Uwe Ohler's Research Group
Duke Publications
Holste D, Ohler U.
Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events.
PLoS Comput Biol. 2008 Jan;4(1):e21. No abstract available.
PMID: 18225947 [PubMed - in process]
Gottwein E, Mukherjee N, Sachse C, Frenzel C, Majoros WH, Chi JT, Braich R, Manoharan M, Soutschek J, Ohler U, Cullen BR.
A viral microRNA functions as an orthologue of cellular miR-155.
Nature. 2007 Dec 13;450(7172):1096-9.
PMID: 18075594 [PubMed - indexed for MEDLINE]
Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN.
A high-resolution root spatiotemporal map reveals dominant expression patterns.
Science. 2007 Nov 2;318(5851):801-6.
PMID: 17975066 [PubMed - indexed for MEDLINE]
Huang W, Nevins JR, Ohler U.
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools.
Genome Biol. 2007 Oct 24;8(10):R225 [Epub ahead of print]
PMID: 17956628 [PubMed - as supplied by publisher]
Majoros WH, Ohler U.
Spatial preferences of microRNA targets in 3' untranslated regions.
BMC Genomics. 2007 Jun 7;8:152.
PMID: 17555584 [PubMed - indexed for MEDLINE]
Ohler U.
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.
Nucleic Acids Res. 2006;34(20):5943-50. Epub 2006 Oct 26.
PMID: 17068082 [PubMed - indexed for MEDLINE]
Bajic VB, Brent MR, Brown RH, Frankish A, Harrow J, Ohler U, Solovyev VV, Tan SL.
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
Genome Biol. 2006;7 Suppl 1:S3.1-13. Epub 2006 Aug 7. Review.
PMID: 16925837 [PubMed - indexed for MEDLINE]
Narlikar L, Gordân R, Ohler U, Hartemink AJ.
Informative priors based on transcription factor structural class improve de novo motif discovery.
Bioinformatics. 2006 Jul 15;22(14):e384-92.
PMID: 16873497 [PubMed - indexed for MEDLINE]
Mace DL, Lee JY, Twigg RW, Colinas J, Benfey PN, Ohler U.
Quantification of transcription factor expression from Arabidopsis images.
Bioinformatics. 2006 Jul 15;22(14):e323-31.
PMID: 16873489 [PubMed - indexed for MEDLINE]
Huang W, Umbach DM, Ohler U, Li L.
Optimized mixed Markov models for motif identification.
BMC Bioinformatics. 2006 Jun 2;7:279.
PMID: 16749929 [PubMed - indexed for MEDLINE]
Lee JY, Colinas J, Wang JY, Mace D, Ohler U, Benfey PN.
Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.
Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):6055-60. Epub 2006 Mar 31.
PMID: 16581911 [PubMed - indexed for MEDLINE]
Pre-Duke Publications
Ruvinsky I, Ohler U, Burge CB, Ruvkun G.
Detection of broadly expressed neuronal genes in C. elegans.
Dev Biol. 2007 Feb 15;302(2):617-26. Epub 2006 Sep 15.
PMID: 17046742 [PubMed - indexed for MEDLINE]
Ohler U, Shomron N, Burge CB.
Recognition of unknown conserved alternatively spliced exons.
PLoS Comput Biol. 2005 Jul;1(2):113-22. Epub 2005 Jul 8.
PMID: 16110330 [PubMed]
Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB.
Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification.
RNA. 2004 Sep;10(9):1309-22.
PMID: 15317971 [PubMed - indexed for MEDLINE]
Lim CY, Santoso B, Boulay T, Dong E, Ohler U, Kadonaga JT.
The MTE, a new core promoter element for transcription by RNA polymerase II.
Genes Dev. 2004 Jul 1;18(13):1606-17.
PMID: 15231738 [PubMed - indexed for MEDLINE]
Ohler U, Liao GC, Niemann H, Rubin GM.
Computational analysis of core promoters in the Drosophila genome.
Genome Biol. 2002;3(12):RESEARCH0087. Epub 2002 Dec 20.
PMID: 12537576 [PubMed - indexed for MEDLINE]
Ohler U, Niemann H, Liao Gc, Rubin GM.
Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.
Bioinformatics. 2001;17 Suppl 1:S199-206.
PMID: 11473010 [PubMed - indexed for MEDLINE]
Ohler U, Niemann H.
Identification and analysis of eukaryotic promoters: recent computational approaches.
Trends Genet. 2001 Feb;17(2):56-60.
PMID: 11173099 [PubMed - indexed for MEDLINE]
Ohler U, Stemmer G, Harbeck S, Niemann H.
Stochastic segment models of eukaryotic promoter regions.
Pac Symp Biocomput. 2000;:380-91.
PMID: 10902186 [PubMed - indexed for MEDLINE]
Ohler U.
Promoter prediction on a genomic scale--the Adh experience.
Genome Res. 2000 Apr;10(4):539-42.
PMID: 10779494 [PubMed - indexed for MEDLINE]
Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE.
Genome annotation assessment in Drosophila melanogaster.
Genome Res. 2000 Apr;10(4):483-501.
PMID: 10779488 [PubMed - indexed for MEDLINE]
Ohler U, Harbeck S, Niemann H, Nöth E, Reese MG.
Interpolated markov chains for eukaryotic promoter recognition.
Bioinformatics. 1999 May;15(5):362-9.
PMID: 10366656 [PubMed - indexed for MEDLINE]