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» Sequence Complexity for Biological Sequence Analysis
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RECOMB
2002
Springer
15 years 10 months ago
Deconvolving sequence variation in mixed DNA populations
We present an original approach to identifying sequence variants in a mixed DNA population from sequence trace data. The heart of the method is based on parsimony: given a wildtyp...
Andy Wildenberg, Steven Skiena, Pavel Sumazin
ISAMI
2010
14 years 7 months ago
Employing Compact Intra-genomic Language Models to Predict Genomic Sequences and Characterize Their Entropy
Probabilistic models of languages are fundamental to understand and learn the profile of the subjacent code in order to estimate its entropy, enabling the verification and predicti...
Sérgio A. D. Deusdado, Paulo Carvalho
BMCBI
2010
156views more  BMCBI 2010»
14 years 10 months ago
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
Background: High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical question...
James H. Bullard, Elizabeth Purdom, Kasper D. Hans...
ICLP
2009
Springer
15 years 10 months ago
Preprocessing for Optimization of Probabilistic-Logic Models for Sequence Analysis
Abstract. A class of probabilistic-logic models is considered, which increases the expressibility from HMM's and SCFG's regular and contextfree languages to, in principle...
Henning Christiansen, Ole Torp Lassen
BMCBI
2007
109views more  BMCBI 2007»
14 years 10 months ago
Computational RNA secondary structure design: empirical complexity and improved methods
Background: We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various cl...
Rosalía Aguirre-Hernández, Holger H....