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» The complexity of stochastic sequences
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WABI
2009
Springer
132views Bioinformatics» more  WABI 2009»
16 years 1 months ago
mpscan: Fast Localisation of Multiple Reads in Genomes
Abstract. With Next Generation Sequencers, sequence based transcriptomic or epigenomic assays yield millions of short sequence reads that need to be mapped back on a reference geno...
Eric Rivals, Leena Salmela, Petteri Kiiskinen, Pet...
BMCBI
2008
132views more  BMCBI 2008»
15 years 6 months ago
The Average Mutual Information Profile as a Genomic Signature
Background: Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also p...
Mark Bauer, Sheldon M. Schuster, Khalid Sayood
CORR
2008
Springer
121views Education» more  CORR 2008»
15 years 6 months ago
Rate-Distortion via Markov Chain Monte Carlo
We propose an approach to lossy source coding, utilizing ideas from Gibbs sampling, simulated annealing, and Markov Chain Monte Carlo (MCMC). The idea is to sample a reconstructio...
Shirin Jalali, Tsachy Weissman
RECOMB
2008
Springer
16 years 6 months ago
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes
The transcriptional regulatory sequences in metazoan genomes often consist of multiple cis-regulatory modules (CRMs). Each CRM contains locally enriched occurrences of binding site...
Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Sel...
BMCBI
2007
106views more  BMCBI 2007»
15 years 6 months ago
Constructing a meaningful evolutionary average at the phylogenetic center of mass
Background: As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the dat...
Eric A. Stone, Arend Sidow