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Items: 1 to 20 of 82

1.

Genome-wide identification of regulatory elements in Sertoli cells.

Maatouk DM, Natarajan A, Shibata Y, Song L, Crawford GE, Ohler U, Capel B.

Development. 2017 Jan 13. pii: dev.142554. doi: 10.1242/dev.142554. [Epub ahead of print]

PMID:
28087634
2.

JACUSA: site-specific identification of RNA editing events from replicate sequencing data.

Piechotta M, Wyler E, Ohler U, Landthaler M, Dieterich C.

BMC Bioinformatics. 2017 Jan 3;18(1):7. doi: 10.1186/s12859-016-1432-8.

3.

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells.

Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO.

Cell Stem Cell. 2016 Dec 8. pii: S1934-5909(16)30402-7. doi: 10.1016/j.stem.2016.11.006. [Epub ahead of print]

PMID:
27939218
4.

Integrative classification of human coding and noncoding genes through RNA metabolism profiles.

Mukherjee N, Calviello L, Hirsekorn A, de Pretis S, Pelizzola M, Ohler U.

Nat Struct Mol Biol. 2017 Jan;24(1):86-96. doi: 10.1038/nsmb.3325.

PMID:
27870833
5.

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.

Li S, Yamada M, Han X, Ohler U, Benfey PN.

Dev Cell. 2016 Nov 21;39(4):508-522. doi: 10.1016/j.devcel.2016.10.012.

PMID:
27840108
6.

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.

Hsu PY, Calviello L, Wu HL, Li FW, Rothfels CJ, Ohler U, Benfey PN.

Proc Natl Acad Sci U S A. 2016 Oct 21. pii: 201614788. [Epub ahead of print]

PMID:
27791167
7.

The mRNA-bound proteome of the early fly embryo.

Wessels HH, Imami K, Baltz AG, Kolinski M, Beldovskaya A, Selbach M, Small S, Ohler U, Landthaler M.

Genome Res. 2016 Jul;26(7):1000-9. doi: 10.1101/gr.200386.115.

8.

Divergent transcription and epigenetic directionality of human promoters.

Lacadie SA, Ibrahim MM, Gokhale SA, Ohler U.

FEBS J. 2016 Dec;283(23):4214-4222. doi: 10.1111/febs.13747. Review.

PMID:
27115538
9.

CSEQ-SIMULATOR: A DATA SIMULATOR FOR CLIP-SEQ EXPERIMENTS.

Kassuhn W, Ohler U, Drewe P.

Pac Symp Biocomput. 2016;21:433-44.

10.

Detecting actively translated open reading frames in ribosome profiling data.

Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U.

Nat Methods. 2016 Feb;13(2):165-70. doi: 10.1038/nmeth.3688.

PMID:
26657557
11.

Perspectives on Unidirectional versus Divergent Transcription.

Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U.

Mol Cell. 2015 Nov 5;60(3):348-9. doi: 10.1016/j.molcel.2015.10.014. No abstract available.

12.

Transcriptional control of tissue formation throughout root development.

Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN.

Science. 2015 Oct 23;350(6259):426-30. doi: 10.1126/science.aad1171.

13.

Identifying RBP Targets with RIP-seq.

Wessels HH, Hirsekorn A, Ohler U, Mukherjee N.

Methods Mol Biol. 2016;1358:141-52. doi: 10.1007/978-1-4939-3067-8_9.

PMID:
26463382
14.

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms.

Mino T, Murakawa Y, Fukao A, Vandenbon A, Wessels HH, Ori D, Uehata T, Tartey S, Akira S, Suzuki Y, Vinuesa CG, Ohler U, Standley DM, Landthaler M, Fujiwara T, Takeuchi O.

Cell. 2015 May 21;161(5):1058-73. doi: 10.1016/j.cell.2015.04.029.

15.

Human promoters are intrinsically directional.

Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U.

Mol Cell. 2015 Feb 19;57(4):674-84. doi: 10.1016/j.molcel.2014.12.029.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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