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Linear separability of gene expression data sets.
IEEE/ACM Trans Comput Biol Bioinform. 2010 Apr-Jun;7(2):375-81
PMID: 20431156 [PubMed - indexed for MEDLINE]
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Approximate maximum parsimony and ancestral maximum likelihood.
IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):183-7
PMID: 20150680 [PubMed - indexed for MEDLINE]
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Genomic DNA k-mer spectra: models and modalities.
Genome Biol. 2009;10(10):R108
PMID: 19814784 [PubMed - indexed for MEDLINE]
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Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network.
BMC Syst Biol. 2009 Sep 3;3:86
PMID: 19728874 [PubMed - indexed for MEDLINE]
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Forbidden penta-peptides.
Protein Sci. 2007 Oct;16(10):2251-9
PMID: 17893362 [PubMed - indexed for MEDLINE]
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Biological networks: comparison, conservation, and evolution via relative description length.
J Comput Biol. 2007 Jul-Aug;14(6):817-38
PMID: 17691896 [PubMed - indexed for MEDLINE]
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Analytic solutions of maximum likelihood on forks of four taxa.
Math Biosci. 2007 Aug;208(2):347-58
PMID: 17664091 [PubMed - indexed for MEDLINE]
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Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression.
Mol Syst Biol. 2007;3:108
PMID: 17486136 [PubMed - indexed for MEDLINE]
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Genetic code symmetry and efficient design of GC-constrained coding sequences.
Bioinformatics. 2007 Jan 15;23(2):e57-63
PMID: 17237106 [PubMed - indexed for MEDLINE]
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Maximum likelihood molecular clock comb: analytic solutions.
J Comput Biol. 2006 Apr;13(3):819-37
PMID: 16706728 [PubMed - indexed for MEDLINE]
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The average common substring approach to phylogenomic reconstruction.
J Comput Biol. 2006 Mar;13(2):336-50
PMID: 16597244 [PubMed - indexed for MEDLINE]
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Maximum likelihood Jukes-Cantor triplets: analytic solutions.
Mol Biol Evol. 2006 Mar;23(3):626-32
PMID: 16319091 [PubMed - indexed for MEDLINE]
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Maximum likelihood of evolutionary trees: hardness and approximation.
Bioinformatics. 2005 Jun;21 Suppl 1:i97-106
PMID: 15961504 [PubMed - indexed for MEDLINE]
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Molecular clock fork phylogenies: closed form analytic maximum likelihood solutions.
Syst Biol. 2004 Dec;53(6):963-7
PMID: 15764563 [PubMed - indexed for MEDLINE]
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Ancestral maximum likelihood of evolutionary trees is hard.
J Bioinform Comput Biol. 2004 Jun;2(2):257-71
PMID: 15297981 [PubMed - indexed for MEDLINE]
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Discovering local structure in gene expression data: the order-preserving submatrix problem.
J Comput Biol. 2003;10(3-4):373-84
PMID: 12935334 [PubMed - indexed for MEDLINE]
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