scAbsolute: measuring single-cell ploidy and replication status

Autor: Michael P. Schneider, Amy E. Cullen, Justina Pangonyte, Jason Skelton, Harvey Major, Elke Van Oudenhove, Maria J. Garcia, Blas Chaves Urbano, Anna M. Piskorz, James D. Brenton, Geoff Macintyre, Florian Markowetz

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-27 (2024)

Abstract Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-cell DNA sequencing information, s

Externí odkaz: https://doaj.org/article/9e368e2318e242c8953f09f4b2805e9d

Correction to: VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer

Autor: Andrew N. Holding, Federico M. Giorgi, Amanda Donnelly, Amy E. Cullen, Sankari Nagarajan, Luke A. Selth, Florian Markowetz

Publikováno v: Genome Biology, Vol 20, Iss 1, Pp 1-2 (2019)

Following publication of the original article [1], the authors reported that Figs. 4 and 5 had mistakenly been transposed. Please find the correct Figs. 4 and 5 below. The original article [1] has been corrected.

Externí odkaz: https://doaj.org/article/5e3c41b12a864729b8883fc2a502ceb2

VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer

Autor: Florian Markowetz, Amy E Cullen, Sankari Nagarajan, Andrew N Holding, Federico M. Giorgi, Amanda Donnelly, Luke A. Selth

Publikováno v: Holding, A N, Giorgi, F M, Donnelly, A, Cullen, A E, Nagarajan, S, Selth, L A & Markowetz, F 2019, ' VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer ', Genome biology, vol. 20, no. 1 . https://doi.org/10.1186/s13059-019-1698-z
Genome Biology, Vol 20, Iss 1, Pp 1-16 (2019)

BackgroundVirtUaL ChIP-seq Analysis through Networks (VULCAN) infers regulatory interactions of transcription factors by overlaying networks generated from publicly available tumor expression data onto ChIP-seq data. We apply our method to dissect th

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::617bf496f488e44f30a5814f52a23286

Network analysis of ChIP-seq data by VULCAN identifies GRHL2 as a key co-regulator of ERa in luminal breast cancer

Autor: Andrew N Holding, Amanda Donnelly, Federico M. Giorgi, Sankari Nagarajan, Luke A. Selth, Amy E Cullen, Florian Markowetz

Background VirtUaL ChIP-seq Analysis through Networks (VULCAN) infers regulatory interactions of transcription factors by overlaying networks generated from publicly available tumor expression data onto ChIP-seq data. We applied our method to dissect

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::217c2c21c577c1e92345167503a2fea9

Novel Quantitative ChIP-seq Methods Measure Absolute Fold-Change in ER Binding Upon Fulvestrant Treatment

Autor: Andrew N Holding, Michael J. Guertin, Amy E Cullen, Florian Markowetz

A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes in occupancy. Analysis-based normalisation methods were developed for transcriptomic data and these are dependent on the underlying assumptio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fd777465a2e126e6592ef77f56459345
https://doi.org/10.1101/182261