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RECOMB
2008
Springer
15 years 9 months ago
Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates
Here we identify duplicated genes in five mammalian genomes and classify these duplicates based on the mechanisms by which they were generated. Retrotransposition accounts for at l...
Paul Ryvkin, Jin Jun, Edward Hemphill, Craig Nelso...
BMEI
2008
IEEE
15 years 3 months ago
A New Approach for Tree Alignment Based on Local Re-Optimization
Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences align...
Feng Yue, Jijun Tang
SP
2008
IEEE
100views Security Privacy» more  SP 2008»
15 years 3 months ago
Towards Practical Privacy for Genomic Computation
Many basic tasks in computational biology involve operations on individual DNA and protein sequences. These sequences, even when anonymized, are vulnerable to re-identification a...
Somesh Jha, Louis Kruger, Vitaly Shmatikov
AAAI
2008
14 years 11 months ago
CRF-OPT: An Efficient High-Quality Conditional Random Field Solver
Conditional random field (CRF) is a popular graphical model for sequence labeling. The flexibility of CRF poses significant computational challenges for training. Using existing o...
Minmin Chen, Yixin Chen, Michael R. Brent
DILS
2008
Springer
14 years 11 months ago
Semi Supervised Spectral Clustering for Regulatory Module Discovery
We propose a novel semi-supervised clustering method for the task of gene regulatory module discovery. The technique uses data on dna binding as prior knowledge to guide the proces...
Alok Mishra, Duncan Gillies