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Citing and Citations

cgatcore has been developed over the past 10 years and has been used in a number of previously published scientific articles. This page provides information on how to cite cgatcore and highlights some of the key publications where it has been used.

Citing cgatcore

When using cgatcore for a publication, please cite the following article in your paper:

ADD CITATION HERE

More references

The following is a list of publications that have used tools developed by CGAT developers. Note that this list is not exhaustive:

  • 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)