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Results: 1 to 20 of 21

1.

Improving MEME via a two-tiered significance analysis.

Tanaka E, Bailey TL, Keich U.

Bioinformatics. 2014 Jul 15;30(14):1965-73. doi: 10.1093/bioinformatics/btu163. Epub 2014 Mar 24.

PMID:
24665130
[PubMed - in process]
2.

High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast.

Liachko I, Youngblood RA, Keich U, Dunham MJ.

Genome Res. 2013 Apr;23(4):698-704. doi: 10.1101/gr.144659.112. Epub 2012 Dec 12.

PMID:
23241746
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Novel features of ARS selection in budding yeast Lachancea kluyveri.

Liachko I, Tanaka E, Cox K, Chung SC, Yang L, Seher A, Hallas L, Cha E, Kang G, Pace H, Barrow J, Inada M, Tye BK, Keich U.

BMC Genomics. 2011 Dec 28;12:633. doi: 10.1186/1471-2164-12-633.

PMID:
22204614
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Target-decoy approach and false discovery rate: when things may go wrong.

Gupta N, Bandeira N, Keich U, Pevzner PA.

J Am Soc Mass Spectrom. 2011 Jul;22(7):1111-20. doi: 10.1007/s13361-011-0139-3. Epub 2011 May 5.

PMID:
21953092
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Improved similarity scores for comparing motifs.

Tanaka E, Bailey T, Grant CE, Noble WS, Keich U.

Bioinformatics. 2011 Jun 15;27(12):1603-9. doi: 10.1093/bioinformatics/btr257. Epub 2011 May 4.

PMID:
21543443
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Alignment constrained sampling.

Ng P, Keich U.

J Comput Biol. 2011 Feb;18(2):155-68. doi: 10.1089/cmb.2010.0220.

PMID:
21314455
[PubMed - indexed for MEDLINE]
7.

Confidently estimating the number of DNA replication origins.

Bhaskar A, Keich U.

Stat Appl Genet Mol Biol. 2010;9:Article28. doi: 10.2202/1544-6115.1544. Epub 2010 Jul 2.

PMID:
20678076
[PubMed - indexed for MEDLINE]
8.

A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.

Liachko I, Bhaskar A, Lee C, Chung SC, Tye BK, Keich U.

PLoS Genet. 2010 May 13;6(5):e1000946. doi: 10.1371/journal.pgen.1000946.

PMID:
20485513
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs.

Oliver HF, Orsi RH, Ponnala L, Keich U, Wang W, Sun Q, Cartinhour SW, Filiatrault MJ, Wiedmann M, Boor KJ.

BMC Genomics. 2009 Dec 30;10:641. doi: 10.1186/1471-2164-10-641.

PMID:
20042087
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast.

Keich U, Gao H, Garretson JS, Bhaskar A, Liachko I, Donato J, Tye BK.

BMC Bioinformatics. 2008 Sep 12;9:372. doi: 10.1186/1471-2105-9-372.

PMID:
18786274
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

GIMSAN: a Gibbs motif finder with significance analysis.

Ng P, Keich U.

Bioinformatics. 2008 Oct 1;24(19):2256-7. doi: 10.1093/bioinformatics/btn408. Epub 2008 Aug 14.

PMID:
18703586
[PubMed - indexed for MEDLINE]
Free Article
12.

A conservative parametric approach to motif significance analysis.

Keich U, Ng P.

Genome Inform. 2007;19:61-72.

PMID:
18546505
[PubMed - indexed for MEDLINE]
13.

FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.

Nagarajan N, Keich U.

Bioinformatics. 2008 Feb 15;24(4):577-8. doi: 10.1093/bioinformatics/btm594. Epub 2008 Jan 6.

PMID:
18180239
[PubMed - indexed for MEDLINE]
Free Article
14.

Factoring local sequence composition in motif significance analysis.

Ng P, Keich U.

Genome Inform. 2008;21:15-26.

PMID:
19425144
[PubMed - indexed for MEDLINE]
15.

Correcting base-assignment errors in repeat regions of shotgun assembly.

Zhi D, Keich U, Pevzner P, Heber S, Tang H.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):54-64.

PMID:
17277413
[PubMed - indexed for MEDLINE]
16.

Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.

Ng P, Nagarajan N, Jones N, Keich U.

Bioinformatics. 2006 Jul 15;22(14):e393-401.

PMID:
16873498
[PubMed - indexed for MEDLINE]
Free Article
17.

Computing the P-value of the information content from an alignment of multiple sequences.

Nagarajan N, Jones N, Keich U.

Bioinformatics. 2005 Jun;21 Suppl 1:i311-8. Erratum in: Bioinformatics. 2005 Sep 15;21(18):3700.

PMID:
15961473
[PubMed - indexed for MEDLINE]
Free Article
18.

sFFT: a faster accurate computation of the p-value of the entropy score.

Keich U.

J Comput Biol. 2005 May;12(4):416-30. Review.

PMID:
15882140
[PubMed - indexed for MEDLINE]
19.

Genome-wide analysis of bacterial promoter regions.

Eskin E, Keich U, Gelfand MS, Pevzner PA.

Pac Symp Biocomput. 2003:29-40.

PMID:
12603015
[PubMed - indexed for MEDLINE]
20.

Subtle motifs: defining the limits of motif finding algorithms.

Keich U, Pevzner PA.

Bioinformatics. 2002 Oct;18(10):1382-90.

PMID:
12376383
[PubMed - indexed for MEDLINE]
Free Article

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