BMC Bioinformatics

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This article is part of the supplement: Neural Information Processing Systems (NIPS) workshop on New Problems and Methods in Computational Biology

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Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering

Manjunatha Jagalur, Chris Pal*, Erik Learned-Miller, R Thomas Zoeller and David Kulp

BMC Bioinformatics 2007, 8(Suppl 10):S5 doi:10.1186/1471-2105-8-S10-S5

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Methodology   Open Access

Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infection

Konstantina Dimitrakopoulou, Charalampos Tsimpouris, George Papadopoulos, Claudia Pommerenke, Esther Wilk, Kyriakos N Sgarbas, Klaus Schughart, Anastasios Bezerianos Journal of Clinical Bioinformatics 2011, 1:27 (21 October 2011)

Software   Open Access

Biblio-MetReS: A bibliometric network reconstruction application and server

Anabel Usié, Hiren Karathia, Ivan Teixidó, Joan Valls, Xavier Faus, Rui Alves, Francesc Solsona BMC Bioinformatics 2011, 12:387 (5 October 2011)

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Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study

Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, Jürgen Kurths BMC Bioinformatics 2011, 12:292 (19 July 2011)

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Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

Franc Llorens, Manuela Hummel, Xavier Pastor, Anna Ferrer, Raquel Pluvinet, Ana Vivancos, Ester Castillo, Susana Iraola, Ana M Mosquera, Eva González, Juanjo Lozano, Matthew Ingham, Juliane C Dohm, Marc Noguera, Robert Kofler, Jose del Río, Mònica Bayés, Heinz Himmelbauer, Lauro Sumoy BMC Genomics 2011, 12:326 (23 June 2011)

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Structural influence of gene networks on their inference: analysis of C3NET

Gökmen Altay, Frank Emmert-Streib Biology Direct 2011, 6:31 (22 June 2011)

Research article   Open Access

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data

Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemysław Biecek, Jerzy Tiuryn, Martin Vingron BMC Bioinformatics 2011, 12:249 (21 June 2011)

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OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson, Morris A Swertz BMC Bioinformatics 2011, 12:218 (29 May 2011)