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Networks analysis

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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141.

Software   Open Access Highly Accessed

Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

Jacek Sroka, Łukasz Bieniasz-Krzywiec, Szymon Gwóźdź, Dariusz Leniowski, Jakub Łącki, Mateusz Markowski, Claudio Avignone-Rossa, Michael E Bushell, Johnjoe McFadden, Andrzej M Kierzek BMC Bioinformatics 2011, 12:196 (24 May 2011)

Abstract | Full text | PDF | PubMed

142.

Research article   Open Access

A Network of SCOP Hidden Markov Models and Its Analysis

Liqing Zhang, Layne T Watson, Lenwood S Heath BMC Bioinformatics 2011, 12:191 (23 May 2011)

Abstract | Full text | PDF | PubMed

143.

Research article   Open Access

The biomedical discourse relation bank

Rashmi Prasad, Susan McRoy, Nadya Frid, Aravind Joshi, Hong Yu BMC Bioinformatics 2011, 12:188 (23 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

144.

Database   Open Access Highly Accessed

Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library

Roderic DM Page BMC Bioinformatics 2011, 12:187 (23 May 2011)

Abstract | Full text | PDF | PubMed

145.

Software   Open Access

Brunn: An open source laboratory information system for microplates with a graphical plate layout design process

Jonathan Alvarsson, Claes Andersson, Ola Spjuth, Rolf Larsson, Jarl ES Wikberg BMC Bioinformatics 2011, 12:179 (20 May 2011)

Abstract | Full text | PDF | PubMed

146.

Database   Open Access Highly Accessed

Web-based metabolic network visualization with a zooming user interface

Mario Latendresse, Peter D Karp BMC Bioinformatics 2011, 12:176 (19 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

147.

Correspondence   Open Access Highly Accessed

Toward an interactive article: integrating journals and biological databases

Arun Rangarajan, Tim Schedl, Karen Yook, Juancarlos Chan, Stephen Haenel, Lolly Otis, Sharon Faelten, Tracey DePellegrin-Connelly, Ruth Isaacson, Marek S Skrzypek, Steven J Marygold, Raymund Stefancsik, J Cherry, Paul W Sternberg, Hans-Michael Müller BMC Bioinformatics 2011, 12:175 (19 May 2011)

Abstract | Full text | PDF | PubMed

148.

Methodology article   Open Access Highly Accessed

Predicting drug side-effect profiles: a chemical fragment-based approach

Edouard Pauwels, Véronique Stoven, Yoshihiro Yamanishi BMC Bioinformatics 2011, 12:169 (18 May 2011)

Abstract | Full text | PDF | PubMed

149.

Research article   Open Access

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

Augustin Luna, Evrim I Karac, Margot Sunshine, Lucas Chang, Ruth Nussinov, Mirit I Aladjem, Kurt W Kohn BMC Bioinformatics 2011, 12:167 (17 May 2011)

Abstract | Full text | PDF | PubMed

150.

Research article   Open Access

CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method

Kai Wang, Fuyan Hu, Kejia Xu, Hua Cheng, Meng Jiang, Ruili Feng, Jing Li, Tieqiao Wen BMC Bioinformatics 2011, 12:164 (17 May 2011)

Abstract | Full text | PDF | PubMed

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