Frost JF, Amante SM, Okae H, Jones EM, Ashley B, Lewis RM, Cleal JK, Caley MP, Arima T, Maffucci T, Branco MR (2023) “Regulation of human trophoblast gene expression by endogenous retroviruses”, Nat Struct Mol Biol, [PDF] [GEO] [Github]

Taylor D, Branco MR (2023) “Inferring protein-DNA binding profiles at interspersed repeats using HiChIP and PAtChER”, Methods in Molecular Biology, 2607:199-214 [PubMed] [Request PDF]

Ashley B, Simner C, Manousopoulou A, Jenkinson C, Hey F, Frost JM, Rezwan FI, White CH, Lofthouse EM, Hyde E, Cooke L, Barton S, Mahon P, Curtis EM, Moon RJ, Crozier SR, Inskip HM, Godfrey KM, Holloway JW, Cooper C, Jones KS, Lewis RM, Hewison M, Garbis SD, Branco MR, Harvey NC, Cleal JK (2022) “Placental uptake and metabolism of 25(OH)vitamin D determine its activity within the fetoplacental unit”, eLife, 11:e71094 [PDF] [GEO]

Taylor D, Lowe R, Philippe C, Cheng KCL, Grant OA, Zabet NR, Cristofari G, Branco MR (2022) “Locus-specific chromatin profiling of evolutionarily young transposable elements”, Nucleic Acids Research, 50:e33 [PDF] [GEO] [Github] [PAtChER]

Pezic D, Weeks S, Varsally W, Dewari PS, Branco MR, Hadjur S (2021) “The cohesin regulator Stag1 promotes cell plasticity through heterochromatin regulation”, bioRxiv, [PDF]

Shendy NAM, Raghu D, Roy S, Perry CH, Safi A, Branco MR, Homayouni R, Abell AN (2020) “Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching”, Communications Biology, 3:475 [PubMed] [PDF] [GEO]

De Borre M, Branco MR (2020) “Oxidative bisulfite sequencing: an experimental and computational protocol”, Methods in Molecular Biology, 2198:333-48 [PubMed] [Request PDF]

Schlesinger S, Branco MR, Mermoud JE (2020) “Roles and regulation of endogenous retroviruses in pluripotency and early development”. In Stem Cell Epigenetics (Translational Epigenetics Series, vol. 17): Academic Press [Request PDF]

Deniz O, Ahmed M, Todd CD, Rio-Machin A, Dawson MA, Branco MR (2020) “Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia”, Nature Communications, 11:3506 [PubMed] [PDF] [GEO] [GitHub]

Antunes C, da Silva JD, Guerra-Gomes S, Alves ND, Ferreira F, Loureiro-Campos E, Branco MR, Sousa N, Reik W, Pinto L, Marques CJ (2020) “Tet3 ablation in adult brain neurons increases anxiety-like behavior and regulates cognitive function in mice”, Molecular Psychiatry, Online ahead of print [PubMed] [Request PDF] [GEO]

Senner CE, Chrysanthou S, Burge S, Lin H-Y, Branco MR, Hemberger M (2020) “TET1 and 5-Hydroxymethylation Preserve the Stem Cell State of Mouse Trophoblast”, Stem Cell Reports, doi: 10.1016/j.stemcr.2020.04.009 [PubMed] [PDF] [GEO]

Branco MR, Chuong EB (2020) “Crossroads between transposons and gene regulation”, Philosophical Transactions of the Royal Society B, 375:20190330 [PubMed] [PDF]

Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Reik W, Sousa N, Pinto L, Branco MR, Marques CJ (2019) “Tet3 regulates cellular identity and DNA methylation in neural progenitor cells”, Cellular and Molecular Life Sciences, 77:2871-83 [PubMed] [PDF] [GEO]

Carrillo-Jimenez A, Deniz O, Niklison-Chirou MV, Ruiz R, Bezerra-Salomao K, Stratoulias V, Amoroux R, Yip PK, Vilalta A, Cheray M, Scott-Egerton AM, Rivas E, Tayara K, Garcia-Dominguez I, Garcia-Revilla J, Fernandez-Martin JC, Espinosa-Oliva AM, Shen X, St George-Hyslop P, Brown GC, Hajkova P, Joseph B, Venero JL, Branco MR, Buguillos M (2019) “TET2 regulates the neuroinflammatory response in microglia”, Cell Reports, 29:697-713 [PubMed] [PDF] [GEO]

Todd CD, Deniz O, Taylor D, Branco MR (2019) “Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells”, eLife, 8:e44344 [PubMed] [PDF] [GEO] [GitHub]

Deniz O, Frost J, Branco MR (2019) “Regulation of transposable elements by DNA modifications”, Nature Reviews Genetics, 20:417-31 [PubMed] [Request PDF]

Schoenfelder S, Mifsud B, Senner CE, Todd CD, Chrysanthou S, Darbo E, Hemberger M, Branco MR (2018) “Divergent wiring of repressive and active chromatin interactions between mouse and trophoblast lineages”, Nature Communications, 9:4189 [PubMed] [PDF] [ArrayExpress]

Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR, Reik W (2018) “Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data”, Genome Biology, 19:33 [PubMed] [PDF] [GEO] [GitHub]

Deniz O, de la Rica L, Cheng KC, Spensberger D, Branco MR (2018) “SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells”, Genome Biology, 19:6 [PubMed] [PDF] [GEO]

Garcia-Gomez A, Li T, Kerick M, Català F, Comet N, Rodríguez-Ubreva J, de la Rica L, Branco MR, Martín J, Ballestar E (2017) “TET2- and TDG-mediated changes are required for the acquisition of distinct histone modifications in divergent terminal differentiation of myeloid cells”, Nucleic Acids Research, 45(17):10002-17 [PubMed] [PDF] [GEO]

Barbieri M, Xie SQ, Triglia ET, Chiariello AM, Bianco S, de Santiago I, Branco MR, Rueda D, Nicodemi M, Pombo A (2017) “Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells”, Nature Structural & Molecular Biology, 24:515-24 [PubMed] [Request PDF]

Beagrie RA, Scialdone A, Schueler M, Kraemer DCA, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas LM, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PAW, Nicodemi M, Pombo A (2017) “Complex multi-enhancer contacts captured by genome architecture mapping (GAM)”, Nature, 543(7646):519-24 [PubMed] [Request PDF] [GEO] [GitHub]

de la Rica L, Deniz O, Cheng KC, Todd CD, Cruz C, Houseley J, Branco MR (2016) “TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells”, Genome Biology, 17:234 [PubMed] [PDF] [GEO]

de la Rica L, Stanley JS, Branco MR (2016) “Profiling DNA methylation and hydroxymethylation at retrotransposable elements”, Methods in Molecular Biology, 1400:387-401 [PubMed] [Request PDF]

Branco MR, King M, Perez-Garcia V, Bogutz AB, Caley M, Fineberg E, Lefebvre L, Cook SJ, Dean W, Hemberger M, Reik W (2016) “Maternal DNA methylation regulates early trophoblast development”, Developmental Cell, 36(2):152-63 [PubMed] [PDF] [GEO]

Selected papers from past labs

Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S (2012) “Quantitative sequencing of 5-methylcytosine and 5-hyroxymethylcytosine at single-base resolution”, Science, 336(6083):934-7 [PubMed] [Request PDF] [ArrayExpress]

Branco MR, Ficz G, Reik W (2011) “Uncovering the role of 5-hydroxymethylcytosine in the epigenome”, Nature Reviews Genetics, 13(1):7-13 [PubMed] [Request PDF]

Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W (2011) “Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation”, Nature, 473(7347):398-402 [PubMed] [Request PDF] [ENA]

Branco MR, Pombo A (2007) “Chromosome organization: new facts, new models”, Trends in Cell Biology, 17(3): 127-34 [PubMed] [Request PDF]

Branco MR, Pombo A (2006) “Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations”, PloS Biology, 4(5): e138 [PubMed] [PDF]

Branco MR, Marinho HS, Cyrne M, Antunes F (2004) “Decrease of H2O2 plasma membrane permeability during adaptation to H2O2 in Saccharomyces cerevisiae”, Journal of Biological Chemistry, 279(8): 6501-6 [PubMed] [PDF]

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