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» Pattern Matching in Degenerate DNA RNA Sequences
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BMCBI
2005
179views more  BMCBI 2005»
14 years 9 months ago
MARS: Microarray analysis, retrieval, and storage system
Background: Microarray analysis has become a widely used technique for the study of geneexpression patterns on a genomic scale. As more and more laboratories are adopting microarr...
Michael Maurer, Robert Molidor, Alexander Sturn, J...
FCCM
2011
IEEE
311views VLSI» more  FCCM 2011»
14 years 1 months ago
String Matching in Hardware Using the FM-Index
—String matching is a ubiquitous problem that arises in a wide range of applications in computing, e.g., packet routing, intrusion detection, web querying, and genome analysis. D...
Edward Fernandez, Walid Najjar, Stefano Lonardi
RECOMB
2007
Springer
15 years 3 months ago
Nucleosome Occupancy Information Improves de novo Motif Discovery
A complete understanding of transcriptional regulatory processes in the cell requires identification of transcription factor binding sites on a genomewide scale. Unfortunately, th...
Leelavati Narlikar, Raluca Gordân, Alexander...
BMCBI
2010
103views more  BMCBI 2010»
14 years 9 months ago
A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements
Background: Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evid...
Alexander G. Churbanov, Igor Vorechovsky, Chindo H...
BMCBI
2010
167views more  BMCBI 2010»
14 years 9 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. ...