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» A Comparison of Functional and Structural Partitioning
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BMCBI
2004
150views more  BMCBI 2004»
13 years 5 months ago
SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters
Background: Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a u...
Chunlin Wang, Elliot J. Lefkowitz
BMCBI
2011
13 years 11 days ago
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community
Background: Caenorhabditis elegans gene-based phenotype information dates back to the 1970’s, beginning with Sydney Brenner and the characterization of behavioral and morphologi...
Gary Schindelman, Jolene Fernandes, Carol Bastiani...
ICALP
2009
Springer
14 years 5 months ago
Counting Subgraphs via Homomorphisms
We introduce a generic approach for counting subgraphs in a graph. The main idea is to relate counting subgraphs to counting graph homomorphisms. This approach provides new algori...
Omid Amini, Fedor V. Fomin, Saket Saurabh
BMCBI
2010
167views more  BMCBI 2010»
13 years 5 months ago
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
Background: Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription fa...
Denitsa Alamanova, Philip Stegmaier, Alexander E. ...
BMCBI
2010
113views more  BMCBI 2010»
13 years 5 months ago
Improving performance of mammalian microRNA target prediction
Background: MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA...
Hui Liu, Dong Yue, Yidong Chen, Shou-Jiang Gao, Yu...