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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 333831

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 open source Bioconductor repository.

Pedro joined the Boroviak Lab at the Centre for Trophoblast Research in 2018. He works on defining transcriptional and epigenetic signatures of embryonic and extraembryonic lineages and to identify primate-specific features and mechanisms in early non-human primate development. 

 

 

 

Publications

Bioinformatics

Madrigal P (2017) fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasetsBioinformatics 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

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

Madrigal P (2015) On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions. Front Bioeng Biotechnol. 3,144. DOI: http://10.3389/fbioe.2015.00144

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J. (2013) Practical guidelines for the comprehensive analysis of ChIP-seq dataPLoS Comput Biol. 9, e1003326. DOI: 10.1371/journal.pcbi.1003326

 

Pluripotency and Stem Cells

Madrigal P, Alasoo K (2018) AP-1 Takes Centre Stage in Enhancer Chromatin Dynamics. Trends Cell Biol. 28, 509-511. DOI: 10.1016/j.tcb.2018.04.009

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) The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotencyNature 555,256-259. DOI: http://10.1038/nature25784

Sampaziotis F, Justin AW, Tysoe OC, Sawiak S, Godfrey EM, Upponi SS, Gieseck RL 3rd, de Brito MC, Berntsen NL, Gómez-Vázquez MJ, Ortmann D, Yiangou L, Ross A, Bargehr J, Bertero A, Zonneveld MCF, Pedersen MT, Pawlowski M, Valestrand L, Madrigal P, Georgakopoulos N, Pirmadjid N, Skeldon GM, Casey J, Shu W, Materek PM, Snijders KE, Brown SE, Rimland CA, Simonic I, Davies SE, Jensen KB, Zilbauer M, Gelson WTH, Alexander GJ, Sinha S, Hannan NRF, Wynn TA, Karlsen TH, Melum E, Markaki AE, Saeb-Parsy K, Vallier L (2017) Reconstruction of the mouse extrahepatic biliary tree using primary human extrahepatic cholangiocyte organoids. Nat Med. 23, 954-963. DOI: http:// 10.1038/nm.4360

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

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

 

Plant Biology

Mateos JL, Tilmes V, Madrigal P, Severing E, Richter R, Rijkenberg CWM, Krajewski P, Coupland G (2017) Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species. PNAS 114, E11037-E11046. DOI: http://10.1073/pnas.1618075114

Mateos JL*, Madrigal P*, Tsuda K, Rawat V, Richter R, Romera-Branchat M, Fornara F, Schneeberger K, Krajewski P, Coupland G (2015) Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biol. 16, 31. DOI: 10.1186/s13059-015-0597-1.

Pajoro A, Madrigal P, Muiño JM, Matus JT, Jin J, Mecchia MA, Debernardi JM, Palatnik JF, Balazadeh S, Arif M, Ó'Maoiléidigh DS, Wellmer F, Krajewski P, Riechmann JL, Angenent GC, Kaufmann K (2014) Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol. 15, R41. DOI: 10.1186/gb-2014-15-3-r41