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  1. Queen Mary University of London
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Publications: DR Miguel Branco

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Vasconcelos S, Moustakas I, Branco MR, Guimarães S, Caniçais C, van der Helm T, Ramalho C ( 2024 ) . Syncytiotrophoblast Markers Are Downregulated in Placentas from Idiopathic Stillbirths . International Journal of Molecular Sciences vol. 25 , ( 10 )
Cheng KCL, Frost JM, Sánchez-Luque FJ, García-Canãdas M, Taylor D, Yang WR, Irayanar B, Sampath S et al. ( 2023 ) . Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation . Epigenetics & Chromatin vol. 16 , ( 1 )
Pezic D, Weeks S, Varsally W, Dewari PS, Pollard S, Branco MR, Hadjur S ( 2023 ) . The N-terminus of Stag1 is required to repress the 2C program by maintaining rRNA expression and nucleolar integrity . Stem Cell Reports vol. 18 , ( 11 ) 2154 - 2173 .
Senner CE, Dong Z, Prater M, Branco MR ( 2023 ) . One-carbon metabolism is required for epigenetic stability in the mouse placenta . Frontiers in Cell and Developmental Biology vol. 11 ,
Pal D, Patel M, Boulet F, Sundarraj J, Grant OA, Branco MR, Basu S, Santos SDM et al. ( 2023 ) . H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function . Nature Structural & Molecular Biology vol. 30 , ( 7 ) 935 - 947 .
( 2023 ) . Endogenous retroviruses control human placental gene expression . Nature Structural & Molecular Biology vol. 30 , ( 4 ) 415 - 416 .
Frost JM, Amante SM, Okae H, Jones EM, Ashley B, Lewis RM, Cleal JK, Caley MP et al. ( 2023 ) . Regulation of human trophoblast gene expression by endogenous retroviruses . Nature Structural & Molecular Biology vol. 30 , ( 4 ) 527 - 538 .
Branco MR, Soler ADM ( 2023 ) . Preface .
Taylor D, Branco MR ( 2022 ) . Inferring Protein-DNA Binding Profiles at Interspersed Repeats Using HiChIP and PAtChER . Methods in Molecular Biology vol. 2607 , 199 - 214 .
Ashley B, Simner C, Manousopoulou A, Jenkinson C, Hey F, Frost JM, Rezwan FI, White CH et al. ( 2022 ) . Placental uptake and metabolism of 25(OH)vitamin D determine its activity within the fetoplacental unit . eLife vol. 11 ,
Taylor D, Lowe R, Philippe C, Cheng KCL, Grant OA, Zabet NR, Cristofari G ( 2021 ) . Locus-specific chromatin profiling of evolutionarily young transposable elements . Nucleic Acids Research vol. 50 , ( 6 ) e33 - e33 .
Pedraza‐Arevalo S, Ibáñez‐Costa A, Blázquez‐Encinas R, Branco MR, Vázquez‐Borrego MC, Herrera‐Martínez AD, Venegas‐Moreno E, Serrano‐Blanch R et al. ( 2021 ) . Epigenetic and post‐transcriptional regulation of somatostatin receptor subtype 5 (SST5) in pituitary and pancreatic neuroendocrine tumors . Molecular Oncology vol. 16 , ( 3 ) 764 - 779 .
Antunes C, Da Silva JD, Guerra-Gomes S, Alves ND, Ferreira F, Branco MR, Sousa N ( 2021 ) . Reduced hippocampal ten-eleven translocation 3 (Tet3) protein expression in Tet3 conditional knockout mice . Molecular Psychiatry vol. 26 , ( 5 ) 1425 - 1425 .
Shendy NAM, Raghu D, Roy S, Perry CH, Safi A, Abell AN ( 2020 ) . Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching . Communications Biology vol. 3 , ( 1 )
De Borre M ( 2020 ) . Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol . Methods in Molecular Biology vol. 2198 , 333 - 348 .
Deniz Ö, Ahmed M, Todd CD, Rio-Machin A, Dawson MA, Branco MR ( 2020 ) . Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia . Nature Communications vol. 11 , ( 1 )
Senner CE, Chrysanthou S, Burge S, Lin H-Y, Branco MR ( 2020 ) . TET1 and 5-Hydroxymethylation Preserve the Stem Cell State of Mouse Trophoblast . Stem Cell Reports vol. 15 , ( 6 ) 1301 - 1316 .
Borkowski‐Tillman T, Garcia‐Rodriguez R, Viñals F, Branco M, Kradjen‐Haratz K ( 2020 ) . Agenesis of the septum pellucidum: Prenatal diagnosis and outcome . Prenatal Diagnosis vol. 40 , ( 6 ) 674 - 680 .
Antunes C, Da Silva JD, Guerra-Gomes S, Alves ND, Ferreira F, Loureiro-Campos E, Branco MR, Reik W et al. ( 2020 ) . Tet3 ablation in adult brain neurons increases anxiety-like behavior and regulates cognitive function in mice . Molecular Psychiatry vol. 26 , ( 5 ) 1445 - 1457 .
Branco MR ( 2020 ) . Crossroads between transposons and gene regulation . Philosophical Transactions of the Royal Society B Biological Sciences vol. 375 , ( 1795 )
Santos AC, Branco M, Martins P ( 2020 ) . Fetal atrial septal aneurysm: a differential diagnosis of aortic arch retrograde flow . BMJ Case Reports vol. 13 , ( 1 )
Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Sousa N ( 2020 ) . Correction to: Tet3 regulates cellular identity and DNA methylation in neural progenitor cells . Cellular and Molecular Life Sciences vol. 77 , ( 14 ) 2885 - 2885 .
Schlesinger S, Branco MR ( 2020 ) . Chapter 7 Roles and regulation of endogenous retroviruses in pluripotency and early development . Stem Cell Epigenetics , Elsevier
Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Sousa N, Branco MR ( 2019 ) . Tet3 regulates cellular identity and DNA methylation in neural progenitor cells . Cellular and Molecular Life Sciences vol. 77 , ( 14 ) 2871 - 2883 .
Carrillo-Jimenez A, Deniz Ö, Niklison-Chirou MV, Ruiz R, Bezerra-Salomão K, Stratoulias V, Amouroux R, Yip PK et al. ( 2019 ) . TET2 Regulates the Neuroinflammatory Response in Microglia . Cell Reports vol. 29 , ( 3 ) 697 - 713.e8 .
Todd CD, Deniz Ö, Taylor D, Branco MR ( 2019 ) . Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells . eLife vol. 8 ,
Deniz Ö, Frost JM, Branco MR ( 2019 ) . Author Correction: Regulation of transposable elements by DNA modifications . Nat Rev Genet
Deniz Ö, Frost JM, Branco MR ( 2019 ) . Regulation of transposable elements by DNA modifications . Nat Rev Genet
Olova N, Krueger F, Andrews S, Oxley D, Berrens RV ( 2019 ) . Correction to: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data . Genome Biology vol. 20 , ( 1 )
Borkowski T, Rodriguez RG, Viñals F, Branco M, Haratz KK, Ben‐Sira L ( 2018 ) . P11.03: Agenesis of the septum pellucidum: prenatal diagnosis and outcome . Ultrasound in Obstetrics and Gynecology vol. 52 , ( S1 ) 164 - 165 .
Schoenfelder S, Mifsud B, Senner CE, Todd CD, Chrysanthou S, Hemberger M ( 2018 ) . Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages . Nature Communications vol. 9 , ( 1 )
Pedraza-Arevalo S, Ibanez-Costa A, Vazquez-Borrego MC, Branco M, Galvez-Moreno MA, Korbonits M, Gahete MD ( 2018 ) . Epigenetic and post-transcriptional regulation of the SSTR5 gene in somatotropinomas . Endocrine Abstracts
Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR ( 2018 ) . Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data . Genome Biology vol. 19 , ( 1 )
Deniz Ö, de la Rica L, Cheng KCL, Spensberger D, Branco MR ( 2018 ) . SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells . Genome Biology vol. 19 , ( 1 )
Garcia-Gomez A, Li T, Kerick M, Català-Moll F, Comet NR, Rodríguez-Ubreva J, de la Rica L ( 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 vol. 45 , ( 17 ) 10002 - 10017 .
Neves AR, Nunes F, Branco M, do Céu Almeida M ( 2017 ) . The role of ultrasound in the prediction of birth weight discordance in twin pregnancies: are we there yet? . Journal of Perinatal Medicine vol. 46 , ( 2 ) 163 - 168 .
Barbieri M, Xie SQ, Torlai Triglia E, Chiariello AM, Bianco S, de Santiago I, Branco MR, Rueda D ( 2017 ) . Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells . Nature Structural & Molecular Biology vol. 24 , ( 6 ) 515 - 524 .
Beagrie RA, Scialdone A, Schueler M, Kraemer DCA, Chotalia M, Barbieri M, de Santiago I, Branco MR et al. ( 2017 ) . Complex multi-enhancer contacts captured by genome architecture mapping . Nature vol. 543 , ( 7646 ) 519 - 524 .
de la Rica L, Deniz Ö, Cheng KCL, Todd CD, Cruz C, Houseley J, Branco MR ( 2016 ) . TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells . Genome Biology vol. 17 , ( 1 )
Neves AR, Nunes F, Branco M, do Céu Almeida M ( 2016 ) . The influence of fetal growth restriction on ultrasound prediction of birth weight discordance in twin pregnancies . European Journal of Obstetrics & Gynecology and Reproductive Biology vol. 206 ,
Oliveira GN, Ramos L ( 2016 ) . Congenital dacryocystocoele with prenatal diagnosis . BMJ Case Reports vol. 2016 ,
de la Rica L, Stanley JS ( 2016 ) . Profiling DNA Methylation and Hydroxymethylation at Retrotransposable Elements . Methods in Molecular Biology vol. 1400 , 387 - 401 .
Branco MR, King M, Perez-Garcia V, Bogutz AB, Caley M, Fineberg E, Lefebvre L, Cook SJ et al. ( 2016 ) . Maternal DNA Methylation Regulates Early Trophoblast Development . Developmental Cell vol. 36 , ( 2 ) 152 - 163 .
Maçães A, Fernandes S, Rodrigues C ( 2015 ) . Interstitial ectopic pregnancy managed with local methotrexate . BMJ Case Reports vol. 2015 ,
Booth MJ, Ost TWB, Beraldi D, Bell NM, Branco MR, Reik W ( 2013 ) . Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine . Nat Protoc vol. 8 , ( 10 ) 1841 - 1851 .
Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Oxley D et al. ( 2013 ) . FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency . Cell Stem Cell vol. 13 , ( 3 ) 351 - 359 .
Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Oxley D et al. ( 2013 ) . FGF signalling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency . Clinical Epigenetics vol. 5 , ( Suppl 1 )
Branco MR ( 2013 ) . Bridging genomics technology and biology . Genome Biol vol. 14 , ( 10 )
Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Paul Y-L et al. ( 2013 ) . FGF signalling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency . Clinical epigenetics vol. 5 , ( Suppl 1 ) S2 - S2 .
Hackett JA, Reddington JP, Nestor CE, Dunican DS, Reichmann J, Reik W ( 2012 ) . Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline . Development vol. 139 , ( 19 ) 3623 - 3632 .
Rego JL, Branco M, Ramos L ( 2012 ) . P33.14: Cytomegalovirus infection in pregnancy . Ultrasound in Obstetrics and Gynecology vol. 40 , ( S1 ) 309 - 309 .
Raiber E-A, Beraldi D, Ficz G, Burgess HE, Branco MR, Murat P, Oxley D, Booth MJ et al. ( 2012 ) . Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase . Genome Biol vol. 13 , ( 8 )
Arand J, Spieler D, Karius T, Branco MR, Meilinger D, Meissner A, Jenuwein T, Wolf V ( 2012 ) . In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases . PLoS Genet vol. 8 , ( 6 )
Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S ( 2012 ) . Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution . Science vol. 336 , ( 6083 ) 934 - 937 .
Ficz G, Hore T, Santos F, Krueger F, Oxley D, Cook SJ, Xu G, Andrews S et al. ( 2012 ) . 2i inhibition of Erk1/2 and Gsk3β drives genome-wide demethylation to the epigenetic ground state of pluripotency . GENETICS RESEARCH . vol. 94 , 355 - 356 .
Pombo A ( 2012 ) . Intermingling of chromosome territories, translocations and interchromosomal associations . MUTAGENESIS . vol. 27 , 118 - 118 .
Krueger C, King MR, Krueger F, Branco MR, Osborne CS, Higgins MJ ( 2012 ) . Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status . PLoS One vol. 7 , ( 7 )
Branco MR, Ficz G, Reik W ( 2011 ) . Uncovering the role of 5-hydroxymethylcytosine in the epigenome . Nat Rev Genet vol. 13 , ( 1 ) 7 - 13 .
Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S et al. ( 2011 ) . Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation . Nature vol. 473 , ( 7347 ) 398 - 402 .
Ramos F, Maia S, Branco M, Raposo J, Sá J, Sousa S, Venâncio M, Ramos L ( 2010 ) . Accuracy of Prenatal Diagnosis in Elective Termination of Pregnancy: 385 Cases from 2000 to 2007 . International Scholarly Research Notices vol. 2011 , ( 1 )
Reik W, Popp C, Ficz G, Branco M, Branco M, Krueger C, Hemberger M, Dean W ( 2010 ) . Epigenetic regulation of imprinting, reprogramming, and lineage commitment in mammals . New Biotechnology . vol. 27 ,
Ferrai C, Xie SQ, Luraghi P, Munari D, Ramirez F, Crippa MP ( 2010 ) . Poised transcription factories prime silent uPA gene prior to activation . PLoS Biol vol. 8 , ( 1 )
Redrup L, Branco MR, Perdeaux ER, Krueger C, Lewis A, Santos F, Nagano T, Cobb BS ( 2009 ) . The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing . DEVELOPMENT vol. 136 , ( 4 ) 525 - 530 .
Branco MR, Oda M, Reik W ( 2008 ) . Safeguarding parental identity: Dnmt1 maintains imprints during epigenetic reprogramming in early embryogenesis . Genes Dev vol. 22 , ( 12 ) 1567 - 1571 .
Noordermeer D, Branco MR, Splinter E, Klous P, van IJcken W, van der Spek P ( 2008 ) . Correction: Transcription and Chromatin Organization of a Housekeeping Gene Cluster Containing an Integrated β-Globin Locus Control Region . PLOS Genetics vol. 4 , ( 3 )
Noordermeer D, Branco MR, Splinter E, Klous P, van Ijcken W, Koutsourakis M, van der Spek P ( 2008 ) . Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region . PLoS Genet vol. 4 , ( 3 )
Branco MR, Branco T, Ramirez F ( 2008 ) . Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH . Chromosome Res vol. 16 , ( 3 ) 413 - 426 .
Pombo A, Branco MR ( 2007 ) . Functional organisation of the genome during interphase . Curr Opin Genet Dev vol. 17 , ( 5 ) 451 - 455 .
Branco MR ( 2007 ) . Chromosome organization: new facts, new models . Trends Cell Biol vol. 17 , ( 3 ) 127 - 134 .
Branco MR, Pombo A ( 2006 ) . Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations . PLoS Biol vol. 4 , ( 5 )
BRANCO M, Xie SQ, Pombo A, Stephens D ( 2006 ) . Correlative microscopy using Tokuyasu cryosections: applications for immunolabeling and in situ hybridization . Cell Imaging , Scion Publishing Ltd
Pombo A, Branco MR ( 2006 ) . Mapping chromosome interactions in the nucleus of mammalian cells . EUROPEAN JOURNAL OF CELL BIOLOGY . vol. 85 , 100 - 100 .
Ferreira I, Laureano C, Branco M, Fonseca M, Almeida MC ( 2005 ) . Chorionicity and adverse perinatal outcome . Acta Médica Portuguesa vol. 18 , ( 3 ) 183 - 188 .
Rodrigues CT, Branco MR, Ferreira ID, Nordeste A, Fonseca M, Silva IS ( 2005 ) . [Multiple gestation epidemiology--15 years survey] . Acta Med Port vol. 18 , ( 2 ) 107 - 111 .
Branco MR, Marinho HS, Cyrne L ( 2004 ) . Decrease of H2O2 plasma membrane permeability during adaptation to H2O2 in Saccharomyces cerevisiae . J Biol Chem vol. 279 , ( 8 ) 6501 - 6506 .
Branco MR, Pedros N, Sousa-Lopes A, Cyrne L ( 2004 ) . Regulation of the permeability of biomembranes to H2O2: Implications for redox compartmentalization . FREE RADICAL BIOLOGY AND MEDICINE . vol. 37 , S60 - S60 .
Barbieri M, Xie SQ, Triglia ET, de Santiago I, Branco MR, Rueda D, Nicodemi M, Pombo A . Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells .
Castela G, Providência J, Monteiro M, Silva S, Brito M, Sá J, Oliveiros B, Murta J et al. . Characterization of The Portuguese Population Diagnosed With Retinoblastoma .
Olova N, Krueger F, Andrews S, Berrens RV . Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data .
Deniz Ö, Ahmed M, Todd CD, Rio-Machin A, Dawson MA, Branco MR . Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia .
Todd CD, Deniz Ö, Branco MR . Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells .
Pal D, Patel M, Boulet F, Sundarraj J, Grant OA, Branco MR, Basu S, Santos S et al. . H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function .
Biguet M, Marno K, Oliveira N, Gibbons JM, Pade C, Jones CE, Branco MR, McKnight A . HIV-1 Vpr alters cellular transcription by targeting the PAF1 complex .
. IAP retrotransposons contribute to the transcriptional diversity of the murine placenta .
Taylor D, Lowe R, Cheng KCL, Grant OA, Zabet NR . Locus-specific chromatin profiling of evolutionarily young transposable elements .
Senner CE, Dong Z, Branco MR, Watson ED . One-carbon metabolism is required for epigenetic stability in the mouse placenta .
Ashley B, Simner C, Manousopoulou A, Jenkinson C, Hey F, Frost JM, Rezwan FI, White CH et al. . Placental uptake and metabolism of 25(OH)Vitamin D determines its activity within the fetoplacental unit .
Branco M, Frost J, Amante S, Okae H, Jones E, Ashley B, Lewis R, Cleal J et al. . Regulation of human trophoblast gene expression by endogenous retroviruses .
Deniz Ö, de la Rica L, Cheng KCL, Spensberger D, Branco MR . SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells .
Carrillo-Jimenez A, Deniz Ö, Niklison-Chirou MV, Ruiz R, Bezerra-Salomão K, Stratoulias V, Amouroux R, Yip PK et al. . TET2 regulates the neuroinflammatory response in microglia .
Pezic D, Weeks S, Varsally W, Dewari PS, Pollard S . The N-terminus of Stag1 is required to repress the 2C program by maintaining rRNA expression and nucleolar integrity .
Cheng KCL, Frost JM, Sánchez-Luque FJ, García-Canãdas M, Taylor D, Yang WR, Irayanar B, Sampath S et al. . Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation .
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