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JCB
2008
90views more  JCB 2008»
13 years 10 months ago
A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast
Resolving the general organizational principles that govern the interactions during transcriptional gene regulation has great relevance for understanding disease progression, biof...
Vladimir Filkov, Nameeta Shah
BMCBI
2010
259views more  BMCBI 2010»
13 years 5 months ago
Rule-based spatial modeling with diffusing, geometrically constrained molecules
Background: We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our appro...
Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Ma...
BMCBI
2008
158views more  BMCBI 2008»
13 years 10 months ago
Discovering gene annotations in biomedical text databases
Currently, most of the discovered biological and biomedical knowledge is available as textual data in scientific papers. And, locating and curating information about a genomic enti...
Ali Cakmak, Gultekin Özsoyoglu
BMCBI
2004
130views more  BMCBI 2004»
13 years 10 months ago
PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability
Background: Regulatory regions that function in DNA replication and gene transcription contain specific sequences that bind proteins as well as less-specific sequences in which th...
Yanlin Huang, David Kowalski
JSC
2010
103views more  JSC 2010»
13 years 8 months ago
Anti-patterns for rule-based languages
Negation is intrinsic to human thinking and most of the time when searching for something, we base our patterns on both positive and negative conditions. This should be naturally ...
Horatiu Cirstea, Claude Kirchner, Radu Kopetz, Pie...