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» Computing with Evolving Proteins
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NAR
2011
267views Computer Vision» more  NAR 2011»
15 years 1 months ago
EcoCyc: a comprehensive database of Escherichia coli biology
EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual...
Ingrid M. Keseler, Julio Collado-Vides, Alberto Sa...
BMCBI
2010
123views more  BMCBI 2010»
15 years 6 months ago
Decoding HMMs using the k best paths: algorithms and applications
Background: Traditional algorithms for hidden Markov model decoding seek to maximize either the probability of a state path or the number of positions of a sequence assigned to th...
Daniel G. Brown 0001, Daniil Golod
248
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ICDE
2007
IEEE
124views Database» more  ICDE 2007»
16 years 8 months ago
Topology Search over Biological Databases
We introduce the notion of a data topology and the problem of topology search over databases. A data topology summarizes the set of all possible relationships that connect a given...
Lin Guo, Jayavel Shanmugasundaram, Golan Yona
IV
2009
IEEE
128views Visualization» more  IV 2009»
16 years 1 months ago
Large Quasi-Tree Drawing: A Neighborhood Based Approach
In this paper, we present an algorithm to lay out a particular class of graphs coming from real case studies: the quasi-tree graph class. Protein and internet mappings projects ha...
Romain Bourqui, David Auber
ACSD
2008
IEEE
130views Hardware» more  ACSD 2008»
16 years 1 months ago
BAM: BioAmbient machine
In recent years it has become clear that techniques developed for concurrent programming are in fact very useful for the analysis of complex systems in biology. To some level of i...
Vinod A. Muganthan, Andrew Phillips, Maria Grazia ...