{"id":798,"date":"2022-06-03T07:48:18","date_gmt":"2022-06-03T07:48:18","guid":{"rendered":"https:\/\/www.embl.org\/groups\/zaugg\/?page_id=798"},"modified":"2024-02-27T11:38:12","modified_gmt":"2024-02-27T11:38:12","slug":"preprints-and-media-coverage","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/zaugg\/preprints-and-media-coverage\/","title":{"rendered":"Preprints &#038; Media Coverage"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h3 class=\"wp-block-heading\">Preprints:<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Daga N, H. Servaas N, Kisand K, Moonen D, Arnold C, Reyes-Palomares A, Kaleviste E, Kingo K, Kuuse R, Ulst K, Steinmetz L, Peterson P, Nakic N, <strong>Zaugg JB<\/strong> (2024). Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells. <em><a rel=\"noreferrer noopener\" href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.01.11.575022v1\" target=\"_blank\">BioRxiv<\/a><\/em><\/li>\n\n\n\n<li>Lobato-Moreno S, Yildiz U, Claringbould A, Servaas N, Vlachou E, Arnold C, Bauersachs H, Campos-Fornes V, Prummel K, Noh K, Marttinen M, <strong>Zaugg JB<\/strong> (2023). Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease. <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2023.12.26.573253v3\" target=\"_blank\" rel=\"noreferrer noopener\"><em>BioRxiv<\/em><\/a><\/li>\n\n\n\n<li>Lai MC, Ruiz-Velasco M, Arnold C, Sigalova O, Bunina D, Berest I, Ding X, Hennrich ML, Poisa-Beiro L, Claringbould A, Mathioudaki A, Pabst C, Ho AD, Gavin A-C &amp; <strong>Zaugg JB<\/strong> (2021) Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits. <a rel=\"noreferrer noopener\" href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.09.03.458728v1\" target=\"_blank\"><em>BioRxiv<\/em><\/a><\/li>\n\n\n\n<li>Bunina D+, Germain P-L, Lopez Tobon A, Fernandez-Novel Marx N, Arnold C, \u00d3 hEachteirn A, Claringbould A, Lai MC, Rangasamy S, Narayanan V, Testa G, <strong><em>Zaugg JB+<\/em><\/strong> &amp; Noh K-M+ (2021) Pathological LSD1 mutations cause HDAC-mediated aberrant gene repression during early cell differentiation. <a rel=\"noreferrer noopener\" href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.08.11.455900v2\" target=\"_blank\"><em>BioRxiv<\/em><\/a>.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">2023<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Mu\u00f1oz A, Kreshuk A, Mahamid J, Zaugg JB (2023) <a href=\"https:\/\/europepmc.org\/abstract\/MED\/36690741\"><strong><em>Convolutional networks for supervised mining of molecular patterns within cellular context.<\/em><\/strong><\/a> Nature Methods.\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.embl.org\/news\/science\/ai-helps-scientists-decipher-cellular-structures\/\">Press release from EMBL Communications<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">2022<\/h3>\n\n\n\n<p>Coming soon<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">2021<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Claringbould A &amp; Zaugg JB (2021) <a rel=\"noreferrer noopener\" href=\"https:\/\/www.cell.com\/trends\/molecular-medicine\/fulltext\/S1471-4914(21)00197-0\" target=\"_blank\"><em><strong>Enhancers in disease: molecular basis and emerging treatment strategies<\/strong><\/em><\/a>. Trends Mol Med 27(11):1060\u20131073.\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.cell.com\/trends\/molecular-medicine\/issue?pii=S1471-4914(20)X0012-8\">Selected for cover of the November issue<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Weidem\u00fcller P, Kholmatov M, Petsalaki E &amp; Zaugg JB (2021) <a rel=\"noreferrer noopener\" href=\"https:\/\/analyticalsciencejournals.onlinelibrary.wiley.com\/doi\/10.1002\/pmic.202000034\" target=\"_blank\"><em><strong>Transcription factors: Bridge between cell signaling and gene regulation<\/strong><\/em><\/a>. Proteomics, e2000034.\n<ul class=\"wp-block-list\">\n<li><a rel=\"noreferrer noopener\" href=\"https:\/\/gitlab.ebi.ac.uk\/pweide\/review-tanscription-factors\" target=\"_blank\">Link to data and analysis<\/a> performed in this study (including annotations and classification of transcription factors)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">2020<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Sigalova OM, Shaeiri A, Forneris M, Furlong EEM+, <strong><u>Zaugg JB+<\/u><\/strong>. <a rel=\"noreferrer noopener\" href=\"https:\/\/www.embopress.org\/doi\/10.15252\/msb.20209539\" target=\"_blank\"><strong><em>Predictive features of gene expression variation reveal mechanistic link with differential expression<\/em><\/strong><\/a> (2020). Molecular Systems Biology 16 (8), e9539\n<ul class=\"wp-block-list\">\n<li>The paper was featured on <a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.org\/news\/science\/predicting-how-gene-expression-varies\/\" target=\"_blank\">EMBL news<\/a><\/li>\n\n\n\n<li>Thanks to the MSB team for selecting the article fo the <a rel=\"noreferrer noopener\" href=\"https:\/\/www.embopress.org\/cms\/asset\/29aeaf69-2ff4-46c7-a8b7-ce0c7cf0850a\/msb.v16.8.cover.jpg\" target=\"_blank\">August cover of the issue<\/a><\/li>\n\n\n\n<li>Code is available <a rel=\"noreferrer noopener\" href=\"https:\/\/git.embl.de\/sigalova\/regulation_of_expression_variation\" target=\"_blank\">here<\/a><\/li>\n\n\n\n<li>Data used in the study (gene-specific features) are available <a href=\"http:\/\/www.zaugg.embl.de\/data-and-tools\/predictive-features-of-expression-variation\/\">here<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, Dalton S, <strong>Zaugg JB<\/strong>, Snyder M.&nbsp;<em><strong><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/articles\/s41586-020-2151-x\" target=\"_blank\">Landscape of cohesin-mediated chromatin loops in the human genome. <\/a><\/strong>Nature<\/em> 583(7818):737-743.\n<ul class=\"wp-block-list\">\n<li>The paper was part of the <a rel=\"noreferrer noopener\" href=\"https:\/\/www.encodeproject.org\" target=\"_blank\">ENCODE project<\/a> and <a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/nature\/volumes\/583\/issues\/7818\" target=\"_blank\">featured on the cover<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Bunina D, Abazova N, Diaz N, Noh K-M+, Krijgsveld J+, <strong>Zaugg JB+<\/strong> (2020): <strong>Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. <\/strong><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2405471220301885\">Cell Systems 10, 6 (2020) 459-460<\/a>\n<ul class=\"wp-block-list\">\n<li>The paper was featured on <a href=\"https:\/\/www.embl.org\/news\/science\/from-stem-cells-to-neurons\/\">EMBL news<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Reyes-Palomares A, Gu M, Grubert F, Berest I, Sa S, Kasowski M, Arnold C, Shuai M, Srivas R, Miao S, Li D, Snyder MP, Rabinovitch M &amp; Judith Zaugg JB (2020). <strong><em>Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. <\/em><\/strong><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/articles\/s41467-020-15463-x\" target=\"_blank\">Nat Commun <strong>11, <\/strong>1673 (2020). https:\/\/doi.org\/10.1038\/s41467-020-15463-x<\/a>\n<ul class=\"wp-block-list\">\n<li>The paper was featured in the <a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/collections\/bhkhbxstgj\/content\/carolina-perdigoto\" target=\"_blank\">monthly highlights of Genomes and Epigenomes at Nature Communications<\/a><\/li>\n\n\n\n<li>For a lay summary: <a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.org\/news\/science\/embl-scientists-investigate-rare-lung-disease\/?_ga=2.126500237.1633244963.1590412948-904307581.1590412948\" target=\"_blank\">check out the article covered on EMBL news<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Ibarra IL, Hollmann NM, Klaus B, Augsten S, Velten B, Hennig J &amp; Zaugg JB (2020). <em><strong>Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. <\/strong><\/em><a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1038\/s41467-019-13888-7\" target=\"_blank\">Nat Commun 11, 124 (2020) doi:10.1038\/s41467-019-13888-7<\/a>\n<ul class=\"wp-block-list\">\n<li>Software is available <a href=\"http:\/\/www.zaugg.embl.de\/data-and-tools\/coop-tf-binding\/\">here<\/a><\/li>\n\n\n\n<li>The paper was featured in the <a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/collections\/bhkhbxstgj\/content\/carolina-perdigoto\" target=\"_blank\">monthly highlights of Genomes and Epigenomics at Nature communications<\/a><\/li>\n\n\n\n<li>For a lay summary: <a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.org\/news\/science\/exploring-how-transcription-factors-work-together\/?_ga=2.207867602.1707683222.1586327779-1238833287.1586327779\" target=\"_blank\">check the article covered on EMBL news<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">2019<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Berest I*, Arnold C*, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB (<strong>2019<\/strong>). <em><strong>Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF. <\/strong><\/em><a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1016\/j.celrep.2019.10.106\" target=\"_blank\">Cell Reports&nbsp;29, 10, 3 (2019) 3147-3159.e12<\/a>\n<ul class=\"wp-block-list\">\n<li>Software is available on our&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/git.embl.de\/grp-zaugg\/diffTF\" target=\"_blank\">git repository<\/a><\/li>\n\n\n\n<li>Documentation is available on <a rel=\"noreferrer noopener\" href=\"https:\/\/difftf.readthedocs.io\/en\/latest\/index.html\" target=\"_blank\">readthedocs<\/a><\/li>\n\n\n\n<li>For a lay summary: <a rel=\"noreferrer noopener\" href=\"https:\/\/news.embl.de\/science\/a-classification-tool-for-transcription-factors\/\" target=\"_blank\">check the article covered on EMBL news<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Garg, S.*, Reyes-Palomares, A.*, He, L., Bergeron, A., Lavall\u00e9e, V.-P., Lemieux, S., Gendron, P., Rohde, C., Xia, J., Jagdhane, P., M\u00fcller-Tidow, C., Lipka, D.B., Imren, S., Humphries, R.K., Waskow, C., Vick, B., Jeremias, I., Richard-Carpentier, G., H\u00e9bert, J., Zaugg, J.B.+, Sauvageau, G.+ and Pabst, C+. 2019. <em><strong>Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML<\/strong>.<\/em><a rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1182\/blood.2018862383\" target=\"_blank\">Blood (2019) 134 (3): 263\u2013276<\/a>.\n<ul class=\"wp-block-list\">\n<li><a rel=\"noreferrer noopener\" href=\"https:\/\/ashpublications.org\/blood\/article\/134\/3\/222\/260707\/Triple-mutant-AML-too-clever-by-HLF\" target=\"_blank\">The paper was highlighted in an editorial at Blood<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">2017<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Ruiz-Velasco M, Kumar M*, Lai ML*, Bhat P, Solis-Pinson AB, Reyes A, Kleinsorg A, Noh K-M, Gibson TJ, Zaugg JB (2017). <strong><em>CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals<\/em><\/strong><em>. <\/em><a href=\"http:\/\/www.cell.com\/cell-systems\/abstract\/S2405-4712(17)30488-X\"><strong>Cell Systems<\/strong>&nbsp;Volume 5 , Issue 6 , 628 &#8211; 637.e6<\/a>&nbsp;;&nbsp;l<a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.de\/download\/zaugg\/CTCF_Splicing\/Ruiz-Velasco_2017.pdf\" target=\"_blank\">ink to download the pdf<\/a>\n<ul class=\"wp-block-list\">\n<li>This&nbsp;article was featured in the <a href=\"https:\/\/news.embl.de\/science\/loops-in-dna-affect-protein-coding\/\">EMBL News<\/a>.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">2015<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Grubert F*, Zaugg JB*, Kasowski M*, Ursu O*, et al. (2015) <strong><em>Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.<\/em><\/strong><a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867415009642\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Cell<\/strong>.<em>&nbsp;162&nbsp;(5):&nbsp;1051-1065<\/em><\/a>\n<ul class=\"wp-block-list\">\n<li>This article was highlighted in&nbsp;<em><a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867415010351\" target=\"_blank\" rel=\"noreferrer noopener\">Cell<\/a>, and&nbsp;<a href=\"http:\/\/www.nature.com\/nrg\/journal\/v16\/n10\/full\/nrg4007.html?WT.ec_id=NRG-201510&amp;spMailingID=49577001&amp;spUserID=MzIzNTQwMjUxMDUS1&amp;spJobID=762469335&amp;spReportId=NzYyNDY5MzM1S0\" target=\"_blank\" rel=\"noreferrer noopener\">Nature Genetics<\/a>,&nbsp;and<\/em>&nbsp;also covered by an&nbsp;<a href=\"http:\/\/news.embl.de\/science\/1508-zaugg\/\" target=\"_blank\" rel=\"noreferrer noopener\">EMBL press release<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Before 2012<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Kotte O, Zaugg JB, Heinemann M. (2010) <strong><em>Bacterial adaptation through distributed sensing of metabolic fluxes<\/em><\/strong>. <a href=\"http:\/\/msb.embopress.org\/content\/6\/1\/355.long\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Mol Syst Biol <\/strong>6: 355.<\/a><\/li>\n\n\n\n<li>Hoskins AA, Morar M, Kappock TJ, Mathews II, Zaugg JB, Barder TE, Peng P, Okamoto A, Ealick SE, Stubbe J. (2007) <strong><em>N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis<\/em><\/strong>.&nbsp;<a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/bi602436g\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Biochemistry<\/strong> 46(10):2842-55.<\/a><\/li>\n<\/ul>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":10,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-798","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/798","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/comments?post=798"}],"version-history":[{"count":11,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/798\/revisions"}],"predecessor-version":[{"id":13177,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/798\/revisions\/13177"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/media?parent=798"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/embl_taxonomy?post=798"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}