RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data

Autor: Zhijian Li, Chao-Chung Kuo, Fabio Ticconi, Mina Shaigan, Julia Gehrmann, Eduardo Gade Gusmao, Manuel Allhoff, Martin Manolov, Martin Zenke, Ivan G. Costa

Publikováno v: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-12 (2023)

Abstract Background Massive amounts of data are produced by combining next-generation sequencing with complex biochemistry techniques to characterize regulatory genomics profiles, such as protein–DNA interaction and chromatin accessibility. Interpr

Externí odkaz: https://doaj.org/article/ebd553fe4f374c11b81204a9c95da07a

Differential roles of STAT1 and STAT2 in the sensitivity of JAK2V617F- vs. BCR-ABL-positive cells to interferon alpha

Autor: Mirle Schemionek, Steffen Koschmieder, Nicolas Chatain, Claudia Schubert, Manuel Allhoff, Daniel B. Lipka, Kristina Feldberg, Tiago Maié, Stefan Tillmann, Julian Baumeister, Tim H. Brümmendorf, Ivan G. Costa

Publikováno v: Journal of hematology & oncology 12, 36 (2019). doi:10.1186/s13045-019-0722-9
Journal of Hematology & Oncology
Journal of Hematology & Oncology, Vol 12, Iss 1, Pp 1-16 (2019)

Background Interferon alpha (IFNa) monotherapy is recommended as the standard therapy in polycythemia vera (PV) but not in chronic myeloid leukemia (CML). Here, we investigated the mechanisms of IFNa efficacy in JAK2V617F- vs. BCR-ABL-positive cells.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ab8df5bd748e5496ea972e8cae129873
https://publications.rwth-aachen.de/record/772716

Analysis of computational footprinting methods for DNase sequencing experiments

Autor: Eduardo G. Gusmao, Ivan G. Costa, Manuel Allhoff, Martin Zenke

Publikováno v: Nature methods. 13(4)

DNase-seq allows nucleotide-level identification of transcription factor binding sites on the basis of a computational search of footprint-like DNase I cleavage patterns on the DNA. Frequently in high-throughput methods, experimental artifacts such a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1547453c54f6fbf88c2e54521084e574
https://pubmed.ncbi.nlm.nih.gov/26901649

Discovering motifs that induce sequencing errors

Autor: Ivan G. Costa, Manuel Allhoff, Marcel Martin, Tobias Marschall, Alexander Schönhuth, Sven Rahmann

Publikováno v: BMC bioinformatics 14(Supplement 5), S1 (2013). doi:10.1186/1471-2105-14-S5-S1
BMC Bioinformatics, 14(Suppl 5)
BMC Bioinformatics

BMC bioinformatics 14(Supplement 5), S1 (2013). doi:10.1186/1471-2105-14-S5-S1
Published by BioMed Central [u.a.], London

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::45727bf0cc7887a26873c0756981bd83