| A Survey of Best Practices for RNA-seq Data Analysis A Conesa, P Madrigal, S Tarazona, D Gomez-Cabrero, A Cervera, ... Genome Biology 17, 13, 2016 | 1623 | 2016 |
| Practical guidelines for the comprehensive analysis of ChIP-seq data T Bailey, P Krajewski, I Ladunga, C Lefebvre, Q Li, T Liu, P Madrigal, ... PLoS Computational Biology 9 (11), e1003326, 2013 | 283 | 2013 |
| Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation F Sampaziotis, M Cardoso de Brito, P Madrigal, A Bertero, K Saeb-Parsy, ... Nature Biotechnology, 2015 | 226 | 2015 |
| Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development A Pajoro, P Madrigal, JM Muiño, JT Matus, J Jin, MA Mecchia, ... Genome biology 15 (3), R41, 2014 | 162 | 2014 |
| The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency A Bertero, S Brown, P Madrigal, A Osnato, D Ortmann, L Yiangou, ... Nature 555 (7695), 256-259, 2018 | 127 | 2018 |
| Reconstruction of the mouse extrahepatic biliary tree using primary human extrahepatic cholangiocyte organoids F Sampaziotis, AW Justin, OC Tysoe, S Sawiak, EM Godfrey, SS Upponi, ... Nature medicine 23 (8), 954, 2017 | 124 | 2017 |
| Reconstruction of the mouse extrahepatic biliary tree using primary human extrahepatic cholangiocyte organoids F Sampaziotis, AW Justin, OC Tysoe, S Sawiak, EM Godfrey, SS Upponi, ... Nature medicine 23 (8), 954, 2017 | 124 | 2017 |
| Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis JL Mateos, P Madrigal, K Tsuda, V Rawat, R Richter, M Romera-Branchat, ... Genome Biology 16, 31, 2015 | 104 | 2015 |
| Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark A Bertero, P Madrigal, A Galli, NC Hubner, I Moreno, D Burks, S Brown, ... Genes & development 29 (7), 702-717, 2015 | 95 | 2015 |
| Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D S Pauklin, P Madrigal, A Bertero, L Vallier Genes & development 30, 421-433, 2016 | 90 | 2016 |
| Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression ASE Cuomo, DD Seaton, DJ McCarthy, I Martinez, MJ Bonder, ... Nature Communications 11, 1-14, 2020 | 50 | 2020 |
| Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data P Madrigal, P Krajewski Frontiers in Genetics 3, 230, 2012 | 44 | 2012 |
| On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions P Madrigal Front. Bioeng. Biotechnol. 3, 144, 2015 | 31 | 2015 |
| Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species JL Mateos, V Tilmes, P Madrigal, E Severing, R Richter, CWM Rijkenberg, ... Proceedings of the National Academy of Sciences, 10.1073/pnas.1618075114, 2017 | 26 | 2017 |
| AP-1 Takes Centre Stage in Enhancer Chromatin Dynamics P Madrigal, K Alasoo Trends in Cell Biology 28 (7), 3, 2018 | 25 | 2018 |
| hiPSC hepatocyte model demonstrates the role of unfolded protein response and inflammatory networks in α1-antitrypsin deficiency CP Segeritz, ST Rashid, M Cardoso de Brito, MS Paola, A Ordonez, ... Journal of Hepatology, 2018 | 17 | 2018 |
| GATA6 Cooperates with EOMES/SMAD2/3 to Deploy the Gene Regulatory Network Governing Human Definitive Endoderm and Pancreas Formation CY Chia, P Madrigal, SLIJ Denil, I Martinez, J Garcia-Bernardo, ... Stem Cell Reports 12 (1), 57-70, 2019 | 15 | 2019 |
| Functional Divergence of the Arabidopsis Florigen-Interacting bZIP Transcription Factors FD and FDP M Romera-Branchat, E Severing, C Pocard, H Ohr, C Vincent, G Née, ... Cell Reports 31 (9), 107717, 2020 | 13 | 2020 |
| Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve transform P Madrigal, P Krajewski BioData Mining 8, 20, 2015 | 12 | 2015 |
| Functional data analysis for computational biology M Cremona, H Xu, K Makova, M Reimherr, F Chiaromonte, P Madrigal Bioinformatics, 2019 | 8 | 2019 |
Ludovic VallierCambridge University and Wellcome Trust Sanger InstituteVerified email at cam.ac.uk
