{"id":816,"date":"2022-06-02T15:59:09","date_gmt":"2022-06-02T15:59:09","guid":{"rendered":"https:\/\/www.embl.org\/groups\/zaugg\/?page_id=816"},"modified":"2024-02-27T10:41:58","modified_gmt":"2024-02-27T10:41:58","slug":"data-and-tools","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/","title":{"rendered":"Resources"},"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\"><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-enhancer-mediated-gene-regulatory-networks\/\"><strong>Gene regulatory networks<\/strong><\/a><\/h3>\n\n\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-inline-end  size-medium is-resized is-style-rounded\"><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-enhancer-mediated-gene-regulatory-networks\/\"><img loading=\"lazy\" decoding=\"async\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/AML_network-1-300x278.jpg\" alt=\"\" class=\"wp-image-13011\" width=\"150\" height=\"139\" srcset=\"https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/AML_network-1-300x278.jpg 300w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/AML_network-1-1024x950.jpg 1024w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/AML_network-1-768x712.jpg 768w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/AML_network-1.jpg 1187w\" sizes=\"auto, (max-width: 150px) 100vw, 150px\" \/><\/a><figcaption class=\"vf-figure__caption\">Enhancer-mediated gene regulatory network (eGRN) inferred with GRaNIE<\/figcaption><\/figure>\n\n\n\n<p><strong>Links: <\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Software: <a rel=\"noreferrer noopener\" href=\"https:\/\/git.embl.de\/grp-zaugg\/GRaNIE\" target=\"_blank\">https:\/\/git.embl.de\/grp-zaugg\/GRaNIE<\/a><\/li>\n\n\n\n<li>Software: <a rel=\"noreferrer noopener\" href=\"https:\/\/git.embl.de\/grp-zaugg\/GRaNPA\" target=\"_blank\">https:\/\/git.embl.de\/grp-zaugg\/GRaNPA<\/a><\/li>\n\n\n\n<li><a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-enhancer-mediated-gene-regulatory-networks\/\" target=\"_blank\">Resources and description<\/a><\/li>\n\n\n\n<li><a rel=\"noreferrer noopener\" href=\"https:\/\/www.embopress.org\/doi\/full\/10.15252\/msb.202311627\" target=\"_blank\"><\/a><a rel=\"noreferrer noopener\" href=\"https:\/\/www.embopress.org\/doi\/full\/10.15252\/msb.202311627\" target=\"_blank\">Publication<\/a>: GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages (<a rel=\"noreferrer noopener\" href=\"https:\/\/www.embopress.org\/doi\/full\/10.15252\/msb.202311627\" target=\"_blank\">Molecular Systems Biology 2023<\/a>)<\/li>\n<\/ul>\n\n\n<hr class=\"vf-divider\">\n\n\n<h3 class=\"wp-block-heading\">DeePiCt: supervised models for segmentation of cryo-electron tomograms<\/h3>\n\n\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-inline-end  size-medium\"><img loading=\"lazy\" decoding=\"async\" width=\"300\" height=\"119\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/41592_2022_1746_Fig5_HTML-copy-300x119.png\" alt=\"\" class=\"wp-image-13007\" srcset=\"https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/41592_2022_1746_Fig5_HTML-copy-300x119.png 300w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/41592_2022_1746_Fig5_HTML-copy-1024x405.png 1024w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/41592_2022_1746_Fig5_HTML-copy-768x304.png 768w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2024\/02\/41592_2022_1746_Fig5_HTML-copy.png 1292w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><figcaption class=\"vf-figure__caption\">Segmentation of cryo electron tomogram with DeePiCt (deep particle picker in cellular context)<\/figcaption><\/figure>\n\n\n\n<p><strong>Links: <\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Software: <a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/ZauggGroup\/DeePiCt\" target=\"_blank\">https:\/\/github.com\/ZauggGroup\/DeePiCt<\/a><\/li>\n\n\n\n<li>Publication: Convolutional networks for supervised mining of molecular patterns within cellular context (<a href=\"https:\/\/www.nature.com\/articles\/s41467-019-13888-7\">Nature Methods 2023<\/a>)<\/li>\n<\/ul>\n\n\n<hr class=\"vf-divider\">\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/coop-tf-binding\/\" data-type=\"page\" data-id=\"834\">Transcription factor cooperative binding <\/a><\/h3>\n\n\n\n<p><strong>Links: <\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/coop-tf-binding\/\">Resources and description<\/a><\/li>\n\n\n\n<li>Publication: Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions (<a href=\"https:\/\/www.nature.com\/articles\/s41467-019-13888-7\"><\/a><a href=\"https:\/\/www.nature.com\/articles\/s41467-019-13888-7\">Nature Communications 2020<\/a>)<\/li>\n<\/ul>\n\n\n<hr class=\"vf-divider\">\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-predictive-features-of-gene-expression-variation-reveal-mechanistic-link-with-differential-expression-mol-sys-biol-2020\/\" data-type=\"page\" data-id=\"820\">Predictive features of gene expression variation <\/a><\/h3>\n\n\n\n<p><strong>Links: <\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-predictive-features-of-gene-expression-variation-reveal-mechanistic-link-with-differential-expression-mol-sys-biol-2020\/\">Resources and description<\/a><\/li>\n\n\n\n<li>Publication: Predictive features of gene expression variation reveal mechanistic link with differential expression (<a rel=\"noreferrer noopener\" href=\"https:\/\/www.embopress.org\/doi\/10.15252\/msb.20209539\" target=\"_blank\"><strong><em>Mol. Sys. Biol. 2020<\/em><\/strong><\/a>)<\/li>\n<\/ul>\n\n\n<hr class=\"vf-divider\">\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-quantification-of-differential-transcription-factor-activity-and-multiomics-based-classification-into-activators-and-repressors-difftf\/\" data-type=\"page\" data-id=\"842\">Quantification of differential transcription factor activity<\/a><\/h3>\n\n\n\n<p><strong>Links<\/strong>: <\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Software: <a rel=\"noreferrer noopener\" href=\"https:\/\/git.embl.de\/grp-zaugg\/diffTF\" target=\"_blank\">https:\/\/git.embl.de\/grp-zaugg\/diffTF<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-quantification-of-differential-transcription-factor-activity-and-multiomics-based-classification-into-activators-and-repressors-difftf\/\">Resources and description<\/a><\/li>\n\n\n\n<li>Publication: Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF (<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2211124719314391\">Cell Reports 2019<\/a>)<\/li>\n<\/ul>\n\n\n<hr class=\"vf-divider\">\n\n\n<h3 class=\"wp-block-heading\"><strong><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/data-and-tools-coop-tf-binding-2\/\" data-type=\"page\" data-id=\"838\">CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals<\/a> <\/strong><\/h3>\n\n\n\n<p><strong>Links: <\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/data-and-tools-coop-tf-binding-2\/\">Resources and description<\/a><\/li>\n\n\n\n<li>Publication: CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals (<a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.de\/download\/zaugg\/CTCF_Splicing\/Ruiz-Velasco_2017.pdf\" target=\"_blank\">Cell Systems 2017<\/a>)<\/li>\n<\/ul>\n\n\n<hr class=\"vf-divider\">\n\n\n<h3 class=\"wp-block-heading\"><strong><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-snphood-investigate-quantify-and-visualise-the-epigenomic-neighbourhood-of-snps-using-ngs-data-bioinformatics-2016\/\" data-type=\"page\" data-id=\"854\">SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data <\/a>(<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/early\/2016\/03\/26\/bioinformatics.btw127.abstract\">Bioinformatics&nbsp;2016<\/a>)<\/strong><\/h3>\n\n\n<hr class=\"vf-divider\">\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/distal-chromatin-qtls\/\" data-type=\"page\" data-id=\"850\">Genetic Control of Chromatin States and Gene Expression in Humans Involves Local and Distal Chromosomal Interactions (Cell 2015)<\/a><strong> (<a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867415009642\">Cell 2015<\/a>)<\/strong><\/h3>\n\n\n<hr class=\"vf-divider\">\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-extensive-variation-in-chromatin-states-across-humans-science-2013\/\" data-type=\"page\" data-id=\"830\">Extensive Variation in Chromatin States Across Humans<\/a> (<a href=\"http:\/\/www.sciencemag.org\/content\/342\/6159\/750\">Science 2013<\/a>)<\/h3>\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-816","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/816","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=816"}],"version-history":[{"count":18,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/816\/revisions"}],"predecessor-version":[{"id":13175,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/816\/revisions\/13175"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/media?parent=816"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/embl_taxonomy?post=816"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}