Terje Ahlquist, Marianne A Merok, Kim Andresen, Rolf I Skotheim, Merete Hektoen, Torleiv O Rognum, Gunn I Meling, Geir Hoff, Michael Bretthauer, Espen Thiis-Evensen, Arild Nesbakken, Ragnhild A Lothe Molecular Cancer 2011, 10:85 (21 July 2011)

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BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets

Mark J Alston, John Seers, Jay CD Hinton, Sacha Lucchini BMC Bioinformatics 2010, 11:73 (3 February 2010)

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Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data

Yvonne JK Edwards, Anna E Lobley, Melissa M Pentony, David T Jones Genome Biology 2009, 10:R50 (11 May 2009)

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Signals for microRNA targeting and ubiquitination are enriched in intrinsically disordered proteins, but some highly disordered proteins can escape rapid degradation.

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)

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