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» Bayesian Non-negative Matrix Factorization
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BMCBI
2010
153views more  BMCBI 2010»
13 years 5 months ago
Metamotifs - a generative model for building families of nucleotide position weight matrices
Background: Development of high-throughput methods for measuring DNA interactions of transcription factors together with computational advances in short motif inference algorithms...
Matias Piipari, Thomas A. Down, Tim J. P. Hubbard
BMCBI
2007
105views more  BMCBI 2007»
13 years 4 months ago
Finding regulatory elements and regulatory motifs: a general probabilistic framework
Over the last two decades a large number of algorithms has been developed for regulatory motif finding. Here we show how many of these algorithms, especially those that model bind...
Erik van Nimwegen
NIPS
2008
13 years 6 months ago
Stochastic Relational Models for Large-scale Dyadic Data using MCMC
Stochastic relational models (SRMs) [15] provide a rich family of choices for learning and predicting dyadic data between two sets of entities. The models generalize matrix factor...
Shenghuo Zhu, Kai Yu, Yihong Gong
BMCBI
2006
98views more  BMCBI 2006»
13 years 4 months ago
Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
Background: Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibiti...
Kannan Tharakaraman, Leonardo Mariño-Ram&ia...