Citing and Citations
cgatcore has been developed over the past 10 years and as such has been used in a number of previously published scientific artciles.
Citing cgatcore
When using cgatcore for a publication, please cite the following article in you paper:
ADD CITATION HERE
More references
A number of publications that have used CGAT-developer tools are listed below, however this list is not an exhastive list:
A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution SV Ramagopalan, A Heger, AJ Berlanga, NJ Maugeri, MR Lincoln, … Genome research 20 (10), 1352-1360 2010
Sequencing depth and coverage: key considerations in genomic analyses D Sims, I Sudbery, NE Ilott, A Heger, CP Ponting Nature Reviews Genetics 15 (2), 121 2014
KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands AM Farcas, NP Blackledge, I Sudbery, HK Long, JF McGouran, NR Rose, … elife 2012
Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment S Cooper, M Dienstbier, R Hassan, L Schermelleh, J Sharif, … Cell reports 7 (5), 1456-1470 2014
Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes NE Ilott, JA Heward, B Roux, E Tsitsiou, PS Fenwick, L Lenzi, I Goodhead, … Nature communications 5, 3979 2014
Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia SN Sansom, N Shikama-Dorn, S Zhanybekova, G Nusspaumer, … Genome research 24 (12), 1918-1931 2014
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates HK Long, D Sims, A Heger, NP Blackledge, C Kutter, ML Wright, … Elife 2 2013
The long non‐coding RNA Paupar regulates the expression of both local and distal genes KW Vance, SN Sansom, S Lee, V Chalei, L Kong, SE Cooper, PL Oliver, … The EMBO journal 33 (4), 296-311 2014
A genome-wide association study implicates the APOE locus in nonpathological cognitive ageing G Davies, SE Harris, CA Reynolds, A Payton, HM Knight, DC Liewald, … Molecular Psychiatry 19 (1), 76 2014
Predicting long non-coding RNAs using RNA sequencing NE Ilott, CP Ponting Methods 63 (1), 50-59 2013
Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy P Rajan, IM Sudbery, MEM Villasevil, E Mui, J Fleming, M Davis, I Ahmad, … European urology 66 (1), 32-39 2014
The long non-coding RNA Dali is an epigenetic regulator of neural differentiation V Chalei, SN Sansom, L Kong, S Lee, JF Montiel, KW Vance, CP Ponting Elife 3 2014
GAT: a simulation framework for testing the association of genomic intervals A Heger, C Webber, M Goodson, CP Ponting, G Lunter Bioinformatics 29 (16), 2046-2048 2013
De novo point mutations in patients diagnosed with ataxic cerebral palsy R Parolin Schnekenberg, EM Perkins, JW Miller, WIL Davies, … Brain 138 (7), 1817-1832 2015
SPG7 mutations are a common cause of undiagnosed ataxia G Pfeffer, A Pyle, H Griffin, J Miller, V Wilson, L Turnbull, K Fawcett, … Neurology 84 (11), 1174-1176 2015
CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes C Laitem, J Zaborowska, NF Isa, J Kufs, M Dienstbier, S Murphy Nature Structural and Molecular Biology 22 (5), 396 2015
IRF5: RelA interaction targets inflammatory genes in macrophages DG Saliba, A Heger, HL Eames, S Oikonomopoulos, A Teixeira, K Blazek, … Cell reports 8 (5), 1308-1317 2014
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy T Smith, A Heger, I Sudbery Genome research 27 (3), 491-499 2017
Long noncoding RNAs in B-cell development and activation TF Brazão, JS Johnson, J Müller, A Heger, CP Ponting, VLJ Tybulewicz Blood 128 (7), e10-e19 2016
CGAT: computational genomics analysis toolkit D Sims, NE Ilott, SN Sansom, IM Sudbery, JS Johnson, KA Fawcett, … Bioinformatics 30 (9), 1290-1291 2014