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» Contextual alignment of biological sequences
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BMCBI
2007
107views more  BMCBI 2007»
13 years 7 months ago
Linking microarray reporters with protein functions
Background: The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biologi...
Stan Gaj, Arie van Erk, Rachel I. M. van Haaften, ...
CSB
2003
IEEE
14 years 28 days ago
LOGOS: a modular Bayesian model for de novo motif detection
The complexity of the global organization and internal structures of motifs in higher eukaryotic organisms raises significant challenges for motif detection techniques. To achiev...
Eric P. Xing, Wei Wu, Michael I. Jordan, Richard M...
METMBS
2004
140views Mathematics» more  METMBS 2004»
13 years 9 months ago
New Techniques for Generation and Analysis of Evolutionary Trees
We introduce new distance measures for the construction and analysis of phylogenies, focusing on thioredoxin-fold proteins. Our distance measures for tree construction are based o...
Chang Wang, Stephen D. Scott, Qingping Tao, Dmitri...
ISMB
2000
13 years 9 months ago
Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data
We have developed a set of methods and tools for automatic discovery of putative regulatory signals in genome sequences. The analysis pipeline consists of gene expression data clu...
Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan J. Ro...
BMCBI
2008
145views more  BMCBI 2008»
13 years 7 months ago
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
Background: Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are ...
Jonathan R. Manning, Emily R. Jefferson, Geoffrey ...