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BIOINFORMATICS
2006
124views more  BIOINFORMATICS 2006»
14 years 12 months ago
Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
Motivation Quantitative estimation of the regulatory relationship between transcription factors and genes is a fundamental stepping stone when trying to develop models of cellular...
Guido Sanguinetti, Neil D. Lawrence, Magnus Rattra...
BMCBI
2006
116views more  BMCBI 2006»
14 years 12 months ago
Optimized mixed Markov models for motif identification
Background: Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challengi...
Weichun Huang, David M. Umbach, Uwe Ohler, Leping ...
BMCBI
2010
117views more  BMCBI 2010»
14 years 12 months ago
New decoding algorithms for Hidden Markov Models using distance measures on labellings
Background: Existing hidden Markov model decoding algorithms do not focus on approximately identifying the sequence feature boundaries. Results: We give a set of algorithms to com...
Daniel G. Brown 0001, Jakub Truszkowski
BMCBI
2004
151views more  BMCBI 2004»
14 years 11 months ago
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
Background: The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include a...
Jens Reeder, Robert Giegerich
CANDC
2007
ACM
14 years 11 months ago
Chromosome segregation in Escherichia coli division: A free energy-driven string model
Although the mechanisms of eukaryotic chromosome segregation and cell division have been elucidated to a certain extent, those for bacteria remain largely unknown. Here we present...
Jianmiao Fan, Kagan Tuncay, Peter J. Ortoleva