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Items: 7

1.

Scalable Workflows and Reproducible Data Analysis for Genomics.

Strozzi F, Janssen R, Wurmus R, Crusoe MR, Githinji G, Di Tommaso P, Belhachemi D, Möller S, Smant G, de Ligt J, Prins P.

Methods Mol Biol. 2019;1910:723-745. doi: 10.1007/978-1-4939-9074-0_24.

PMID:
31278683
2.

HOT or not: examining the basis of high-occupancy target regions.

Wreczycka K, Franke V, Uyar B, Wurmus R, Bulut S, Tursun B, Akalin A.

Nucleic Acids Res. 2019 Jun 20;47(11):5735-5745. doi: 10.1093/nar/gkz460.

3.

Global identification of functional microRNA-mRNA interactions in Drosophila.

Wessels HH, Lebedeva S, Hirsekorn A, Wurmus R, Akalin A, Mukherjee N, Ohler U.

Nat Commun. 2019 Apr 9;10(1):1626. doi: 10.1038/s41467-019-09586-z.

4.

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.

Karabacak Calviello A, Hirsekorn A, Wurmus R, Yusuf D, Ohler U.

Genome Biol. 2019 Feb 21;20(1):42. doi: 10.1186/s13059-019-1654-y.

5.

PiGx: reproducible genomics analysis pipelines with GNU Guix.

Wurmus R, Uyar B, Osberg B, Franke V, Gosdschan A, Wreczycka K, Ronen J, Akalin A.

Gigascience. 2018 Dec 1;7(12). doi: 10.1093/gigascience/giy123.

6.

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.

7.

DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.

Blin K, Dieterich C, Wurmus R, Rajewsky N, Landthaler M, Akalin A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D160-7. doi: 10.1093/nar/gku1180. Epub 2014 Nov 21.

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