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Networks analysis Section edited by Igor Jurisica

This section incorporates all aspects of network analysis including but not limited to: methods for predicting, analyzing and visualizing networks, and applications to systems biology.

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1.

Research article   Open Access

Statistical Analysis of Dendritic Spine Distributions in Rat Hippocampal Cultures

Aruna Jammalamadaka, Sourav Banerjee, Kenneth S Kosik, Bangalore S Manjunath BMC Bioinformatics 2013, 14:287 (2 October 2013)

Abstract | Provisional PDF

2.

Research article   Open Access

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

Mingzhu Zhu, Jeremy L Dahmen, Gary Stacey, Jianlin Cheng BMC Bioinformatics 2013, 14:278 (22 September 2013)

Abstract | Provisional PDF | PubMed

3.

Research article   Open Access Highly Accessed

Learning a Markov Logic network for supervised gene regulatory network inference

Céline Brouard, Christel Vrain, Julie Dubois, David Castel, Marie-Anne Debily, Florence d’Alché-Buc BMC Bioinformatics 2013, 14:273 (12 September 2013)

Abstract | Full text | PDF | PubMed

4.

Software   Open Access Highly Accessed

Pathway-PDT: a flexible pathway analysis tool for nuclear families

Yo Park, Michael Schmidt, Eden R Martin, Margaret A Pericak-Vance, Ren-Hua Chung BMC Bioinformatics 2013, 14:267 (4 September 2013)

Abstract | Full text | PDF | ePUB | PubMed

5.

Methodology article   Open Access Highly Accessed

Conversion of KEGG metabolic pathways to SBGN maps including automatic layout

Tobias Czauderna, Michael Wybrow, Kim Marriott, Falk Schreiber BMC Bioinformatics 2013, 14:250 (16 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

6.

Software   Open Access Highly Accessed

Robust flux balance analysis of multiscale biochemical reaction networks

Yuekai Sun, Ronan MT Fleming, Ines Thiele, Michael A Saunders BMC Bioinformatics 2013, 14:240 (30 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

7.

Research article   Open Access Highly Accessed

A new approach for prediction of tumor sensitivity to targeted drugs based on functional data

Noah Berlow, Lara E Davis, Emma L Cantor, Bernard Séguin, Charles Keller, Ranadip Pal BMC Bioinformatics 2013, 14:239 (29 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

8.

Software   Open Access Highly Accessed

The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases

Panagiotis Moulos, Julie Klein, Simon Jupp, Robert Stevens, Jean-Loup Bascands, Joost P Schanstra BMC Bioinformatics 2013, 14:235 (24 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

9.

Research article   Open Access

Alternate virtual populations elucidate the type I interferon signature predictive of the response to rituximab in rheumatoid arthritis

Brian J Schmidt, Fergal P Casey, Thomas Paterson, Jason R Chan BMC Bioinformatics 2013, 14:221 (10 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

10.

Software   Open Access Highly Accessed

RCytoscape: tools for exploratory network analysis

Paul T Shannon, Mark Grimes, Burak Kutlu, Jan J Bot, David J Galas BMC Bioinformatics 2013, 14:217 (9 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

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