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» Gene finding in novel genomes
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BMCBI
2006
166views more  BMCBI 2006»
13 years 8 months ago
Extraction of phylogenetic network modules from the metabolic network
Background: In bio-systems, genes, proteins and compounds are related to each other, thus forming complex networks. Although each organism has its individual network, some organis...
Takuji Yamada, Minoru Kanehisa, Susumu Goto
BMCBI
2007
164views more  BMCBI 2007»
13 years 8 months ago
SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA
Background: Computational methods to predict transcription factor binding sites (TFBS) based on exhaustive algorithms are guaranteed to find the best patterns but are often limite...
Fathi Elloumi, Martha Nason
BMCBI
2007
123views more  BMCBI 2007»
13 years 8 months ago
Robust clustering in high dimensional data using statistical depths
Background: Mean-based clustering algorithms such as bisecting k-means generally lack robustness. Although componentwise median is a more robust alternative, it can be a poor cent...
Yuanyuan Ding, Xin Dang, Hanxiang Peng, Dawn Wilki...
RECOMB
2005
Springer
14 years 8 months ago
RNA-RNA Interaction Prediction and Antisense RNA Target Search
Abstract. Recent studies demonstrating the existence of special non-coding "antisense" RNAs used in post-transcriptional gene regulation have received considerable attent...
Can Alkan, Emre Karakoç, Joseph H. Nadeau, ...
RECOMB
2003
Springer
14 years 8 months ago
Combining phylogenetic and hidden Markov models in biosequence analysis
A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process c...
Adam C. Siepel, David Haussler