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Dr Pedro Madrigal

Single-cell computational approaches to define transcriptional and epigenetic signatures of embryonic and extraembryonic lineages in early non-human primate development
Dr Pedro Madrigal

Computational Scientist / Bioinformatician


Office Phone: +44 (0)1223 333886

Research Interests

Pedro originates from Murcia in Spain and is a postdoctoral computational scientist with a background in engineering. He was awarded his PhD in Bioinformatics from the Adam Mickiewicz University in Poland with the support of a EU Marie Curie fellowship.  In 2013, he moved to the UK to join the laboratory of Prof. Ludovic Vallier at the Wellcome Trust-MRC Cambridge Stem Cell Institute and the Wellcome Trust Sanger Institute as a computational biologist. There he studied the influence of epigenome and transcriptome dynamics upon differentiation of human pluripotent stem cells towards definitive endoderm. Pedro has expertise in next-generation sequencing data analysis, especially in developing new statistical methodologies using Functional Data Analysis and as a contributor of software packages to the Bioconductor repository. Pedro joined the Boroviak Lab at the Centre for Trophoblast Research in 2018. His project is about defining transcriptional and epigenetic signatures of embryonic and extraembryonic lineages and to identify primate-specific features and mechanisms in early non-human primate development.

Collaborators

Thorsten Bovoriak
Russel Hamilton

 

Key Publications

Bertero A*,   Brown S*, Madrigal P, Osnato A, Ortmann D, Yiangou L, Kadiwala J, Hubner NC, Ruiz de los Mozos I, Sadee C, Lenaerts A, Nakanoh S, Grandy R, Farnell E, Ule J, Stunnenberg HG, Mendjan S, Vallier L (2018, in press) The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency. Nature

Madrigal P (2017) fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets. Bioinformatics 33, 746-748. DOI: 10.1093/bioinformatics/btw724

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. (2016) A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 13. DOI: 10.1186/s13059-016-0881-8

Pauklin S, Madrigal P, Bertero A, Vallier L. (2016) Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D. Genes Dev. 30, 421-33. DOI: 10.1101/gad.271452.115

Madrigal P, Krajewski P. (2015) Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve transform. BioData Min. 8, 20. DOI: 10.1186/s13040-015-0051-7

Bertero A, Madrigal P, Galli A, Hubner NC, Moreno I, Burks D, Brown S, Pedersen RA, Gaffney D, Mendjan S, Pauklin S, Vallier L. (2015) Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark. Genes Dev. 29, 702-17. DOI: 10.1101/gad.255984.114

Sampaziotis F, de Brito MC*, Madrigal P*, Bertero A, Saeb-Parsy K, Soares FAC, Schrumpf E, Melum E, Karlsen TH, Bradley JA, Gelson WT, Davies S, Baker A, Kaser A, Alexander GJ, Hannan NRF, Vallier L. (2015) Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation. Nat Biotechnol. 33, 845-852. DOI: 10.1038/nbt.3275