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Jason Piper


As of December 2014, I have completed my PhD. Please see my LinkedIn profile for my current whereabouts, or contact me via


2011-2014 PhD Systems Biology University of Warwick
2010-2011 MSc Systems Biology University of Warwick
2006-2010 BSc Biochemistry (with a Year in Industry at the MRC NIMR) University of York


Cauchy P, James SR, Zacarias-Cabeza J, Ptasinska A, Imperato MR, Assi SA, Piper J, Canestraro M, Hoogenkamp M, Raghavan M, Loke J, Akiki S, Clokie SJ, Richards SJ, Westhead DR, Griffiths MJ, Ott S, Bonifer C, Cockerill PN Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature. Cell Reports 12(5):821-36, 2015 (PDF Document)

Ptasinska, A, Assi SA, Martinez-Soria N, Imperato MR, Piper J, Cauchy P, Pickin A, James SR, Hoogenkamp M, Williamson D, Wu M, Tenen DG, Ott S, Westhead DR, Cockerill PN, Heidenreich O, Bonifer C. Identification of a dynamic core transcriptional network in t(8;21) AML regulating differentiation block and self-renewal. Cell Reports, 8: 1-15, 2014 (PDF Document)

Piper, J; Elze, MC; Cauchy P ; Cockerill PN; Bonifer C; Ott S. Wellington: A novel method for the accurate identification of digital genomic footprints from DNase-seq data, Nucleic Acids Research 2013 (PDF Document)

PhD Research Project

Supervised by Prof. Constanze Bonifer (Birmingham) & Dr. Sascha Ott (Warwick)

  • Mapping DNA footprints (Protein-DNA binding sites) in DNase-seq datasets.

As part of this project, I developed a python library for analysing DNase-seq cut sites (instead of pile-ups that ChIP-seq software uses) in Python (pyDNase) along with a novel algorithm (Wellington) for mapping DNA footprints on a genomic scale.

Past Research Projects

For my undergraduate dissertation I developed computational tools in Python for the construction and analysis of complex social networks of academics within the department of biology at the University of York based on a mix of curated and non-curated sources. This involved data mining and sanitation from multiple sources by writing different scrapers and also the subsequent construction, visualisation and analysis of these networks using available software such as Visone and by programming my own statistics by using the igraph library.

I spent my Year in Industry at the NIMR studying the epigenetic modification of HPV-16 episomes after transfection and infection with genetically modified pseudovirions produced by myself.


Teaching assistant for BS918, CH923, and MIBTP masterclasses on Statistics, Bioinformatics, and Genomics.