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Items: 1 to 50 of 98

1.

Deciphering human ribonucleoprotein regulatory networks.

Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Ghanbari M, Garzia A, Munteanu A, Yusuf D, Farazi T, Hoell JI, Akat KM, Akalin A, Tuschl T, Ohler U.

Nucleic Acids Res. 2019 Jan 25;47(2):570-581. doi: 10.1093/nar/gky1185.

2.

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.

Drewe-Boss P, Wessels HH, Ohler U.

Genome Biol. 2018 Nov 1;19(1):183. doi: 10.1186/s13059-018-1521-2.

3.

Determinants of promoter and enhancer transcription directionality in metazoans.

Ibrahim MM, Karabacak A, Glahs A, Kolundzic E, Hirsekorn A, Carda A, Tursun B, Zinzen RP, Lacadie SA, Ohler U.

Nat Commun. 2018 Oct 26;9(1):4472. doi: 10.1038/s41467-018-06962-z.

4.

Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation.

Qu Y, Legen J, Arndt J, Henkel S, Hoppe G, Thieme C, Ranzini G, Muino JM, Weihe A, Ohler U, Weber G, Ostersetzer O, Schmitz-Linneweber C.

Front Plant Sci. 2018 Oct 4;9:1453. doi: 10.3389/fpls.2018.01453. eCollection 2018.

5.

SSMART: sequence-structure motif identification for RNA-binding proteins.

Munteanu A, Mukherjee N, Ohler U.

Bioinformatics. 2018 Dec 1;34(23):3990-3998. doi: 10.1093/bioinformatics/bty404.

PMID:
29893814
6.

Finding RNA structure in the unstructured RBPome.

Orenstein Y, Ohler U, Berger B.

BMC Genomics. 2018 Feb 20;19(1):154. doi: 10.1186/s12864-018-4540-1.

7.

Redundant regulation.

Lacadie SA, Ohler U.

Nat Ecol Evol. 2018 Mar;2(3):418-419. doi: 10.1038/s41559-018-0479-5. No abstract available.

PMID:
29379186
8.

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.

Hafez D, Karabacak A, Krueger S, Hwang YC, Wang LS, Zinzen RP, Ohler U.

Genome Biol. 2017 Oct 26;18(1):199. doi: 10.1186/s13059-017-1316-x.

9.

Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP.

Hinze F, Drewe-Boss P, Milek M, Ohler U, Landthaler M, Gotthardt M.

RNA Biol. 2018 Mar 4;15(3):359-368. doi: 10.1080/15476286.2017.1384120. Epub 2018 Jan 24.

10.

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.

Heller D, Krestel R, Ohler U, Vingron M, Marsico A.

Nucleic Acids Res. 2017 Nov 2;45(19):11004-11018. doi: 10.1093/nar/gkx756.

11.

RNA localization is a key determinant of neurite-enriched proteome.

Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M.

Nat Commun. 2017 Sep 19;8(1):583. doi: 10.1038/s41467-017-00690-6.

12.

Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome.

Calviello L, Ohler U.

Trends Genet. 2017 Oct;33(10):728-744. doi: 10.1016/j.tig.2017.08.003. Epub 2017 Sep 5. Review.

PMID:
28887026
13.

DDX54 regulates transcriptome dynamics during DNA damage response.

Milek M, Imami K, Mukherjee N, Bortoli F, Zinnall U, Hazapis O, Trahan C, Oeffinger M, Heyd F, Ohler U, Selbach M, Landthaler M.

Genome Res. 2017 Aug;27(8):1344-1359. doi: 10.1101/gr.218438.116. Epub 2017 Jun 8.

14.

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R.

Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409.

15.

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation.

Backofen R, Engelhardt J, Erxleben A, Fallmann J, Grüning B, Ohler U, Rajewsky N, Stadler PF.

J Biotechnol. 2017 Nov 10;261:76-84. doi: 10.1016/j.jbiotec.2017.05.019. Epub 2017 May 26. Review.

16.

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A.

Nucleic Acids Res. 2017 Jun 2;45(10):e91. doi: 10.1093/nar/gkx120.

17.

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 Feb 15;144(4):720-730. doi: 10.1242/dev.142554. Epub 2017 Jan 13.

18.

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.

19.

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. 2017 Feb 2;20(2):205-217.e8. doi: 10.1016/j.stem.2016.11.006. Epub 2016 Dec 8.

20.

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. Epub 2016 Nov 21.

PMID:
27870833
21.

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. Epub 2016 Nov 10.

22.

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 Nov 8;113(45):E7126-E7135. doi: 10.1073/pnas.1614788113. Epub 2016 Oct 21.

23.

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. Epub 2016 Apr 28.

24.

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. Epub 2016 May 11. Review.

25.

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

Kassuhn W, Ohler U, Drewe P.

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

26.

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. Epub 2015 Dec 14.

PMID:
26657557
27.

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.

28.

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.

29.

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
30.

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):1058-1073. doi: 10.1016/j.cell.2015.04.029.

31.

Human promoters are intrinsically directional.

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

Mol Cell. 2015 Feb 19;57(4):674-684. doi: 10.1016/j.molcel.2014.12.029. Epub 2015 Jan 29.

32.

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.

33.

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
34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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