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BMCBI
2010
126views more  BMCBI 2010»
15 years 6 months ago
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes
Background: The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes w...
Joel Arrais, João Fernandes, João Pe...
BMCBI
2010
139views more  BMCBI 2010»
15 years 6 months ago
A global optimization algorithm for protein surface alignment
Background: A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined w...
Paola Bertolazzi, Concettina Guerra, Giampaolo Liu...
BMCBI
2010
146views more  BMCBI 2010»
15 years 6 months ago
On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference
Background: Transcriptional regulatory network inference (TRNI) from large compendia of DNA microarrays has become a fundamental approach for discovering transcription factor (TF)...
Elissa J. Cosgrove, Timothy S. Gardner, Eric D. Ko...
BMCBI
2010
149views more  BMCBI 2010»
15 years 6 months ago
RuleMonkey: software for stochastic simulation of rule-based models
Background: The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be...
Joshua Colvin, Michael I. Monine, Ryan N. Gutenkun...
BMCBI
2008
163views more  BMCBI 2008»
15 years 6 months ago
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Background: High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpre...
Frédéric Chalmel, Michael Primig