Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer.

Autor: Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G Stunnenberg, Sampsa Hautaniemi

Publikováno v: PLoS Computational Biology, Vol 9, Iss 6, p e1003100 (2013)

Identification of responsive genes to an extra-cellular cue enables characterization of pathophysiologically crucial biological processes. Deep sequencing technologies provide a powerful means to identify responsive genes, which creates a need for co

Externí odkaz: https://doaj.org/article/0e84788c4dd94d04b5fec045a77ecd66

Predicting stimulation-dependent enhancer-promoter interactions from chip-seq time course data

Autor: Filomena Matarese, Henk Stunnenberg, George Reid, Korbinian Grote, Antti Honkela, Iryna Charapitsa, Tomasz Dzida, Magnus Rattray, Mudassar Iqbal

Publikováno v: PeerJ, 5, 1-23
PeerJ
PeerJ, 5, pp. 1-23
PeerJ, Vol 5, p e3742 (2017)

We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II)

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::65286b604d4225b2b332a2fc86d38fe2
http://hdl.handle.net/2066/177896

A transient ischemic environment induces reversible compaction of chromatin

Autor: Aleksander Szczurek, Michael U. Musheev, Christoph Cremer, Ina Kirmes, George Reid, Udo Birk, Kirti Prakash, Karolina Fornalczyk, Florian Schock, Christina Heiser, Dongyu Ma, Iryna Charapitsa

Publikováno v: Genome Biology

Background Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule loc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eeada4fb4179b6b94715e8a675bff113

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

Autor: George Reid, Neil D. Lawrence, Hande Topa, Jaakko Peltonen, Filomena Matarese, Hendrik G. Stunnenberg, Iryna Charapitsa, Antti Honkela, Korbinian Grote, Magnus Rattray

Publikováno v: Proceedings of the National Academy of Sciences USA, 112, 42, pp. 13115-13120
Proceedings of the National Academy of Sciences USA, 112, 13115-13120

Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a splicing-associated RNA

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::021000259721afa809d824dbfedc872d
https://doi.org/10.1073/pnas.1420404112

Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer

Autor: George Reid, Alejandra Cervera, Iryna Charapitsa, Martin Seifert, Chengyu Liu, Hendrik G. Stunnenberg, Korbinian Grote, Filomena Matarese, Kristian Ovaska, Sampsa Hautaniemi

Publikováno v: PLoS Computational Biology
PLoS Computational Biology, Vol 9, Iss 6, p e1003100 (2013)

Identification of responsive genes to an extra-cellular cue enables characterization of pathophysiologically crucial biological processes. Deep sequencing technologies provide a powerful means to identify responsive genes, which creates a need for co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bb6b4109a7e3c426188bf24aed1c8211
https://doi.org/10.1371/journal.pcbi.1003100