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» An integrative approach to modeling biological networks
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BMCBI
2010
175views more  BMCBI 2010»
14 years 12 months ago
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
Background: Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to fle...
Martijn P. van Iersel, Alexander R. Pico, Thomas K...
BMCBI
2010
127views more  BMCBI 2010»
14 years 12 months ago
PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactom
Background: Signal transduction events often involve transient, yet specific, interactions between structurally conserved protein domains and polypeptide sequences in target prote...
Khader Shameer, Lalima L. Madan, Shivamurthy Veera...
BMCBI
2006
147views more  BMCBI 2006»
14 years 12 months ago
A case study in pathway knowledgebase verification
Background: Biological databases and pathway knowledgebases are proliferating rapidly. We are developing software tools for computer-aided hypothesis design and evaluation, and we...
Stephen A. Racunas, Nigam Shah, Nina V. Fedoroff
SAB
2010
Springer
117views Optimization» more  SAB 2010»
14 years 10 months ago
Indirectly Encoding Neural Plasticity as a Pattern of Local Rules
Biological brains can adapt and learn from past experience. In neuroevolution, i.e. evolving artificial neural networks (ANNs), one way that agents controlled by ANNs can evolve t...
Sebastian Risi, Kenneth O. Stanley
RECOMB
2006
Springer
16 years 4 days ago
Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes
Abstract. Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription fa...
Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam ...