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» On Compressibility of Protein Sequences
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BMCBI
2011
15 years 1 months ago
Shape-based peak identification for ChIP-Seq
Background: The identification of binding targets for proteins using ChIP-Seq has gained popularity as an alternative to ChIP-chip. Sequencing can, in principle, eliminate artifac...
Valerie Hower, Steven N. Evans, Lior Pachter
EVOW
2009
Springer
16 years 25 days ago
A Memetic Algorithm for Phylogenetic Reconstruction with Maximum Parsimony
The Maximum Parsimony problem aims at reconstructing a phylogenetic tree from DNA, RNA or protein sequences while minimizing the number of evolutionary changes. Much work has been ...
Jean-Michel Richer, Adrien Goëffon, Jin-Kao H...
BIBM
2007
IEEE
162views Bioinformatics» more  BIBM 2007»
16 years 12 days ago
Multiple Interacting Subcellular Structure Tracking by Sequential Monte Carlo Method
With the wide application of green fluorescent protein (GFP) in the study of live cells, there is a surging need for the computer-aided analysis on the huge amount of image seque...
Quan Wen, Jean Gao, Kate Luby-Phelps
ISBRA
2007
Springer
16 years 6 days ago
Clustering Algorithms Optimizer: A Framework for Large Datasets
Clustering algorithms are employed in many bioinformatics tasks, including categorization of protein sequences and analysis of gene-expression data. Although these algorithms are r...
Roy Varshavsky, David Horn, Michal Linial
IPPS
2006
IEEE
16 years 2 days ago
Parallel implementation of a quartet-based algorithm for phylogenetic analysis
This paper describes a parallel implementation of our recently developed algorithm for phylogenetic analysis on the IBM BlueGene/L cluster [15]. This algorithm constructs evolutio...
Bing Bing Zhou, Daniel Chu, Monther Tarawneh, Ping...