{"id":13,"date":"2014-06-01T14:52:22","date_gmt":"2014-06-01T12:52:22","guid":{"rendered":"http:\/\/vaquerizaslab.org\/dev22\/?page_id=13"},"modified":"2023-09-11T23:41:08","modified_gmt":"2023-09-11T21:41:08","slug":"publications","status":"publish","type":"page","link":"https:\/\/vaquerizaslab.org\/dev22\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<div class=\"entry-content\">\n<p><script src=\"https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js\" type=\"text\/javascript\"><\/script><\/p>\n<h3>Selected Publications<\/h3>\n<h5>(Full list of publications: <a href=\"https:\/\/scholar.google.de\/citations?user=rm7KRmUAAAAJ&amp;hl=en&amp;oi=ao\" target=\"_blank\" rel=\"noopener noreferrer\">Google Scholar<\/a> &#8211; <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=vaquerizas_jm&amp;sort=date\" target=\"_blank\" rel=\"noopener noreferrer\">PubMed<\/a>)<\/h5>\n<h4>2022<\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1101\/gr.275655.121\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Chang NC*, <strong>Rovira Q*<\/strong>, Wells J*, Feschotte C# &amp; <strong>Vaquerizas JM#<\/strong>. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression<br \/>\n<em><strong>Genome Research<\/strong><\/em>, 32(7):1408-1423<br \/>\n<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34987056\/\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"http:\/\/genome.cshlp.org\/cgi\/pmidlookup?view=long&amp;pmid=34987056\" target=\"_blank\" rel=\"noopener noreferrer\">Journal OA<\/a>|<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.04.08.439009v1\" target=\"_blank\" rel=\"noopener noreferrer\">bioRxiv<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1016\/j.ceb.2021.12.004\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Ing-Simmons E, Rigau M, &amp; Vaquerizas JM<\/strong>. Emerging mechanisms and dynamics of three-dimensional genome organisation at zygotic genome activation<br \/>\n<em><strong>Current Opinion Cell Biology<\/strong><\/em>, 74:37-46<br \/>\n<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35065445\/\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0955-0674(21)00120-4\" target=\"_blank\" rel=\"noopener noreferrer\">Journal OA<\/a><\/p>\n<h4>2021<\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1038\/s41588-021-00799-x\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Ing-Simmons E<\/strong>, Vaid R, Bing XY, Levine M, Mannervik M &amp; <strong>Vaquerizas JM<\/strong>. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning<br \/>\n<em><strong>Nature Genetics<\/strong><\/em>, 53(4):487-499<br \/>\n<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33795866\/\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/www.nature.com\/articles\/s41588-021-00799-x\" target=\"_blank\" rel=\"noopener noreferrer\">Journal OA<\/a>|<a href=\"https:\/\/www.nature.com\/ng\/volumes\/53\/issues\/4\" target=\"_blank\" rel=\"noopener noreferrer\">Journal cover<\/a>|<a href=\"https:\/\/www.nature.com\/articles\/s41588-021-00813-2\" target=\"_blank\" rel=\"noopener noreferrer\">News &amp; Views<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1016\/j.stemcr.2021.03.001\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Chanoumidou K, <strong>Hern\u00e1ndez-Rodr\u00edguez B<\/strong>, Windener F, Thomas C, Stehling M, Mozafari S, Albrecht S, Ottoboni L, Antel J, Kim KP, Velychko S, Cui QL, Xu YKT, Martino G, Winkler J, Sch\u00f6ler HR, Baron-Van Evercooren A, Boespflug-Tanguy O, <strong>Vaquerizas JM<\/strong>, Ehrlich M &amp; Kuhlmann T. One-step Reprogramming of Human Fibroblasts into Oligodendrocyte-like Cells by SOX10, OLIG2, and NKX6.2<br \/>\n<em><strong>Stem Cell Reports<\/strong><\/em>, 16(4):771-783<br \/>\n<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33770499\/\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/www.cell.com\/stem-cell-reports\/fulltext\/S2213-6711(21)00129-6\" target=\"_blank\" rel=\"noopener noreferrer\">Journal OA<\/a><\/p>\n<h4>2020<\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1186\/s13059-020-02215-9\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Kruse K<\/strong>, <strong>Hug CB<\/strong> &amp; <strong>Vaquerizas JM<\/strong>. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data<br \/>\n<em><strong>Genome Biology<\/strong><\/em>, 21(1):303. doi: 10.1186\/s13059-020-02215-9<br \/>\n<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33334380\/\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-020-02215-9\" target=\"_blank\" rel=\"noopener noreferrer\">Journal full text<\/a>|<a href=\"https:\/\/github.com\/vaquerizaslab\/fanc\" target=\"_blank\" rel=\"noopener noreferrer\">Software<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1038\/s41588-020-00712-y\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Galan S*<\/strong>, <strong>Machnik N*<\/strong>, <strong>Kruse K<\/strong>, <strong>D\u00edaz N<\/strong>, Marti-Renom MA &amp; <strong>Vaquerizas JM<\/strong>. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction<br \/>\n<em><strong>Nature Genetics<\/strong><\/em>, 52(11):1247-1255<br \/>\n<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33077914\/\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/www.nature.com\/articles\/s41588-020-00712-y\" target=\"_blank\" rel=\"noopener noreferrer\">Journal<\/a>|<a href=\"https:\/\/rdcu.be\/b8IW2\" target=\"_blank\" rel=\"noopener noreferrer\">Full text<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1101\/2020.07.07.186791\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Ing-Simmons E<\/strong>, Vaid R, Mannervik M &amp; <strong>Vaquerizas JM<\/strong>. Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning.<br \/>\n<em><strong>bioRxiv<\/strong><\/em>, doi: https:\/\/doi.org\/10.1101\/2020.07.07.186791<br \/>\n<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.07.07.186791v1\" target=\"_blank\" rel=\"noopener noreferrer\">bioRxiv<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1016\/j.stem.2020.11.001\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Takayama N, Murison A, Takayanagi SI, Arlidge C, Zhou S, Garcia-Prat L, Chan-Seng-Yue M, Zandi S, Gan OI, Boutzen H, Kaufmann KB, Trotman-Grant A, Schoof E, Kron K, <strong>D\u00edaz N<\/strong>, Lee JJY, Medina T, De Carvalho DD, Taylor MD, <strong>Vaquerizas JM<\/strong>, Xie SZ, Dick JE, Lupien M. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization.<br \/>\n<em><strong>Cell Stem Cell<\/strong><\/em>, S1934-5909(20)30539-7 doi: 10.1016\/j.stem.2020.11.001<br \/>\n<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33242413\/\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S1934590920305397\" target=\"_blank\" rel=\"noopener noreferrer\">Journal<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1038\/s41556-020-0536-6\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Burton A, Brochard V, Galan C, Ruiz-Morales ER, <strong>Rovira Q<\/strong>, Rodriguez-Terrones D, <strong>Kruse K<\/strong>, Le Gras S, Udayakumar VS, Chin HG, Eid A, Liu X, Wang C, Gao S, Pradhan S, <strong>Vaquerizas JM<\/strong>, Beaujean N, Jenuwein T &amp; Torres-Padilla ME. Heterochromatin Establishment During Early Mammalian Development Is Regulated by Pericentromeric RNA and Characterized by Non-Repressive H3K9me3.<br \/>\n<em><strong>Nature Cell Biology<\/strong><\/em>, 22(7):767-778<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/32601371\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/www.nature.com\/articles\/s41556-020-0536-6\" target=\"_blank\" rel=\"noopener noreferrer\">Full text<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1016\/j.celrep.2019.12.057\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Rhodes JDP*, Feldmann A*, <strong>Hern\u00e1ndez-Rodr\u00edguez B*<\/strong>, <strong>D\u00edaz N*<\/strong>, Brown JM, Fursova NA, Blackledge NP, Prathapan P, Dobrinic P, Huseyin M, Szczurek A, <strong>Kruse K<\/strong>, Nasmyth KA, Buckle VJ, <strong>Vaquerizas JM#<\/strong> &amp; Klose RJ#. Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells.<br \/>\n<em><strong>Cell Reports<\/strong><\/em>, 30(3):820-835.e10<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/31968256\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/www.cell.com\/cell-reports\/fulltext\/S2211-1247(19)31714-0\" target=\"_blank\" rel=\"noopener noreferrer\">Full text<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1101\/2020.02.03.932517\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Kruse K<\/strong>, <strong>Hug CB<\/strong>, &amp; <strong>Vaquerizas JM<\/strong>. FAN-C: A Feature-rich Framework for the Analysis and Visualisation of C data.<br \/>\n<em><strong>bioRxiv<\/strong><\/em>, doi: https:\/\/doi.org\/10.1101\/2020.02.03.932517<br \/>\n<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2020.02.03.932517v1\" target=\"_blank\" rel=\"noopener noreferrer\">bioRxiv<\/a><\/p>\n<h4>2019<\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1242\/dev.177162\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Ing-Simmons E<\/strong> &amp; <strong>Vaquerizas JM<\/strong>. Visualising three-dimensional genome organisation in two dimensions.<br \/>\n<em><strong>Development<\/strong><\/em>, <span class=\"highwire-cite-metadata-volume highwire-cite-metadata\">146:&nbsp;<\/span><span class=\"highwire-cite-metadata-pages highwire-cite-metadata\">dev177162<\/span><br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/31558569\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/vaquerizaslab.org\/dev22\/wp-content\/uploads\/2019\/10\/Ing-Simmons_Vaquerizas-Development_2019-dev177162.full_.pdf\">Full text<\/a>|<a href=\"https:\/\/dev.biologists.org\/content\/146\/19\/dev177162.long\" target=\"_blank\" rel=\"noopener noreferrer\">Publisher<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1101\/523712\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Kruse K<\/strong>, <strong>D\u00edaz N<\/strong>, <strong>Enriquez-Gasca R<\/strong>, Gaume X, Torres-Padilla ME &amp; <strong>Vaquerizas JM<\/strong>. Transposable elements drive reorganisation of 3D chromatin during early embryogenesis.<br \/>\n<em><strong>bioRxiv<\/strong><\/em>, doi: https:\/\/doi.org\/10.1101\/523712<br \/>\n<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/523712v1\" target=\"_blank\" rel=\"noopener noreferrer\">bioRxiv<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.7554\/eLife.45863\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Lux\u00e1n G, Stewen J, <strong>D\u00edaz N<\/strong>, Kato K, Maney SK, Aravamudhan A, Berkenfeld F, Nagelmann N, Drexler HC, Zeuschner D, Faber C, Schillers H, Hermann S, Wiseman J, <strong>Vaquerizas JM<\/strong>, Pitulescu ME &amp; Adams RH. Endothelial EphB4 maintains vascular integrity and transport function in adult heart.<br \/>\n<em><strong>eLife<\/strong><\/em>, 8. pii: e45863<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/31782728\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/elifesciences.org\/articles\/45863\" target=\"_blank\" rel=\"noopener noreferrer\">Full text<\/a><\/p>\n<h4>2018<\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"30498195\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>D\u00edaz N*<\/strong>, <strong>Kruse K*<\/strong>, Erdmann T, Staiger AM, Ott G, Lenz G &amp; <strong>Vaquerizas JM<\/strong>. Chromatin conformation analysis of primary patient tissue using a low input Hi-C method.<br \/>\n<em><strong>Nature Communications<\/strong><\/em>, 9: 4938<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/30498195\" target=\"_blank\" rel=\"noopener noreferrer\">Pubmed<\/a>|<a href=\"https:\/\/www.nature.com\/articles\/s41467-018-06961-0\" target=\"_blank\" rel=\"noopener noreferrer\">Full text<\/a>|<a href=\"https:\/\/www.biorxiv.org\/content\/early\/2018\/07\/19\/372789.1\" target=\"_blank\" rel=\"noopener noreferrer\">bioRxiv<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.1016\/j.tig.2018.09.002\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Hug BC<\/strong>&nbsp;&amp; <strong>Vaquerizas JM<\/strong>. The Birth of the 3D Genome during Early Embryonic Development.<br \/>\n<em><strong>Trends in Genetics<\/strong><\/em>,&nbsp;34:903-914<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/30292539\" target=\"_blank\" rel=\"noopener noreferrer\">PubMed<\/a>|<a href=\"https:\/\/doi.org\/10.1016\/j.tig.2018.09.002\" target=\"_blank\" rel=\"noopener noreferrer\">Full text<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-doi=\"10.3791\/57001\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Hug BC<\/strong>&nbsp;&amp; <strong>Vaquerizas JM<\/strong>. Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos.<br \/>\n<em><strong>JoVE<\/strong><\/em>, DOI: https:\/\/doi.org\/10.3791\/57001<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/30346395\" target=\"_blank\" rel=\"noopener noreferrer\">PubMed<\/a>|<a href=\"https:\/\/www.jove.com\/video\/57001\" target=\"_blank\" rel=\"noopener noreferrer\">Full text<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"29255263\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Rodriguez-Terrones D, Gaume X, Ishiuchi T, Weiss A, Kopp A, <strong>Kruse K<\/strong>, Penning A, <strong>Vaquerizas JM<\/strong>, Brino L &amp; Torres-Padilla ME. A molecular roadmap for the emergence of early-embryonic-like cells in culture.<br \/>\n<em><strong>Nature Genetics<\/strong><\/em>, 50:106-119<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29255263\" target=\"_blank\" rel=\"noopener noreferrer\">PubMed<\/a>|<a href=\"https:\/\/www.nature.com\/articles\/s41588-017-0016-5\" target=\"_blank\" rel=\"noopener noreferrer\">Publisher<\/a><\/p>\n<h4>2017<\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"28388407\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Hug CB<\/strong>, <strong>Grimaldi AG<\/strong>, <strong>Kruse K<\/strong> &amp;&nbsp;<strong>Vaquerizas JM<\/strong>. Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.<br \/>\n<em><strong>Cell<\/strong><\/em>, 169:216\u2013228<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28388407\" target=\"_blank\" rel=\"noopener noreferrer\">PubMed<\/a>|<a href=\"https:\/\/www.cell.com\/cell\/fulltext\/S0092-8674(17)30343-4\" target=\"_blank\" rel=\"noopener noreferrer\">Full text<\/a>|<a href=\"http:\/\/www.cell.com\/cell\/fulltext\/S0092-8674(17)30345-8\" target=\"_blank\" rel=\"noopener noreferrer\">Preview<\/a>|<a href=\"http:\/\/www.nature.com\/nrg\/journal\/vaop\/ncurrent\/full\/nrg.2017.37.html\" target=\"_blank\" rel=\"noopener noreferrer\">Research highlight<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"28959057\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Jeong HW, <strong>Hern\u00e1ndez-Rodr\u00edguez B<\/strong>, Kim J, Kim KP, <strong>Enriquez-Gasca R<\/strong>, Yoon J, Adams S, Sch\u00f6ler HR,&nbsp;<b>Vaquerizas<\/b>&nbsp;<strong>JM#<\/strong> &amp; Adams RH#. Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis.<br \/>\n<em><strong>Nature Communications<\/strong><\/em>, 8:726<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28959057\" target=\"_blank\" rel=\"noopener noreferrer\">PubMed<\/a>|<a href=\"https:\/\/www.nature.com\/articles\/s41467-017-00738-7\" target=\"_blank\" rel=\"noopener noreferrer\">Publisher<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"28218908\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Langen UH, Pitulescu ME, Kim JM, <strong>Enriquez-Gasca R<\/strong>, Sivaraj KK, Kusumbe AP, <strong>Singh A<\/strong>, Di Russo J, Bixel MG, Zhou B, Sorokin L, <strong>Vaquerizas JM<\/strong> &amp; Adams RH. Cell\u2013matrix signals specify bone endothelial cells during developmental osteogenesis.<br \/>\n<em><strong>Nature Cell Biology<\/strong><\/em>, 19:189-201<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28218908\">PubMed<\/a>|<a href=\"http:\/\/www.nature.com\/ncb\/journal\/vaop\/ncurrent\/full\/ncb3476.html\">Publisher<\/a><\/p>\n<h4>2016<\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"27626372\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Vaquerizas JM<\/strong> &amp; Torres-Padilla ME. Developmental biology: Panoramic views of the early epigenome.<br \/>\n<em><strong>Nature<\/strong><\/em>, 537:494-496<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27626372\">PubMed<\/a>|<a href=\"http:\/\/www.nature.com\/nature\/journal\/v537\/n7621\/full\/nature19468.html\">Publisher<\/a>|<a href=\"http:\/\/www.nature.com\/nature\/podcast\/index-2016-09-15.html\">Podcast<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"27318199\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Kruse* K<\/strong>, <strong>Hug* CB<\/strong>, <strong>Hern\u00e1ndez-Rodr\u00edguez B<\/strong> &amp;&nbsp;<strong>Vaquerizas JM<\/strong>. TADtool: Visual Parameter Identification for TAD-calling Algorithms.<br \/>\n<em><strong>Bioinformatics<\/strong><\/em>, doi:10.1093\/bioinformatics\/btw368<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27318199\">PubMed<\/a>|<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/early\/2016\/06\/16\/bioinformatics.btw368.abstract\">Publisher<\/a>|<a href=\"https:\/\/github.com\/vaquerizaslab\/tadtool\" target=\"_blank\" rel=\"noopener noreferrer\">Software<\/a><\/p>\n<h4>2015<\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"26237512\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Ishiuchi T, <strong>Enriquez-Gasca R<\/strong>, Mizutani E, Bo\u0161kovi\u0107 A, Ziegler-Birling C, Rodriguez-Terrones D, Wakayama T, <strong>Vaquerizas JM<\/strong> &amp; Torres-Padilla ME. Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly.<br \/>\n<em><strong>Nature Structural Molecular Biology<\/strong><\/em>, 22:662-671<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26237512\">PubMed<\/a>|<a href=\"https:\/\/www.nature.com\/articles\/nsmb.3066\">Publisher<\/a>|<a href=\"http:\/\/www.nature.com\/nsmb\/journal\/v22\/n9\/full\/nsmb.3081.html\" target=\"_blank\" rel=\"noopener noreferrer\">News&amp;Views<\/a>|<a href=\"http:\/\/www.wn.de\/Muenster\/2066702-Max-Planck-Institut-fuer-Biomedizin-Muenster-Stammzellen-aus-dem-Labor\">Media coverage<\/a>|<a href=\"http:\/\/www.deutschlandfunk.de\/zellforschung-vom-vielkoenner-zum-alleskoenner.676.de.html?dram:article_id=327362\">Media coverage<\/a><\/p>\n<h4><strong>2012-2008<\/strong><\/h4>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"22723752\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Lam KC*, M\u00fchlpfordt F*, <strong>Vaquerizas JM*<\/strong>, Raja SJ, Holz H, Luscombe NM, Manke T &amp; Akhtar A. 2012. The NSL Complex Regulates Housekeeping Genes in Drosophila.<br \/>\n<em><strong>PLoS Genetics<\/strong><\/em>, 8:e1002736<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22723752\">PubMed<\/a>|<a href=\"http:\/\/www.plosgenetics.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pgen.1002736\">Publisher<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"22955616\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>The ENCODE Project Consortium (including <strong>Vaquerizas JM<\/strong>). 2012. An Integrated Encyclopedia of DNA Elements in the Human Genome.<br \/>\n<em><strong>Nature<\/strong><\/em>, 489:57-74<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22955616\">PubMed<\/a>|<a href=\"http:\/\/www.nature.com\/nature\/journal\/v489\/n7414\/full\/nature11247.html\">Publisher<\/a>|<a href=\"http:\/\/www.nature.com\/nature\/journal\/v489\/n7414\/index.html#about-the-cover\">Journal cover<\/a>|<a href=\"http:\/\/www.bbc.co.uk\/news\/health-19202141\">Media coverage<\/a>|<a href=\"http:\/\/www.nytimes.com\/2012\/09\/06\/science\/far-from-junk-dna-dark-matter-proves-crucial-to-health.html\">Media coverage<\/a>|<a href=\"http:\/\/www.nature.com\/encode\/#\/threads\">Website<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"20174442\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Vaquerizas JM*<\/strong>, Suyama R*, Kind J*, Miura K, Luscombe NM &amp; Akhtar A. 2010. Nuclear pore proteins Nup153 and Megator define transcriptionally active regions in the Drosophila genome.<br \/>\n<em><strong>PLoS Genetics<\/strong><\/em>, 6:e1000846<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/20174442\">PubMed<\/a>|<a href=\"http:\/\/www.plosgenetics.org\/article\/info:doi\/10.1371\/journal.pgen.1000846\">Publisher<\/a>|<a href=\"http:\/\/www.plosgenetics.org\/article\/info:doi\/10.1371\/journal.pgen.1000861\">Perspective<\/a>|<a href=\"http:\/\/www.ploscollections.org\/article\/browseIssue.action?issue=info%3Adoi%2F10.1371%2Fissue.pcol.v01.i07\">Epigenetics 2010<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"19274049\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p><strong>Vaquerizas JM<\/strong>, Kummerfeld SK, Teichmann SA &amp; Luscombe NM. 2009. A census of human transcription factors: function, expression and evolution.<br \/>\n<em><strong>Nature Reviews Genetics<\/strong><\/em>, 10:252-63<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19274049\">PubMed<\/a>|<a href=\"http:\/\/www.nature.com\/nrg\/journal\/v10\/n4\/abs\/nrg2538.html\">Publisher<\/a>|<a href=\"http:\/\/www.nature.com\/nrg\/journal\/v10\/n4\/covers\/index.html\">Journal cover<\/a><\/p>\n<div class=\"altmetric-embed\" style=\"float: right;\" data-badge-popover=\"right\" data-badge-type=\"donut\" data-pmid=\"18510926\" data-condensed=\"true\" data-hide-no-mentions=\"true\">&nbsp;<\/div>\n<p>Kind J*, <strong>Vaquerizas JM*<\/strong>, Gebhardt P, Gentzel M, Luscombe NM, Bertone P &amp; Akhtar A. 2008. Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.<br \/>\n<em><strong>Cell<\/strong><\/em>, 133:813-828<br \/>\n<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18510926\">PubMed<\/a>|<a href=\"https:\/\/www.cell.com\/cell\/fulltext\/S0092-8674(08)00610-7\">Publisher<\/a>|<a href=\"https:\/\/www.cell.com\/cell\/fulltext\/S0092-8674(08)00626-0\">Perspective<\/a>|<a href=\"http:\/\/www.nature.com\/nrg\/journal\/v9\/n7\/full\/nrg2412.html#Epigenetics\">NRG Research Highlight<\/a>|<a href=\"http:\/\/www.elpais.com\/articulo\/futuro\/enzima\/distingue\/sexo\/cromosoma\/X\/elpepusocfut\/20080604elpepifut_1\/Tes\">Media coverage<\/a>|<a href=\"http:\/\/lescienze.espresso.repubblica.it\/articolo\/Le_due_facce_del_cromosoma_X\/1331505\">Media coverage<\/a><\/p>\n<p><em>#: co-corresponding authors; *: joint first authors<\/em><\/p>\n<p>Click <strong><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=vaquerizas_jm\" target=\"_blank\" rel=\"noopener noreferrer\">here<\/a><\/strong> for Juanma&#8217;s full list of publications.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Selected Publications (Full list of publications: Google Scholar &#8211; PubMed) 2022 &nbsp; Chang NC*, Rovira Q*, Wells J*, Feschotte C# &amp; Vaquerizas JM#. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression Genome Research, 32(7):1408-1423 Pubmed|Journal OA|bioRxiv &nbsp; Ing-Simmons E, Rigau M, &amp; Vaquerizas JM. Emerging mechanisms and dynamics of three-dimensional [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v15.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/vaquerizaslab.org\/dev22\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - Vaquerizas Lab\" \/>\n<meta property=\"og:description\" content=\"Selected Publications (Full list of publications: Google Scholar &#8211; PubMed) 2022 &nbsp; Chang NC*, Rovira Q*, Wells J*, Feschotte C# &amp; Vaquerizas JM#. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression Genome Research, 32(7):1408-1423 Pubmed|Journal OA|bioRxiv &nbsp; Ing-Simmons E, Rigau M, &amp; Vaquerizas JM. Emerging mechanisms and dynamics of three-dimensional [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/vaquerizaslab.org\/dev22\/publications\/\" \/>\n<meta property=\"og:site_name\" content=\"Vaquerizas Lab\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-11T21:41:08+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@vaquerizas_lab\" \/>\n<meta name=\"twitter:site\" content=\"@vaquerizas_lab\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\">\n\t<meta name=\"twitter:data1\" content=\"admin\">\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\">\n\t<meta name=\"twitter:data2\" content=\"4 minutes\">\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Organization\",\"@id\":\"https:\/\/vaquerizaslab.org\/dev22\/#organization\",\"name\":\"Vaquerizas Laboratory\",\"url\":\"https:\/\/vaquerizaslab.org\/dev22\/\",\"sameAs\":[\"https:\/\/www.linkedin.com\/in\/vaquerizasjm\/\",\"https:\/\/twitter.com\/vaquerizas_lab\"],\"logo\":{\"@type\":\"ImageObject\",\"@id\":\"https:\/\/vaquerizaslab.org\/dev22\/#logo\",\"inLanguage\":\"en-GB\",\"url\":\"https:\/\/vaquerizaslab.org\/dev22\/wp-content\/uploads\/2020\/06\/vaquerizaslab_sqsq.png\",\"width\":1316,\"height\":1321,\"caption\":\"Vaquerizas Laboratory\"},\"image\":{\"@id\":\"https:\/\/vaquerizaslab.org\/dev22\/#logo\"}},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/vaquerizaslab.org\/dev22\/#website\",\"url\":\"https:\/\/vaquerizaslab.org\/dev22\/\",\"name\":\"Vaquerizas Lab\",\"description\":\"Developmental Epigenomics group @ MRC London Institute of Medical Sciences | Imperial College London\",\"publisher\":{\"@id\":\"https:\/\/vaquerizaslab.org\/dev22\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":\"https:\/\/vaquerizaslab.org\/dev22\/?s={search_term_string}\",\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-GB\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/vaquerizaslab.org\/dev22\/publications\/#webpage\",\"url\":\"https:\/\/vaquerizaslab.org\/dev22\/publications\/\",\"name\":\"Publications - Vaquerizas Lab\",\"isPartOf\":{\"@id\":\"https:\/\/vaquerizaslab.org\/dev22\/#website\"},\"datePublished\":\"2014-06-01T12:52:22+00:00\",\"dateModified\":\"2023-09-11T21:41:08+00:00\",\"inLanguage\":\"en-GB\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/vaquerizaslab.org\/dev22\/publications\/\"]}]}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","_links":{"self":[{"href":"https:\/\/vaquerizaslab.org\/dev22\/wp-json\/wp\/v2\/pages\/13"}],"collection":[{"href":"https:\/\/vaquerizaslab.org\/dev22\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/vaquerizaslab.org\/dev22\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/vaquerizaslab.org\/dev22\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/vaquerizaslab.org\/dev22\/wp-json\/wp\/v2\/comments?post=13"}],"version-history":[{"count":56,"href":"https:\/\/vaquerizaslab.org\/dev22\/wp-json\/wp\/v2\/pages\/13\/revisions"}],"predecessor-version":[{"id":808,"href":"https:\/\/vaquerizaslab.org\/dev22\/wp-json\/wp\/v2\/pages\/13\/revisions\/808"}],"wp:attachment":[{"href":"https:\/\/vaquerizaslab.org\/dev22\/wp-json\/wp\/v2\/media?parent=13"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}