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» A framework for framework documentation
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86
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BMCBI
2005
107views more  BMCBI 2005»
15 years 18 days ago
Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach
Background: In testing for differential gene expression involving multiple serial analysis of gene expression (SAGE) libraries, it is critical to account for both between and with...
Jun Lu, John K. Tomfohr, Thomas B. Kepler
95
Voted
BMCBI
2005
89views more  BMCBI 2005»
15 years 18 days ago
An empirical analysis of training protocols for probabilistic gene finders
Background: Generalized hidden Markov models (GHMMs) appear to be approaching acceptance as a de facto standard for state-of-the-art ab initio gene finding, as evidenced by the re...
William H. Majoros, Steven Salzberg
124
Voted
BMCBI
2005
147views more  BMCBI 2005»
15 years 18 days ago
GATA: a graphic alignment tool for comparative sequence analysis
Background: Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved se...
David A. Nix, Michael B. Eisen
166
Voted
BMCBI
2005
169views more  BMCBI 2005»
15 years 18 days ago
Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthe
Background: Synthetic lethality experiments identify pairs of genes with complementary function. More direct functional associations (for example greater probability of membership...
Yan Qi 0003, Ping Ye, Joel S. Bader
110
Voted
BMCBI
2005
93views more  BMCBI 2005»
15 years 18 days ago
Multiple sequence alignment accuracy and evolutionary distance estimation
Background: Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pai...
Michael S. Rosenberg
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