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» Factored A* Search for Models over Sequences and Trees
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BMCBI
2007
247views more  BMCBI 2007»
13 years 7 months ago
A survey of DNA motif finding algorithms
Background: Unraveling the mechanisms that regulate gene expression is a major challenge in biology. An important task in this challenge is to identify regulatory elements, especi...
Modan K. Das, Ho-Kwok Dai
BMCBI
2006
100views more  BMCBI 2006»
13 years 7 months ago
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Background: Horizontal gene transfer (HGT) has allowed bacteria to evolve many new capabilities. Because transferred genes perform many medically important functions, such as conf...
Micah Hamady, M. D. Betterton, Rob Knight
ICPPW
2009
IEEE
13 years 5 months ago
A Scalable Parallel Approach for Peptide Identification from Large-Scale Mass Spectrometry Data
Identifying peptides, which are short polymeric chains of amino acid residues in a protein sequence, is of fundamental importance in systems biology research. The most popular appr...
Gaurav Ramesh Kulkarni, Ananth Kalyanaraman, Willi...
FOCS
2009
IEEE
14 years 2 months ago
Instance-Optimal Geometric Algorithms
We prove the existence of an algorithm A for computing 2-d or 3-d convex hulls that is optimal for every point set in the following sense: for every set S of n points and for ever...
Peyman Afshani, Jérémy Barbay, Timot...
WSDM
2010
ACM
166views Data Mining» more  WSDM 2010»
14 years 4 months ago
Ranking Mechanisms in Twitter-Like Forums
We study the problem of designing a mechanism to rank items in forums by making use of the user reviews such as thumb and star ratings. We compare mechanisms where forum users rat...
Anish Das Sarma, Atish Das Sarma, Sreenivas Gollap...