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138 results
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Supervised detection of regulatory motifs in DNA sequences.
Keles S, van der Laan MJ, Dudoit S, Xing B, Eisen MB. Keles S, et al. Among authors: eisen mb. Stat Appl Genet Mol Biol. 2003;2:Article5. doi: 10.2202/1544-6115.1015. Epub 2003 Aug 25. Stat Appl Genet Mol Biol. 2003. PMID: 16646783
Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles.
Chiang DY, Brown PO, Eisen MB. Chiang DY, et al. Among authors: eisen mb. Bioinformatics. 2001;17 Suppl 1:S49-55. doi: 10.1093/bioinformatics/17.suppl_1.s49. Bioinformatics. 2001. PMID: 11472992
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.
Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. Berman BP, et al. Among authors: eisen mb. Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):757-62. doi: 10.1073/pnas.231608898. Proc Natl Acad Sci U S A. 2002. PMID: 11805330 Free PMC article.
Identification of regulatory elements using a feature selection method.
Keleş S, van der Laan M, Eisen MB. Keleş S, et al. Among authors: eisen mb. Bioinformatics. 2002 Sep;18(9):1167-75. doi: 10.1093/bioinformatics/18.9.1167. Bioinformatics. 2002. PMID: 12217908
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts.
Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB. Chiang DY, et al. Among authors: eisen mb. Genome Biol. 2003;4(7):R43. doi: 10.1186/gb-2003-4-7-r43. Epub 2003 Jun 26. Genome Biol. 2003. PMID: 12844359 Free PMC article.
Benchmarking tools for the alignment of functional noncoding DNA.
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Pollard DA, et al. Among authors: eisen mb. BMC Bioinformatics. 2004 Jan 21;5:6. doi: 10.1186/1471-2105-5-6. BMC Bioinformatics. 2004. PMID: 14736341 Free PMC article.
Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.
Moses AM, Chiang DY, Eisen MB. Moses AM, et al. Among authors: eisen mb. Pac Symp Biocomput. 2004:324-35. doi: 10.1142/9789812704856_0031. Pac Symp Biocomput. 2004. PMID: 14992514
Detecting DNA regulatory motifs by incorporating positional trends in information content.
Kechris KJ, van Zwet E, Bickel PJ, Eisen MB. Kechris KJ, et al. Among authors: eisen mb. Genome Biol. 2004;5(7):R50. doi: 10.1186/gb-2004-5-7-r50. Epub 2004 Jun 24. Genome Biol. 2004. PMID: 15239835 Free PMC article.
Conservation and evolution of cis-regulatory systems in ascomycete fungi.
Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB. Gasch AP, et al. Among authors: eisen mb. PLoS Biol. 2004 Dec;2(12):e398. doi: 10.1371/journal.pbio.0020398. Epub 2004 Nov 9. PLoS Biol. 2004. PMID: 15534694 Free PMC article.
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB. Moses AM, et al. Among authors: eisen mb. Genome Biol. 2004;5(12):R98. doi: 10.1186/gb-2004-5-12-r98. Epub 2004 Nov 30. Genome Biol. 2004. PMID: 15575972 Free PMC article.
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