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Results: 1 to 20 of 67

1.

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.

Yardımcı GG, Frank CL, Crawford GE, Ohler U.

Nucleic Acids Res. 2014 Oct 29;42(19):11865-78. doi: 10.1093/nar/gku810. Epub 2014 Oct 7.

PMID:
25294828
[PubMed - in process]
Free PMC Article
2.

JAMM: a peak finder for joint analysis of NGS replicates.

Ibrahim MM, Lacadie SA, Ohler U.

Bioinformatics. 2015 Jan 1;31(1):48-55. doi: 10.1093/bioinformatics/btu568. Epub 2014 Sep 15.

PMID:
25223640
[PubMed - in process]
3.

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M.

Plant Cell. 2014 Jul;26(7):2746-60. doi: 10.1105/tpc.114.125617. Epub 2014 Jul 17.

PMID:
25035402
[PubMed - in process]
4.

COUGER--co-factors associated with uniquely-bound genomic regions.

Munteanu A, Ohler U, Gordân R.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W461-7. doi: 10.1093/nar/gku435. Epub 2014 May 26.

PMID:
24861628
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets.

Farazi TA, Leonhardt CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T.

RNA. 2014 Jul;20(7):1090-102. doi: 10.1261/rna.045005.114. Epub 2014 May 23.

PMID:
24860013
[PubMed - indexed for MEDLINE]
6.

Improved transcript isoform discovery using ORF graphs.

Majoros WH, Lebeck N, Ohler U, Li S.

Bioinformatics. 2014 Jul 15;30(14):1958-64. doi: 10.1093/bioinformatics/btu160. Epub 2014 Mar 22.

PMID:
24659106
[PubMed - indexed for MEDLINE]
7.

Global target mRNA specification and regulation by the RNA-binding protein ZFP36.

Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U.

Genome Biol. 2014 Jan 8;15(1):R12. doi: 10.1186/gb-2014-15-1-r12.

PMID:
24401661
[PubMed - in process]
Free PMC Article
8.

Using machine learning to identify disease-relevant regulatory RNAs.

Ohler U.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15516-7. doi: 10.1073/pnas.1315199110. Epub 2013 Sep 17. No abstract available.

PMID:
24046375
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.

Ni T, Yang Y, Hafez D, Yang W, Kiesewetter K, Wakabayashi Y, Ohler U, Peng W, Zhu J.

BMC Genomics. 2013 Sep 11;14:615. doi: 10.1186/1471-2164-14-615.

PMID:
24025092
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.

Megraw M, Mukherjee S, Ohler U.

Genome Biol. 2013 Aug 23;14(8):R85. doi: 10.1186/gb-2013-14-8-r85.

PMID:
23972209
[PubMed - in process]
Free PMC Article
11.

Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of mammalian sex determination.

Munger SC, Natarajan A, Looger LL, Ohler U, Capel B.

PLoS Genet. 2013;9(7):e1003630. doi: 10.1371/journal.pgen.1003630. Epub 2013 Jul 11.

PMID:
23874228
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.

Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U.

Genome Res. 2013 Oct;23(10):1730-9. doi: 10.1101/gr.149310.112. Epub 2013 Jul 1.

PMID:
23816784
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields.

Pruteanu-Malinici I, Majoros WH, Ohler U.

Bioinformatics. 2013 Jul 1;29(13):i27-35. doi: 10.1093/bioinformatics/btt206.

PMID:
23812993
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.

Hafez D, Ni T, Mukherjee S, Zhu J, Ohler U.

Bioinformatics. 2013 Jul 1;29(13):i108-16. doi: 10.1093/bioinformatics/btt233.

PMID:
23812974
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

MicroRNA target site identification by integrating sequence and binding information.

Majoros WH, Lekprasert P, Mukherjee N, Skalsky RL, Corcoran DL, Cullen BR, Ohler U.

Nat Methods. 2013 Jul;10(7):630-3. doi: 10.1038/nmeth.2489. Epub 2013 May 26.

PMID:
23708386
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

FMRP targets distinct mRNA sequence elements to regulate protein expression.

Ascano M Jr, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, Williams Z, Ohler U, Tuschl T.

Nature. 2012 Dec 20;492(7429):382-6. doi: 10.1038/nature11737. Epub 2012 Dec 12.

PMID:
23235829
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.

Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG.

Genome Biol. 2012 Oct 3;13(10):R88. doi: 10.1186/gb-2012-13-10-r88.

PMID:
23034120
[PubMed - in process]
Free PMC Article
18.

A microfluidic device and computational platform for high-throughput live imaging of gene expression.

Busch W, Moore BT, Martsberger B, Mace DL, Twigg RW, Jung J, Pruteanu-Malinici I, Kennedy SJ, Fricke GK, Clark RL, Ohler U, Benfey PN.

Nat Methods. 2012 Nov;9(11):1101-6. doi: 10.1038/nmeth.2185. Epub 2012 Sep 30.

PMID:
23023597
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes.

Katzenberger RJ, Rach EA, Anderson AK, Ohler U, Wassarman DA.

PLoS One. 2012;7(9):e45009. doi: 10.1371/journal.pone.0045009. Epub 2012 Sep 11.

PMID:
22984601
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Predicting cell-type-specific gene expression from regions of open chromatin.

Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U.

Genome Res. 2012 Sep;22(9):1711-22. doi: 10.1101/gr.135129.111.

PMID:
22955983
[PubMed - indexed for MEDLINE]
Free PMC Article

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