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Cambridge Cardiovascular



Statistical and regulatory genomics in human induced pluripotent stem cells

My research focuses on gene regulation in human cells through combining methods in statistical genetics and comparative genomics with high-throughput experimental techniques, such as ChIP-seq and DNaseI-seq.

My group uses naturally occurring human genetic variation as a model system to test hypotheses about gene regulation. we are also interested in developing evolutionary models of gene regulation to understand how changes at the molecular level drive gene expression divergence between species.


Key publications: 

Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark. Bertero A, Madrigal P, Galli A, Hubner NC, Moreno I, Burks D, Brown S, Pedersen RA, Gaffney D, Mendjan S, Pauklin S, Vallier L. Genes Dev. 2015 Apr 1;29(7):702-17.

Genetic background drives transcriptional variation in human induced pluripotent stem cells. Rouhani F, Kumasaka N, de Brito MC, Bradley A, Vallier L, Gaffney D. PLoS Genet. 2014 Jun 5;10(6):e1004432.

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation. Aldridge S, Watt S, Quail MA, Rayner T, Lukk M, Bimson MF, Gaffney D, Odom DT. Genome Biol. 2013 Nov 7;14(11):R124.

Global properties and functional complexity of human gene regulatory variation. Gaffney DJ. PLoS Genet. 2013 May;9(5):e1003501.

CDF Group Leader (Sanger Institute)
Dr Daniel  Gaffney

Contact Details


Collaborator profiles: 
Person keywords: 
iPS (induced pluripotent stem cells)
stem cells