{"id":28,"date":"2024-01-06T20:19:40","date_gmt":"2024-01-06T20:19:40","guid":{"rendered":"https:\/\/vladyslavbondarenko.com\/?page_id=28"},"modified":"2024-01-06T22:17:18","modified_gmt":"2024-01-06T22:17:18","slug":"page-1","status":"publish","type":"page","link":"https:\/\/vladyslavbondarenko.com\/?page_id=28","title":{"rendered":""},"content":{"rendered":"<p class=\"fonts-plugin-block \" style=\"font-family: palatino;font-weight: normal;font-size: 35px;text-align: center\">Research Overview<\/p>\n\n\n<div class=\"wp-block-group alignwide\"><div class=\"wp-block-group__inner-container is-layout-constrained wp-block-group-is-layout-constrained\">\n<div class=\"wp-block-group alignfull\"><div class=\"wp-block-group__inner-container is-layout-constrained wp-block-group-is-layout-constrained\">\n<div class=\"wp-block-group is-vertical is-content-justification-center is-layout-flex wp-container-core-group-is-layout-20d0575b wp-block-group-is-layout-flex\">\n<style>\n\t#hotspot-1028 .hotspots-image-container,\n\t#hotspot-1028 .leaflet-container {\n\t\tbackground: #ffffff\t}\n\n\t#hotspot-1028 .hotspots-placeholder {\n\t\tbackground: #c1c1c1;\n\t\tborder: 0 #c1c1c1 solid;\n\t\tcolor: #000000;\n\t}\n\n\t#hotspot-1028 .hotspot-title {\n\t\tcolor: #000000;\n\t}\n\n\t\t\t#hotspot-1028 .hotspot-default {\n\t\t\tstroke-width: 2;\n\t\t\tfill: #ffffff;\n\t\t\tfill-opacity: 0;\n\t\t\tstroke: #ffffff;\n\t\t\tstroke-opacity: 0;\n\t\t}\n\t\t#hotspot-1028 .hotspot-default:hover,\n\t\t#hotspot-1028 .hotspot-default:focus,\n\t\t#hotspot-1028 .hotspot-default.hotspot-active {\n\t\t\tfill: #000000;\n\t\t\tfill-opacity: 0.51;\n\t\t\tstroke: #000000;\n\t\t\tstroke-opacity: 0.01;\n\t\t}\n\t\t#hotspot-1028 .leaflet-tooltip,\n\t#hotspot-1028 .leaflet-rrose-content-wrapper {\n\t\tbackground: #c1c1c1;\n\t\tborder-color: #c1c1c1;\n\t\tcolor: #000000;\n\t}\n\n\t#hotspot-1028 a.leaflet-rrose-close-button {\n\t\tcolor: #000000;\n\t}\n\n\t#hotspot-1028 .leaflet-rrose-tip {\n\t\tbackground: #c1c1c1;\n\t}\n\n\t#hotspot-1028 .leaflet-popup-scrolled {\n\t\tborder-bottom-color: #000000;\n\t\tborder-top-color: #000000;\n\t}\n\n\t#hotspot-1028 .leaflet-tooltip-top:before {\n\t\tborder-top-color: #c1c1c1;\n\t}\n\n\t#hotspot-1028 .leaflet-tooltip-bottom:before {\n\t\tborder-bottom-color: #c1c1c1;\n\t}\n\t#hotspot-1028 .leaflet-tooltip-left:before {\n\t\tborder-left-color: #c1c1c1;\n\t}\n\t#hotspot-1028 .leaflet-tooltip-right:before {\n\t\tborder-right-color: #c1c1c1;\n\t}\n<\/style>\n\n\n\t<div class=\"hotspots-container  layout-left event-click\" id=\"hotspot-1028\" data-layout=\"left\" data-trigger=\"click\">\n\t\t<div class=\"hotspots-interaction\">\n\t\t\t\t<div class=\"hotspots-placeholder\" id=\"content-hotspot-1028\">\n\t\t<div class=\"hotspot-initial\">\n\t\t\t\t\t\t\t\t\t<h2 class=\"hotspot-title\">\n\t\t\t\tClick on different image panels for the overview\t\t\t<\/h2>\n\t\t\t\t\t\t<div class=\"hotspot-content\">\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t<\/div>\n<div class=\"hotspots-image-container\">\n\t<img\n\t\twidth=\"2560\"\n\t\theight=\"2560\"\n\t\tsrc=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Research-v3-1-scaled.jpg\"\n\t\talt=\"Click on different image panels for the overview\"\n\t\tclass=\"hotspots-image skip-lazy\"\n\t\tusemap=\"#hotspots-image-1028\"\n\t\tdata-image-title=\"Click on different image panels for the overview\"\n\t\tdata-image-description=\"\"\n\t\tdata-event-trigger=\"click\"\n\t\tdata-always-visible=\"false\"\n\t\tdata-id=\"1028\"\n\t\tdata-no-lazy=\"1\"\n\t\tdata-lazy-src=\"\"\n\t\tdata-lazy=\"false\"\n\t\tloading=\"eager\"\n\t\tdata-skip-lazy=\"1\"\n\t\t>\n<\/div>\t\t<\/div>\n\t\t<map name=\"hotspots-image-1028\" class=\"hotspots-map\">\n\t\t\t\t\t\t\t\t\t\t\t<area\n\t\t\t\t\tshape=\"polygon\"\n\t\t\t\t\tcoords=\"1333,1385,1337,1,5,-1\"\n\t\t\t\t\thref=\"#hotspot-hotspot-1028-0\"\n\t\t\t\t\trel=\"\"\n\t\t\t\t\ttitle=\"Advanced Imaging\"\n\t\t\t\t\talt=\"Advanced Imaging\"\n\t\t\t\t\tdata-action=\"\"\n\t\t\t\t\tdata-color-scheme=\"\"\n\t\t\t\t\ttarget=\"\"\n\t\t\t\t\tclass=\"more-info-area\"\n\t\t\t\t\t>\n\t\t\t\t\t\t\t\t\t\t\t<area\n\t\t\t\t\tshape=\"polygon\"\n\t\t\t\t\tcoords=\"1336,1,2560,1,1335,1386\"\n\t\t\t\t\thref=\"#hotspot-hotspot-1028-1\"\n\t\t\t\t\trel=\"\"\n\t\t\t\t\ttitle=\"Bioengineering\"\n\t\t\t\t\talt=\"Bioengineering\"\n\t\t\t\t\tdata-action=\"\"\n\t\t\t\t\tdata-color-scheme=\"\"\n\t\t\t\t\ttarget=\"\"\n\t\t\t\t\tclass=\"more-info-area\"\n\t\t\t\t\t>\n\t\t\t\t\t\t\t\t\t\t\t<area\n\t\t\t\t\tshape=\"polygon\"\n\t\t\t\t\tcoords=\"1,-2,1334,1385,-5,2568\"\n\t\t\t\t\thref=\"#hotspot-hotspot-1028-2\"\n\t\t\t\t\trel=\"\"\n\t\t\t\t\ttitle=\"Stem Cell Embryo Models\"\n\t\t\t\t\talt=\"Stem Cell Embryo Models\"\n\t\t\t\t\tdata-action=\"\"\n\t\t\t\t\tdata-color-scheme=\"\"\n\t\t\t\t\ttarget=\"\"\n\t\t\t\t\tclass=\"more-info-area\"\n\t\t\t\t\t>\n\t\t\t\t\t\t\t\t\t\t\t<area\n\t\t\t\t\tshape=\"polygon\"\n\t\t\t\t\tcoords=\"2560,0,1334,1388,2560,2558\"\n\t\t\t\t\thref=\"#hotspot-hotspot-1028-3\"\n\t\t\t\t\trel=\"\"\n\t\t\t\t\ttitle=\"In Vivo Development\"\n\t\t\t\t\talt=\"In Vivo Development\"\n\t\t\t\t\tdata-action=\"\"\n\t\t\t\t\tdata-color-scheme=\"\"\n\t\t\t\t\ttarget=\"\"\n\t\t\t\t\tclass=\"more-info-area\"\n\t\t\t\t\t>\n\t\t\t\t\t\t\t\t\t\t\t<area\n\t\t\t\t\tshape=\"polygon\"\n\t\t\t\t\tcoords=\"1334,1385,2560,2558,1331,2557\"\n\t\t\t\t\thref=\"#hotspot-hotspot-1028-4\"\n\t\t\t\t\trel=\"\"\n\t\t\t\t\ttitle=\"Theoretical modeling\"\n\t\t\t\t\talt=\"Theoretical modeling\"\n\t\t\t\t\tdata-action=\"\"\n\t\t\t\t\tdata-color-scheme=\"\"\n\t\t\t\t\ttarget=\"\"\n\t\t\t\t\tclass=\"more-info-area\"\n\t\t\t\t\t>\n\t\t\t\t\t\t\t\t\t\t\t<area\n\t\t\t\t\tshape=\"polygon\"\n\t\t\t\t\tcoords=\"4,2558,668,2560,1330,2559,1333,1385\"\n\t\t\t\t\thref=\"#hotspot-hotspot-1028-5\"\n\t\t\t\t\trel=\"\"\n\t\t\t\t\ttitle=\"Computational Biology\"\n\t\t\t\t\talt=\"Computational Biology\"\n\t\t\t\t\tdata-action=\"\"\n\t\t\t\t\tdata-color-scheme=\"\"\n\t\t\t\t\ttarget=\"\"\n\t\t\t\t\tclass=\"more-info-area\"\n\t\t\t\t\t>\n\t\t\t\t\t<\/map>\n\n\t\t\n\t\t\t\t\t\n\t\t\t\t\t\t<div class=\"hotspot-info \" id=\"hotspot-hotspot-1028-0\">\n\t\t\t\t\n\t\t\t\t<h2 class=\"hotspot-title\">Advanced Imaging<\/h2>\t\t\t\t\t\t\t\t\t<div class=\"hotspot-thumb\">\n\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"1024\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-research-1-1024x1024.jpg\" class=\"attachment-large size-large\" alt=\"\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-research-1-1024x1024.jpg 1024w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-research-1-300x300.jpg 300w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-research-1-150x150.jpg 150w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-research-1-768x768.jpg 768w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-research-1-1536x1536.jpg 1536w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-research-1-2048x2048.jpg 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<div class=\"hotspot-content\">\n\t\t\t\t\t<p>Engineering solutions for long-term live imaging of complex 3D samples such as developing embryos using light-sheet microscopy.<\/p>\n<p>Bondarenko V, et al., EMBO J. (2023)<\/p>\n<p>Bondarenko V, et al., EP23162464.4 (2023)<\/p>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t\n\t\t\t\t\t\t<div class=\"hotspot-info \" id=\"hotspot-hotspot-1028-1\">\n\t\t\t\t\n\t\t\t\t<h2 class=\"hotspot-title\">Bioengineering<\/h2>\t\t\t\t\t\t\t\t\t<div class=\"hotspot-thumb\">\n\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"789\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/3E-uterus-1024x789.jpg\" class=\"attachment-large size-large\" alt=\"\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/3E-uterus-1024x789.jpg 1024w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/3E-uterus-300x231.jpg 300w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/3E-uterus-768x592.jpg 768w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/3E-uterus-1536x1184.jpg 1536w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/3E-uterus.jpg 1920w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<div class=\"hotspot-content\">\n\t\t\t\t\t<p><em>Ex vivo<\/em> Engineering Uterine micro-Environment with topographically patterned hydrogels (3E-uterus) for development of the whole mouse embryo during implantation<\/p>\n<p>Bondarenko V, et al., <em>EMBO J.<\/em> (2023)<\/p>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t\n\t\t\t\t\t\t<div class=\"hotspot-info \" id=\"hotspot-hotspot-1028-2\">\n\t\t\t\t\n\t\t\t\t<h2 class=\"hotspot-title\">Stem Cell Embryo Models<\/h2>\t\t\t\t\t\t\t\t\t<div class=\"hotspot-thumb\">\n\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"1024\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Black-600-dpi-4.5K-x-4.5K-1024x1024.jpg\" class=\"attachment-large size-large\" alt=\"\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Black-600-dpi-4.5K-x-4.5K-1024x1024.jpg 1024w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Black-600-dpi-4.5K-x-4.5K-300x300.jpg 300w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Black-600-dpi-4.5K-x-4.5K-150x150.jpg 150w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Black-600-dpi-4.5K-x-4.5K-768x768.jpg 768w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Black-600-dpi-4.5K-x-4.5K-1536x1536.jpg 1536w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Black-600-dpi-4.5K-x-4.5K-2048x2048.jpg 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<div class=\"hotspot-content\">\n\t\t\t\t\t<p>Using human embryonic stem cells to model early post-implantation human embryo development.<\/p>\n<p>Oldak B*, Wildschutz E*, Bondarenko V*, et al., <em>Nature<\/em> (2023)<\/p>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t\n\t\t\t\t\t\t<div class=\"hotspot-info \" id=\"hotspot-hotspot-1028-3\">\n\t\t\t\t\n\t\t\t\t<h2 class=\"hotspot-title\">In Vivo Development<\/h2>\t\t\t\t\t\t\t\t\t<div class=\"hotspot-thumb\">\n\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"683\" height=\"1024\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/2020_10_26_E5.25decidua_slide8_section_8_sample_h_DAPI_GFP-booster-488_Phal-Rhod_panLAM-Cy5_optimal_Out_Stitch-200x300-1-683x1024.jpg\" class=\"attachment-large size-large\" alt=\"\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/2020_10_26_E5.25decidua_slide8_section_8_sample_h_DAPI_GFP-booster-488_Phal-Rhod_panLAM-Cy5_optimal_Out_Stitch-200x300-1-683x1024.jpg 683w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/2020_10_26_E5.25decidua_slide8_section_8_sample_h_DAPI_GFP-booster-488_Phal-Rhod_panLAM-Cy5_optimal_Out_Stitch-200x300-1-200x300.jpg 200w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/2020_10_26_E5.25decidua_slide8_section_8_sample_h_DAPI_GFP-booster-488_Phal-Rhod_panLAM-Cy5_optimal_Out_Stitch-200x300-1-768x1152.jpg 768w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/2020_10_26_E5.25decidua_slide8_section_8_sample_h_DAPI_GFP-booster-488_Phal-Rhod_panLAM-Cy5_optimal_Out_Stitch-200x300-1-1024x1536.jpg 1024w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/2020_10_26_E5.25decidua_slide8_section_8_sample_h_DAPI_GFP-booster-488_Phal-Rhod_panLAM-Cy5_optimal_Out_Stitch-200x300-1-1365x2048.jpg 1365w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/2020_10_26_E5.25decidua_slide8_section_8_sample_h_DAPI_GFP-booster-488_Phal-Rhod_panLAM-Cy5_optimal_Out_Stitch-200x300-1-scaled.jpg 1707w\" sizes=\"auto, (max-width: 683px) 100vw, 683px\" \/>\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<div class=\"hotspot-content\">\n\t\t\t\t\t<p>Dissecting <em style=\"font-size: 1.0625em\">in vivo<\/em> uterine tissue context and development <span style=\"font-size: 1.0625em\">using various imaging and spatial multiomics techniques.<\/span><\/p>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t\n\t\t\t\t\t\t<div class=\"hotspot-info \" id=\"hotspot-hotspot-1028-4\">\n\t\t\t\t\n\t\t\t\t<h2 class=\"hotspot-title\">Theoretical modeling<\/h2>\t\t\t\t\t\t\t\t\t<div class=\"hotspot-thumb\">\n\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"463\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Modeling-1024x463.jpg\" class=\"attachment-large size-large\" alt=\"\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Modeling-1024x463.jpg 1024w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Modeling-300x136.jpg 300w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Modeling-768x348.jpg 768w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Modeling.jpg 1074w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<div class=\"hotspot-content\">\n\t\t\t\t\t<p>Applying concepts from theoretical physics to understand biological systems dynamics, such as multicellular coordination during embryo implantation into the uterus.<\/p>\n<p>Bondarenko V, et al., <em>EMBO J <\/em>(2023)<\/p>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t\n\t\t\t\t\t\t<div class=\"hotspot-info \" id=\"hotspot-hotspot-1028-5\">\n\t\t\t\t\n\t\t\t\t<h2 class=\"hotspot-title\">Computational Biology<\/h2>\t\t\t\t\t\t\t\t<div class=\"hotspot-content\">\n\t\t\t\t\t<p>Utilizing computational methods of functional genomics and bioimage data analysis to study gene regulation and development.<\/p>\n<p><span style=\"text-decoration: underline\">Bondarenko V<\/span>, et al., <em>EMBO J<\/em> (2023)<\/p>\n<p>Mikhaylichenko O*, <span style=\"text-decoration: underline\">Bondarenko V*<\/span>, Harnett D* et al., <em>Genes &amp; Development<\/em>\u00a0(2018)<\/p>\n<p>Kuznetsov VA, <span style=\"text-decoration: underline\">Bondarenko V<\/span>, et al., <i>Nucleic Acids Research.<\/i> (2018)<\/p>\n<p><span style=\"text-decoration: underline\">Bondarenko V<\/span>, Gelfand <em>PLOS One<\/em>\u00a0(2016)<\/p>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t<\/div>\n\n<\/div>\n<\/div><\/div>\n<\/div><\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\"><p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 22px\"><strong>Modeling human early embryonic development with stem cells<\/strong><\/p>\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 15px\">The ability to study human embryogenesis remains limited owing to ethical and technical challenges associated with intrauterine development after implantation. <strong>Stem cells<\/strong> exhibit the self-organization capacities to model the aspects of embryonic development. However, embryo-like models with <strong>the spatial organization<\/strong> of all defining embryonic and extra-embryonic tissues of the post-implantation human conceptus are lacking. We used human embryonic stem cells, induced toward the embryonic and extra-embryonic lineages, to establish their capacity to organize into an embryo-like structure. The ensuing integrated stem cell embryo model (SEM) has the spatial organization of the embryonic epiblast, extra-embryonic hypoblast, mesoderm, and the surrounding syncytial trophoblast layer, reminiscent of the human embryo at the second week of intrauterine development.<br><br><em>This study provides a potential stem cell-based platform for studying experimentally inaccessible windows of human early post-implantation development.<\/em><\/p>\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Publication<\/summary>\n<p class=\"wp-block-paragraph\">Oldak B*, Wildschutz E*,&nbsp;<strong>Bondarenko V<\/strong>*, Comar M-Y, Zhao C, Aguilera-Castrejon A, Tarazi S, Viukov S, Pham THA, Ashouokhi S, Lokshtanov D, Roncato F, Ariel E, Rose M, Livnat N, Shani N, Joubran C, Cohen R, Addadi Y, Chemla M, Kedmi M, Keren-Shaul H, Pasque V, Petropoulos S, Lanner F, Novershtern N &amp; Hanna J. H (2023).<br><strong>Reconstitution of Complete Human Post-Implantation Embryo Models up to Day 14 from ESCs.<\/strong>&nbsp;<em>Nature<\/em>&nbsp;622, 562\u2013573. (Cover article)<br><em>*These authors contributed equally to this work<\/em><br><em><br><\/em><a href=\"https:\/\/www.nature.com\/articles\/s41586-023-06604-5#citeas\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Online<\/strong><\/a><\/p>\n<\/details>\n\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Collaborations<\/summary>\n<p class=\"wp-block-paragraph\">Prof. Dr. F Lanner; <em>Karolinska Institutet<\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Dr. S. Petropoulos; <em>Karolinska Institutet<\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Dr. V. Pasque; <em>KU Leuven<\/em><\/p>\n<\/details>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\">\n<figure class=\"wp-block-video aligncenter\"><video height=\"720\" style=\"aspect-ratio: 954 \/ 720;\" width=\"954\" autoplay controls loop src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SEM-movie-1.mp4\" playsinline><\/video><figcaption class=\"wp-element-caption\"><strong>3D reconstruction of a day\u20098 human SEM<\/strong>. Immunofluorescence for epiblast-like (OCT4, cyan), hypoblast-like (SOX17, yellow), trophoblast-like (CK7, magenta) compartments, and nuclei (DAPI, white). 0\u20133\u2009seconds: 3D view of the outer trophoblast-like layer with enlarged multinuclear cells. 4\u201311\u2009s and 19\u201321\u2009s: 3D segmentation of the epiblast-like (cyan) and hypoblast-like (yellow) structures with DAPI. 11\u201319\u2009s: inner SEM structure comprising a bilaminar disc-like structure with amnion-like and YS-like compartments, surrounded by connective tissue and trophoblast-like cells. <em>Video created by V. Bondarenko using Imaris.<\/em> J. <em>Hanna lab, WIS.<\/em><\/figcaption><\/figure>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-dots\"\/>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\"><p class=\"fonts-plugin-block \" style=\"font-family: arial;font-weight: 700;font-size: 22px\">Mouse peri-implantation development inside the uterine crypt<\/p>\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 15px\">By establishing the embryo\u2010maternal interaction, implantation represents a critical developmental stage in mammalian species. Mammalian development begins with generating <span style=\"text-decoration: underline\"><em>extraembryonic lineages, trophectoderm (TE)<\/em><\/span>, and primitive endoderm (PrE), in addition to the <span style=\"text-decoration: underline\"><em>embryonic epiblast (EPI)<\/em><\/span> in the blastocyst by embryonic day (E) 3.5. In mice, at E4.5, the TE differentiates into EPI\u2010attaching<em> <\/em>polar TE<em> <\/em>(pTE) and <em><span style=\"text-decoration: underline\">EPI\u2010distant mural TE (mTE)<\/span><\/em>, which adheres to the uterine wall and initiates implantation. pTE generates the <em><span style=\"text-decoration: underline\">extraembryonic ectoderm (ExE)<\/span><\/em> and mTE differentiates into <span style=\"text-decoration: underline\"><em>giant trophoblast (GT)<\/em><\/span>, while EPI and ExE proliferate and elongate to form an <span style=\"text-decoration: underline\"><em>\u201cegg cylinder\u201d<\/em> <\/span>by E5.25<em> <\/em><span style=\"text-decoration: underline\"><em>inside the crypt formed by the uterine tissue<\/em>.<\/span> The extraembryonic lineages neighboring the EPI, ExE, and visceral endoderm (VE) derived from PrE, play a key role in embryonic growth, patterning, and body axis formation via signaling and formation of placenta.<br><br><em>However, the peri\u2010implantation development of the extraembryonic trophoblast together with the embryonic egg cylinder remains challenging to recapitulate\u00a0ex vivo\u00a0and study with the available 2D and 3D culture systems.<\/em><\/p><\/div>\n\n\n\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\">\n<figure class=\"wp-block-video aligncenter\"><video height=\"640\" style=\"aspect-ratio: 640 \/ 640;\" width=\"640\" autoplay controls loop src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2024\/01\/Movie-EV1-480pt.mov\" playsinline><\/video><figcaption class=\"wp-element-caption\"><strong>Schematic animation of the mouse embryo inside the uterus<\/strong>. At E3.5, the embryo is floating within the uterine lumen and is surrounded by Zona Pellucida; by E4.5, the Zona Pellucida is absent, and the embryo starts attaching to the uterine epithelium by mural trophectoderm. At E5.25, the embryo becomes fully embedded into the&nbsp;<strong>uterine crypt<\/strong>&nbsp;and develops a typical&nbsp;<strong>egg cylinder<\/strong>&nbsp;morphology.&nbsp;<em>Video created by V. Bondarenko using Blender.<\/em><\/figcaption><\/figure>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-dots\"\/>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\"><p class=\"fonts-plugin-block \" style=\"font-family: arial;font-weight: 700;font-size: 22px\">Engineering murine uterine-like microenvironment<\/p>\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 15px\">In my Ph.D. study, I applied <strong>microfabrication<\/strong> and<strong> bioengineering<\/strong> <strong>to model biomechanical cues of the uterine microenvironment<\/strong>. I identified that <strong>tissue geometry<\/strong> and <strong>adhesion are critical for peri-implantation mouse embryo development<\/strong>.<br><br><em>Engineering ex vivo<\/em> <em>uterine environment <\/em>(3E-uterus) supports mouse blastocyst morphogenesis throughout implantation and egg cylinder formation. Embryos robustly form the Reichert\u2019s membrane and all extraembryonic tissues, including ExE and GT. To study cell and tissue dynamics, I integrated this new approach with light-sheet microscopy for <em>in toto<\/em> live imaging and quantitative image analysis.<br><br><i>This study provides a new method platform for ex vivo peri-implantation mouse embryo culture, live imaging, experimental perturbation, and quantitative analysis of <\/i><em style=\"font-style: italic\">the <\/em><em style=\"font-style: italic\">single-cell and whole-embryo<\/em> <em>dynamics.<\/em><\/p>\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Publication<\/summary>\n<p class=\"wp-block-paragraph\"><strong>Bondarenko V<\/strong>, Nikolaev M, Kromm D, Belousov R, Wolny A, Blotenburg M, Zeller P, Rezakhani S, Hugger J, Uhlmann V, Hufnagel L, Kreshuk A, Ellenberg J, van Oudenaarden A, Erzberger A, Lutolf MP, Hiiragi T (2023).<strong><br>Embryo-uterine interaction coordinates mouse embryogenesis during implantation.<\/strong><em> <\/em><em>EMBO J<\/em>, 42 (issue 17): e113280. (Cover article)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/www.embopress.org\/doi\/full\/10.15252\/embj.2022113280\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Online<\/strong><\/a><\/p>\n<\/details>\n\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Collaborations<\/summary>\n<p class=\"wp-block-paragraph\">Prof. Dr. M. Lutolf, Dr. M. Nikolaev; <em>EPFL\/IHB Roche<\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Prof. Dr. J. Ellenberg, Dr. D. Kromm; <em>EMBL Heidelberg<\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Prof. Dr. A. V. Oudenaarden, Dr. M. Blotenburg, P. Zeller; <em>Hubrecht Institute<\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Dr. A. Kreshuk, Dr. A. Wolny, J. Hugger; <em>EMBL Heidelberg<\/em><\/p>\n<\/details>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\">\n<figure class=\"wp-block-video aligncenter\"><video height=\"1080\" style=\"aspect-ratio: 1514 \/ 1080;\" width=\"1514\" autoplay controls loop src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Hiiragi-paper-footage-edited-crop-video.mp4\" playsinline><\/video><figcaption class=\"wp-element-caption\">Summary of the 3E-uterus protocol. <em>Video created by V. Bondarenko using Blender and Imaris.<\/em><\/figcaption><\/figure>\n\n\n\n<figure data-wp-context=\"{&quot;imageId&quot;:&quot;6a6a789abbbbc&quot;}\" data-wp-interactive=\"core\/image\" data-wp-key=\"6a6a789abbbbc\" class=\"wp-block-image size-large wp-lightbox-container\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"637\" data-wp-class--hide=\"state.isContentHidden\" data-wp-class--show=\"state.isContentVisible\" data-wp-init=\"callbacks.setButtonStyles\" data-wp-on--click=\"actions.showLightbox\" data-wp-on--load=\"callbacks.setButtonStyles\" data-wp-on--pointerdown=\"actions.preloadImage\" data-wp-on--pointerenter=\"actions.preloadImageWithDelay\" data-wp-on--pointerleave=\"actions.cancelPreload\" data-wp-on-window--resize=\"callbacks.setButtonStyles\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-3-1024x637.jpg\" alt=\"\" class=\"wp-image-918\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-3-1024x637.jpg 1024w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-3-300x187.jpg 300w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-3-768x478.jpg 768w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-3-1536x956.jpg 1536w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/SPIM-3-2048x1275.jpg 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><button\n\t\t\tclass=\"lightbox-trigger\"\n\t\t\ttype=\"button\"\n\t\t\taria-haspopup=\"dialog\"\n\t\t\tdata-wp-bind--aria-label=\"state.thisImage.triggerButtonAriaLabel\"\n\t\t\tdata-wp-init=\"callbacks.initTriggerButton\"\n\t\t\tdata-wp-on--click=\"actions.showLightbox\"\n\t\t\tdata-wp-style--right=\"state.thisImage.buttonRight\"\n\t\t\tdata-wp-style--top=\"state.thisImage.buttonTop\"\n\t\t>\n\t\t\t<svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"12\" height=\"12\" fill=\"none\" viewBox=\"0 0 12 12\">\n\t\t\t\t<path fill=\"#fff\" d=\"M2 0a2 2 0 0 0-2 2v2h1.5V2a.5.5 0 0 1 .5-.5h2V0H2Zm2 10.5H2a.5.5 0 0 1-.5-.5V8H0v2a2 2 0 0 0 2 2h2v-1.5ZM8 12v-1.5h2a.5.5 0 0 0 .5-.5V8H12v2a2 2 0 0 1-2 2H8Zm2-12a2 2 0 0 1 2 2v2h-1.5V2a.5.5 0 0 0-.5-.5H8V0h2Z\" \/>\n\t\t\t<\/svg>\n\t\t<\/button><\/figure>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-dots\"\/>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\"><p class=\"fonts-plugin-block \" style=\"font-family: arial;font-weight: normal;font-size: 22px;text-align: left\"><strong>Biomechanics of embryo implantation<\/strong><\/p>\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 15px\">Implantation into the uterus redefines the physical context for the developing embryo. I am interested in elucidating <strong>the role of biomechanics in embryo-uterine coordination and development<\/strong>.<br><br>Using <strong>bioengineering<\/strong>, <strong>quantitative live imaging<\/strong>, and <strong>physical theory<\/strong>, I approached embryo implantation as a quantitative biomechanical phenomenon, allowing the understanding of the embryo-uterine interaction mechanisms via a <em>theoretical physics framework of droplet wetting<\/em>. In particular, I found that the <em>integrin-mediated adhesion by the mTE<\/em> provides the mechanism of TE tension release, driving morphogenesis of <em>the pTE and ExE<\/em> within the uterine geometric tissue context. The uterine tissue geometry spatially coordinates collective trophoblast migration to delineate space for egg cylinder growth.<br><br><em>Applying 3E-uterus revealed a new mechanism of <em>coordination<\/em><\/em> <em>between extra-embryonic and embryonic tissue morphogenesis by the uterine microenvironment.<\/em><\/p>\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Publication<\/summary>\n<p class=\"wp-block-paragraph\"><strong>Bondarenko V<\/strong>, Nikolaev M, Kromm D, Belousov R, Wolny A, Blotenburg M, Zeller P, Rezakhani S, Hugger J, Uhlmann V, Hufnagel L, Kreshuk A, Ellenberg J, van Oudenaarden A, Erzberger A, Lutolf MP, Hiiragi T (2023).<strong><br>Embryo-uterine interaction coordinates mouse embryogenesis during implantation.<\/strong><em>EMBO J<\/em>, 42 (issue 17): e113280. (Cover article)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/www.embopress.org\/doi\/full\/10.15252\/embj.2022113280\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Online<\/strong><\/a><\/p>\n<\/details>\n\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Collaborations<\/summary>\n<p class=\"wp-block-paragraph\">Dr. A. Erzberger, Dr. R. Belousov; <em>EMBL Heidelberg<\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Prof. Dr. M. Lutolf, Dr. M. Nikolaev; <em>EPFL\/IHB Roche<\/em><\/p>\n<\/details>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<figure class=\"wp-block-video aligncenter\"><video height=\"1080\" style=\"aspect-ratio: 1160 \/ 1080;\" width=\"1160\" autoplay controls loop src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Movie-EV7.mp4\" playsinline><\/video><figcaption class=\"wp-element-caption\">Pink color denotes the embryo (cell plasma membrane, mT). Top, experiment; bottom, model. The surface of the 3E-uterus microwell is outlined.<em> Image courtesy: V. Bondarenko and R. Belousov, EMBL.<\/em><\/figcaption><\/figure>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 25px;text-align: center\"><strong>Previous Research<\/strong><\/p>\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 17px\">I&#8217;ve made a transition to experimental research from initially computational training. Between 2013 and 2017, I performed my research in gene regulation, population, and comparative genomics.<\/p>\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-8f761849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\"><p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 20px;text-align: center\"><strong>Gene regulation during development<\/strong><\/p>\n\n<div class=\"wp-block-image\">\n<figure data-wp-context=\"{&quot;imageId&quot;:&quot;6a6a789abcb8c&quot;}\" data-wp-interactive=\"core\/image\" data-wp-key=\"6a6a789abcb8c\" class=\"aligncenter size-large wp-lightbox-container\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"441\" data-wp-class--hide=\"state.isContentHidden\" data-wp-class--show=\"state.isContentVisible\" data-wp-init=\"callbacks.setButtonStyles\" data-wp-on--click=\"actions.showLightbox\" data-wp-on--load=\"callbacks.setButtonStyles\" data-wp-on--pointerdown=\"actions.preloadImage\" data-wp-on--pointerenter=\"actions.preloadImageWithDelay\" data-wp-on--pointerleave=\"actions.cancelPreload\" data-wp-on-window--resize=\"callbacks.setButtonStyles\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/GenesDev-paper-7-1024x441.jpg\" alt=\"\" class=\"wp-image-857\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/GenesDev-paper-7-1024x441.jpg 1024w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/GenesDev-paper-7-300x129.jpg 300w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/GenesDev-paper-7-768x331.jpg 768w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/GenesDev-paper-7.jpg 1280w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><button\n\t\t\tclass=\"lightbox-trigger\"\n\t\t\ttype=\"button\"\n\t\t\taria-haspopup=\"dialog\"\n\t\t\tdata-wp-bind--aria-label=\"state.thisImage.triggerButtonAriaLabel\"\n\t\t\tdata-wp-init=\"callbacks.initTriggerButton\"\n\t\t\tdata-wp-on--click=\"actions.showLightbox\"\n\t\t\tdata-wp-style--right=\"state.thisImage.buttonRight\"\n\t\t\tdata-wp-style--top=\"state.thisImage.buttonTop\"\n\t\t>\n\t\t\t<svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"12\" height=\"12\" fill=\"none\" viewBox=\"0 0 12 12\">\n\t\t\t\t<path fill=\"#fff\" d=\"M2 0a2 2 0 0 0-2 2v2h1.5V2a.5.5 0 0 1 .5-.5h2V0H2Zm2 10.5H2a.5.5 0 0 1-.5-.5V8H0v2a2 2 0 0 0 2 2h2v-1.5ZM8 12v-1.5h2a.5.5 0 0 0 .5-.5V8H12v2a2 2 0 0 1-2 2H8Zm2-12a2 2 0 0 1 2 2v2h-1.5V2a.5.5 0 0 0-.5-.5H8V0h2Z\" \/>\n\t\t\t<\/svg>\n\t\t<\/button><figcaption class=\"wp-element-caption\"><strong>A continuum of eRNA directionality and levels reflects&nbsp;cis-regualtory function.<\/strong> Schematic representation of gene promoters, alternative gene promoters, and enhancers showing the heterogeneity of transcription directionality (arrowhead orientation), abundance (arrow height), and stability (arrow thickness) across regulatory elements.<\/figcaption><\/figure>\n<\/div>\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 15px\">The initiation and regulation of transcription are attributed to <strong>promoters<\/strong> and <strong>enhancers<\/strong>, respectively, but both regulatory elements are transcriptionally active. In my M.Sc. study, I addressed <strong>the functional activity of enhancers and promoters in relation to their transcriptional properties.<\/strong><br>\u00a0<br>Using bioinformatics and computational data analysis, I studied the genome-wide relationship between the regulatory activity of promoters and enhancers during <em>Drosophila<\/em> development and their transcriptional properties, such as the levels and the directionality of enhancer RNA (eRNA) transcription.<br>\u00a0<br><em>This study suggested the \u2018continuum\u2019 model of cis-regulation, where the balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the regulatory element.<\/em><\/p>\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Publication<\/summary>\n<p class=\"wp-block-paragraph\">Mikhaylichenko, O*,&nbsp;<strong>Bondarenko V*<\/strong>, Harnett D*, Schor IE, Males M, Viales RR, Furlong EE (2018).&nbsp;<strong>The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription.<\/strong>&nbsp;<em>Genes &amp; Development<\/em>. 32 (issue 1): 42-57. (Cover article)<br><br><em>* These authors contributed equally to this work<\/em><br><a href=\"https:\/\/genesdev.cshlp.org\/content\/32\/1\/42.long\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Online<\/strong><\/a><\/p>\n<\/details>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\"><p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 20px;text-align: center\"><strong>R-loops in the regulatory genome<\/strong><\/p>\n\n<div class=\"wp-block-image\">\n<figure data-wp-context=\"{&quot;imageId&quot;:&quot;6a6a789abd220&quot;}\" data-wp-interactive=\"core\/image\" data-wp-key=\"6a6a789abd220\" class=\"aligncenter size-large is-resized wp-lightbox-container\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"445\" data-wp-class--hide=\"state.isContentHidden\" data-wp-class--show=\"state.isContentVisible\" data-wp-init=\"callbacks.setButtonStyles\" data-wp-on--click=\"actions.showLightbox\" data-wp-on--load=\"callbacks.setButtonStyles\" data-wp-on--pointerdown=\"actions.preloadImage\" data-wp-on--pointerenter=\"actions.preloadImageWithDelay\" data-wp-on--pointerleave=\"actions.cancelPreload\" data-wp-on-window--resize=\"callbacks.setButtonStyles\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Rloop-2-1024x445.jpg\" alt=\"\" class=\"wp-image-864\" style=\"width:383px;height:auto\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Rloop-2-1024x445.jpg 1024w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Rloop-2-300x130.jpg 300w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Rloop-2-768x334.jpg 768w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Rloop-2-1536x668.jpg 1536w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Rloop-2-2048x890.jpg 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><button\n\t\t\tclass=\"lightbox-trigger\"\n\t\t\ttype=\"button\"\n\t\t\taria-haspopup=\"dialog\"\n\t\t\tdata-wp-bind--aria-label=\"state.thisImage.triggerButtonAriaLabel\"\n\t\t\tdata-wp-init=\"callbacks.initTriggerButton\"\n\t\t\tdata-wp-on--click=\"actions.showLightbox\"\n\t\t\tdata-wp-style--right=\"state.thisImage.buttonRight\"\n\t\t\tdata-wp-style--top=\"state.thisImage.buttonTop\"\n\t\t>\n\t\t\t<svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"12\" height=\"12\" fill=\"none\" viewBox=\"0 0 12 12\">\n\t\t\t\t<path fill=\"#fff\" d=\"M2 0a2 2 0 0 0-2 2v2h1.5V2a.5.5 0 0 1 .5-.5h2V0H2Zm2 10.5H2a.5.5 0 0 1-.5-.5V8H0v2a2 2 0 0 0 2 2h2v-1.5ZM8 12v-1.5h2a.5.5 0 0 0 .5-.5V8H12v2a2 2 0 0 1-2 2H8Zm2-12a2 2 0 0 1 2 2v2h-1.5V2a.5.5 0 0 0-.5-.5H8V0h2Z\" \/>\n\t\t\t<\/svg>\n\t\t<\/button><figcaption class=\"wp-element-caption\"><strong>Structural model of R-loop Forming Sequence (RLFS)<\/strong>: short G-cluster-rich region thought to be responsible for the initiation of R-loop formation (RIZ), structurally non-specified short linker (linker) and linker downstream of long high-\/moderate-G-density region (called R-loop elongation zone or REZ). REZ could provide for RNA:DNA hybrid\/R-loop stabilization.<\/figcaption><\/figure>\n<\/div>\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 15px\"><strong>R-loops<\/strong> are three-stranded RNA:DNA hybrid structures that form during transcription.<br><br>I conducted a<strong> comprehensive comparative analysis of R-loop forming DNA regions with the experimental functional genomics data<\/strong>. Using statistics and bioinformatics tools, I characterized the genome-wide association of R-loop forming DNA sequences with gene promoters, U1 splice sites, gene ends, enhancers, and non-B DNA structures, such as G-quadruplexes. The co-localization of R-loop forming DNA sequences with promoters and transcriptionally active enhancers suggested new models for\u00a0<em>in cis<\/em>\u00a0and\u00a0<em>in trans<\/em>\u00a0regulation of transcription initiation by RNA:DNA hybrids.<br><br><em>This study provides a rationale and a computational prediction for the experimental study of the non-B DNA regulatory structures involved in the formation of the RNA:DNA interactome.<\/em><\/p>\n\n\n<details class=\"wp-block-details is-layout-flow wp-block-details-is-layout-flow\"><summary>Publication<\/summary>\n<p class=\"wp-block-paragraph\">Kuznetsov VA,&nbsp;<strong>Bondarenko V<\/strong>, Wongsurawat T, Yenamandra SP, Jenjaroenpun P (2018).&nbsp;<strong>Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers.<\/strong>&nbsp;<em>Nucleic Acids Research.<\/em>&nbsp;46 (15): 7566-7585.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/academic.oup.com\/nar\/article\/46\/15\/7566\/5045338?login=true\"><strong>Online<\/strong><\/a><\/p>\n<\/details>\n<\/div>\n<\/div>\n\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 20px;text-align: center\"><strong>Population and comparative genomics<\/strong><\/p>\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 17px\">Bergman CM, Han S, Nelson MG,\u00a0<strong><span style=\"text-decoration: underline\">Bondarenko V<\/span><\/strong>, Kozeretska IA (2017).\u00a0<strong>Genomic analysis of P elements in natural populations of\u00a0<em>Drosophila melanogaster<\/em>.<\/strong>\u00a0<em>PeerJ<\/em>. 15.5: e3824.<br><a href=\"https:\/\/peerj.com\/articles\/3824\/\"><strong>Online<\/strong><\/a><\/p>\n\n<p class=\"fonts-plugin-block \" style=\"font-weight: normal;font-size: 17px\"><strong><span style=\"text-decoration: underline\">Bondarenko V<\/span><\/strong>, Gelfand MS (2016). <strong>Evolution of the exon-intron structure in Ciliates.<\/strong> <em>PLOS One.<\/em> 11(9): e0161476. <br><a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0161476\"><strong>Online<\/strong><\/a><\/p>\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n<div class=\"wp-block-image is-style-rounded\">\n<figure data-wp-context=\"{&quot;imageId&quot;:&quot;6a6a789abe03e&quot;}\" data-wp-interactive=\"core\/image\" data-wp-key=\"6a6a789abe03e\" class=\"aligncenter size-full is-resized wp-lightbox-container\"><img loading=\"lazy\" decoding=\"async\" width=\"638\" height=\"638\" data-wp-class--hide=\"state.isContentHidden\" data-wp-class--show=\"state.isContentVisible\" data-wp-init=\"callbacks.setButtonStyles\" data-wp-on--click=\"actions.showLightbox\" data-wp-on--load=\"callbacks.setButtonStyles\" data-wp-on--pointerdown=\"actions.preloadImage\" data-wp-on--pointerenter=\"actions.preloadImageWithDelay\" data-wp-on--pointerleave=\"actions.cancelPreload\" data-wp-on-window--resize=\"callbacks.setButtonStyles\" src=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Embryo-placenta-939x939-2-edited.jpg\" alt=\"\" class=\"wp-image-916\" style=\"width:89px;height:auto\" srcset=\"https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Embryo-placenta-939x939-2-edited.jpg 638w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Embryo-placenta-939x939-2-edited-300x300.jpg 300w, https:\/\/vladyslavbondarenko.com\/wp-content\/uploads\/2023\/12\/Embryo-placenta-939x939-2-edited-150x150.jpg 150w\" sizes=\"auto, (max-width: 638px) 100vw, 638px\" \/><button\n\t\t\tclass=\"lightbox-trigger\"\n\t\t\ttype=\"button\"\n\t\t\taria-haspopup=\"dialog\"\n\t\t\tdata-wp-bind--aria-label=\"state.thisImage.triggerButtonAriaLabel\"\n\t\t\tdata-wp-init=\"callbacks.initTriggerButton\"\n\t\t\tdata-wp-on--click=\"actions.showLightbox\"\n\t\t\tdata-wp-style--right=\"state.thisImage.buttonRight\"\n\t\t\tdata-wp-style--top=\"state.thisImage.buttonTop\"\n\t\t>\n\t\t\t<svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"12\" height=\"12\" fill=\"none\" viewBox=\"0 0 12 12\">\n\t\t\t\t<path fill=\"#fff\" d=\"M2 0a2 2 0 0 0-2 2v2h1.5V2a.5.5 0 0 1 .5-.5h2V0H2Zm2 10.5H2a.5.5 0 0 1-.5-.5V8H0v2a2 2 0 0 0 2 2h2v-1.5ZM8 12v-1.5h2a.5.5 0 0 0 .5-.5V8H12v2a2 2 0 0 1-2 2H8Zm2-12a2 2 0 0 1 2 2v2h-1.5V2a.5.5 0 0 0-.5-.5H8V0h2Z\" \/>\n\t\t\t<\/svg>\n\t\t<\/button><\/figure>\n<\/div>\n\n\n<p class=\"wp-block-paragraph\">\u2002<\/p>\n\n\n\n<div class=\"wp-block-group has-background-color has-background is-vertical is-layout-flex wp-container-core-group-is-layout-3789e7aa wp-block-group-is-layout-flex\" style=\"background-color:#f8f8f8f7;margin-top:0;margin-bottom:0;padding-top:var(--wp--preset--spacing--40);padding-right:var(--wp--preset--spacing--30);padding-bottom:var(--wp--preset--spacing--40);padding-left:var(--wp--preset--spacing--30)\">\n<div class=\"wp-block-group alignwide is-content-justification-space-between is-layout-flex wp-container-core-group-is-layout-b14186be wp-block-group-is-layout-flex\">\n<p class=\"wp-block-paragraph\" style=\"font-size:16px\"><strong>Impressum and Intellectual Property Clause<\/strong><\/p>\n\n\n\n<div class=\"wp-block-group is-layout-flex wp-block-group-is-layout-flex\"><nav class=\"has-small-font-size is-responsive items-justified-left wp-block-navigation is-content-justification-left is-layout-flex wp-container-core-navigation-is-layout-ac8bf23f wp-block-navigation-is-layout-flex\" aria-label=\"Navigation\" \n\t\t data-wp-interactive=\"core\/navigation\" data-wp-context='{\"overlayOpenedBy\":{\"click\":false,\"hover\":false,\"focus\":false},\"type\":\"overlay\",\"roleAttribute\":\"\",\"ariaLabel\":\"Menu\"}'><button aria-haspopup=\"dialog\" aria-label=\"Open menu\" class=\"wp-block-navigation__responsive-container-open\" \n\t\t\t\tdata-wp-on--click=\"actions.openMenuOnClick\"\n\t\t\t\tdata-wp-on--keydown=\"actions.handleMenuKeydown\"\n\t\t\t><svg width=\"24\" height=\"24\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" viewBox=\"0 0 24 24\" aria-hidden=\"true\" focusable=\"false\"><path d=\"M4 7.5h16v1.5H4z\"><\/path><path d=\"M4 15h16v1.5H4z\"><\/path><\/svg><\/button>\n\t\t\t\t<div class=\"wp-block-navigation__responsive-container\"  id=\"modal-1\" \n\t\t\t\tdata-wp-class--has-modal-open=\"state.isMenuOpen\"\n\t\t\t\tdata-wp-class--is-menu-open=\"state.isMenuOpen\"\n\t\t\t\tdata-wp-watch=\"callbacks.initMenu\"\n\t\t\t\tdata-wp-on--keydown=\"actions.handleMenuKeydown\"\n\t\t\t\tdata-wp-on--focusout=\"actions.handleMenuFocusout\"\n\t\t\t\ttabindex=\"-1\"\n\t\t\t>\n\t\t\t\t\t<div class=\"wp-block-navigation__responsive-close\" tabindex=\"-1\">\n\t\t\t\t\t\t<div class=\"wp-block-navigation__responsive-dialog\" \n\t\t\t\tdata-wp-bind--aria-modal=\"state.ariaModal\"\n\t\t\t\tdata-wp-bind--aria-label=\"state.ariaLabel\"\n\t\t\t\tdata-wp-bind--role=\"state.roleAttribute\"\n\t\t\t>\n\t\t\t\t\t\t\t<button aria-label=\"Close menu\" class=\"wp-block-navigation__responsive-container-close\" \n\t\t\t\tdata-wp-on--click=\"actions.closeMenuOnClick\"\n\t\t\t><svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" viewBox=\"0 0 24 24\" width=\"24\" height=\"24\" aria-hidden=\"true\" focusable=\"false\"><path d=\"m13.06 12 6.47-6.47-1.06-1.06L12 10.94 5.53 4.47 4.47 5.53 10.94 12l-6.47 6.47 1.06 1.06L12 13.06l6.47 6.47 1.06-1.06L13.06 12Z\"><\/path><\/svg><\/button>\n\t\t\t\t\t\t\t<div class=\"wp-block-navigation__responsive-container-content\" \n\t\t\t\tdata-wp-watch=\"callbacks.focusFirstElement\"\n\t\t\t id=\"modal-1-content\">\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div><\/nav><\/div>\n<\/div>\n\n\n\n<p class=\"has-small-font-size wp-block-paragraph\">This <em>website<\/em> and its original content, features, and functionality are <em>owned by Vladyslav Bondarenko<\/em> and are protected by international copyright, trademark, patent, trade secret, and other intellectual property or proprietary rights laws.<br><br>One must not under any circumstances:<br>&#8211; Modify any materials and their copies from this <em>website<\/em> without formal approval from the <em>owner<\/em> <em>(Vladyslav Bondarenko)<\/em>.<br>&#8211; Use any illustrations, images, photos, video or audio sequences or any graphics separately from the accompanying text, including original captions on the <em>website<\/em>. The source (Vladyslav Bondarenko &amp; other involved and indicated persons) must always be acknowledged.<br>&#8211; Delete or alter any copyright, trademark, or other proprietary rights notices from copies of materials from the <em>website<\/em>.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>\u2002 Impressum and Intellectual Property Clause This website and its original content, features, and functionality are owned by Vladyslav Bondarenko and are protected by international&#8230;<\/p>\n<div class=\"more-link-wrapper\"><a class=\"more-link\" href=\"https:\/\/vladyslavbondarenko.com\/?page_id=28\">Continue Reading<span class=\"screen-reader-text\"><\/span><\/a><\/div>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-28","page","type-page","status-publish","hentry","entry"],"_links":{"self":[{"href":"https:\/\/vladyslavbondarenko.com\/index.php?rest_route=\/wp\/v2\/pages\/28","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/vladyslavbondarenko.com\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/vladyslavbondarenko.com\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/vladyslavbondarenko.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/vladyslavbondarenko.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=28"}],"version-history":[{"count":383,"href":"https:\/\/vladyslavbondarenko.com\/index.php?rest_route=\/wp\/v2\/pages\/28\/revisions"}],"predecessor-version":[{"id":1153,"href":"https:\/\/vladyslavbondarenko.com\/index.php?rest_route=\/wp\/v2\/pages\/28\/revisions\/1153"}],"wp:attachment":[{"href":"https:\/\/vladyslavbondarenko.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=28"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}