{"id":12707,"date":"2023-07-13T14:07:19","date_gmt":"2023-07-13T12:07:19","guid":{"rendered":"https:\/\/new.sano.science\/?post_type=people&p=12707"},"modified":"2026-02-24T11:17:26","modified_gmt":"2026-02-24T10:17:26","slug":"tomasz-kosciolek","status":"publish","type":"people","link":"https:\/\/sano.science\/people\/tomasz-kosciolek\/","title":{"rendered":"Tomasz Ko\u015bci\u00f3\u0142ek"},"excerpt":{"rendered":"

Research Team Leader<\/p>\n","protected":false},"featured_media":28732,"template":"","people_teams":[19,114],"class_list":["post-12707","people","type-people","status-publish","has-post-thumbnail","hentry","people_teams-research","people_teams-structural-and-functional-genomics-group"],"yoast_head":"\nTomasz Ko\u015bci\u00f3\u0142ek - Centre for Computational Personalized Medicine<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sano.science\/people\/tomasz-kosciolek\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tomasz Ko\u015bci\u00f3\u0142ek\" \/>\n<meta property=\"og:description\" content=\"Research Team Leader\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sano.science\/people\/tomasz-kosciolek\/\" \/>\n<meta property=\"og:site_name\" content=\"Centre for Computational Personalized Medicine\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/sano.science\/\" \/>\n<meta property=\"article:modified_time\" content=\"2026-02-24T10:17:26+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/Tomasz-Kosciolek.png\" \/>\n\t<meta property=\"og:image:width\" content=\"650\" \/>\n\t<meta property=\"og:image:height\" content=\"650\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@sanoscience\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/tomasz-kosciolek\\\/\",\"url\":\"https:\\\/\\\/sano.science\\\/people\\\/tomasz-kosciolek\\\/\",\"name\":\"Tomasz Ko\u015bci\u00f3\u0142ek - 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In years 2016-2019 he was a post-doctoral research associate in Rob Knight\u2019s group at University of California San Diego (USA) and 2019-2022 we was a group leader in bioinformatics at the Ma\u0142opolska Centre of Biotechnology, Jagiellonian University in Krak\u00f3w. He is working on the development and application of computational methods to better understand the function and dynamics of the human gut microbiome. He has contributed to the development of a suite of tools commonly used in microbiome analyses – QIIME 2 and Qiita – and he is also working on state-of-the-art machine learning and statistical methods to predict protein function (deepFRI) or to model the dysbiosis and dynamics of the microbiome. The goal of his group is to build a multi-level understanding of the microbiome from genes, through structures, to functions and therapies.<\/p>\n<p> <\/p>\n<p><iframe loading=\"lazy\" title=\"Meet Your Scientist - Tomasz Ko\u015bci\u00f3\u0142ek\" width=\"500\" height=\"281\" src=\"https:\/\/www.youtube.com\/embed\/2hQAclptjkQ?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe><\/p>\n<blockquote><p> <\/p>\n<p>Interview with Tomasz Ko\u015bci\u00f3\u0142ek on Radio WNET entitled “How do microbiomes affect the world? A tiny world with a huge impact on life.”<\/p>\n<p> <\/p><\/blockquote>\n<p><iframe loading=\"lazy\" title=\"Jak mikrobiomy wp\u0142ywaj\u0105 na \u015bwiat? Mini \u015bwiat, ale maxi wp\u0142yw na \u017cycie | Audycja LIMES INFERIOR\" width=\"500\" height=\"281\" src=\"https:\/\/www.youtube.com\/embed\/bBvSe87Bd_A?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe><\/p>\n<p><strong>Explore the interactive tool<\/strong> <a href=\"https:\/\/protein-structure-landscape.sano.science\/\">protein-structure-landscape.sano.science<\/a><\/p>\n","email":"","social_media":[{"icon":{"ID":11992,"id":11992,"title":"orcid","filename":"orcid.svg","filesize":15590,"url":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/orcid.svg","link":"https:\/\/sano.science\/people\/maciej-malawski\/orcid\/","alt":"","author":"5","description":"","caption":"","name":"orcid","status":"inherit","uploaded_to":531,"date":"2023-07-06 11:21:29","modified":"2023-07-06 11:21:29","menu_order":0,"mime_type":"image\/svg+xml","type":"image","subtype":"svg+xml","icon":"https:\/\/sano.science\/wp-includes\/images\/media\/default.png","width":1,"height":1,"sizes":{"thumbnail":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/orcid.svg","thumbnail-width":150,"thumbnail-height":150,"medium":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/orcid.svg","medium-width":300,"medium-height":300,"medium_large":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/orcid.svg","medium_large-width":768,"medium_large-height":1,"large":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/orcid.svg","large-width":1024,"large-height":1024,"1536x1536":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/orcid.svg","1536x1536-width":1,"1536x1536-height":1,"2048x2048":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/orcid.svg","2048x2048-width":1,"2048x2048-height":1}},"link":"https:\/\/orcid.org\/0000-0002-9915-7387","name":"ORCID"},{"icon":{"ID":11986,"id":11986,"title":"google","filename":"google.svg","filesize":14070,"url":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/google.svg","link":"https:\/\/sano.science\/people\/maciej-malawski\/google\/","alt":"","author":"5","description":"","caption":"","name":"google","status":"inherit","uploaded_to":531,"date":"2023-07-06 10:59:21","modified":"2023-07-06 10:59:21","menu_order":0,"mime_type":"image\/svg+xml","type":"image","subtype":"svg+xml","icon":"https:\/\/sano.science\/wp-includes\/images\/media\/default.png","width":1,"height":1,"sizes":{"thumbnail":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/google.svg","thumbnail-width":150,"thumbnail-height":150,"medium":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/google.svg","medium-width":300,"medium-height":300,"medium_large":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/google.svg","medium_large-width":768,"medium_large-height":1,"large":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/google.svg","large-width":1024,"large-height":1024,"1536x1536":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/google.svg","1536x1536-width":1,"1536x1536-height":1,"2048x2048":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/google.svg","2048x2048-width":1,"2048x2048-height":1}},"link":"https:\/\/scholar.google.com\/citations?user=1Mi0KMMAAAAJ&hl=pl","name":"GOOGLE SCHOLAR"}],"tabs":false,"quote":"","publications":[{"ID":29318,"post_author":"8","post_date":"2026-02-24 11:10:52","post_date_gmt":"2026-02-24 10:10:52","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-8A8gyW\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">A new paper co-authored by <a href=\"https:\/\/sano.science\/people\/tomasz-kosciolek\/\" type=\"people\" id=\"12707\">Tomasz Ko\u015bci\u00f3\u0142ek<\/a>, Research Team Leader of the Structural and Functional Genomics Group at Sano, has been published in the <strong>American Journal of Obstetrics & Gynecology<\/strong>. <\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-fTzQJt\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-8A8gyW\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">The study titled \u201c<strong>A Systematic Review of Maternal Microbial Transfer in Cesarean-Delivered Newborns<\/strong>\u201d (authors: Jan Jurgiel, Tomasz Gromowski, Joanna Kr\u00f3l, Dorota Bomba-Opo\u0144, Tomasz Ko\u015bci\u00f3\u0142ek, Miros\u0142aw Wielgo\u015b) reviews existing research on maternal microbial transfer and explores approaches aimed at restoring the natural microbiome in infants born <em>via<\/em> cesarean section. The findings highlight potential benefits in microbial diversity and the safety of the procedure, while emphasizing the need for further research. <\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-fTzQJt\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_699d798fcc8fc\",\"name\":\"acf\/button\",\"data\":{\"title\":\"Read the article\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.ajog.org\/article\/S0002-9378(25)00651-9\/fulltext\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_blank\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-fTzQJt\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-cd7WC6\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Authors: <\/strong>Jurgiel Jan, Gromowski Tomasz, Kr\u00f3l Joanna, Bomba-Opo\u0144 Dorota, Ko\u015bci\u00f3\u0142ek Tomasz, Wielgo\u015b Miros\u0142aw <\/p>\n<!-- \/wp:paragraph -->","post_title":"The impact of maternal microbial transfer on the infant gut microbiome after cesarean delivery: a systematic review\u00a0","post_excerpt":"","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"the-impact-of-maternal-microbial-transfer-on-the-infant-gut-microbiome-after-cesarean-delivery-a-systematic-review","to_ping":"","pinged":"","post_modified":"2026-02-24 11:17:00","post_modified_gmt":"2026-02-24 10:17:00","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=29318","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":19114,"post_author":"8","post_date":"2024-10-04 15:58:27","post_date_gmt":"2024-10-04 13:58:27","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-DgozF9\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\" id=\"h-lukasz-m-szydlowski-nbsp-alper-a-bulbul-nbsp-anna-c-simpson-nbsp-deniz-e-kaya-nbsp-nitin-k-singh-nbsp-ugur-o-sezerman-nbsp-pawel-p-labaj-nbsp-tomasz-kosciolek-nbsp-kasthuri-venkateswaran-nbsp\">Lukasz M. Szydlowski, Alper A. Bulbul, Anna C. Simpson, Deniz E. Kaya, Nitin K. Singh, Ugur O. Sezerman, Pawe\u0142 P. \u0141abaj, Tomasz Kosciolek, Kasthuri Venkateswaran <\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-olQC3k\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-B8vIuB\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">In our study, we used a deep learning-based tool, deepFRI, to analyze the genomes of five newly discovered Gram-positive bacterial species from the ISS, four of which are non-spore-forming and one spore-forming. This allowed for precise annotation of nearly all protein-coding genes. Comparative genomic analysis revealed common traits across all studied species, as well as unique genetic features specific to ISS microorganisms. Proteome analysis reflected these patterns, indicating adaptations to life in space, such as managing hypoosmotic stress related to microgravity, enhanced DNA repair activity to counteract increased radiation exposure, and the presence of mobile genetic elements that improve metabolism. Additionally, our findings suggest the evolution of genetic traits that may possess pathogenic capabilities, such as small molecule and peptide synthesis and ATP-dependent transporters, which could explain previous reports of increased antibiotic resistance and pathogenicity in microbes exposed to space conditions. These results suggest that the ISS microorganisms we studied have adapted to life in space, which is significant for future space missions, both in terms of bioproduction and potential therapeutic targets.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-olQC3k\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-2EctuW\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Authors<\/strong>: <a href=\"https:\/\/sano.science\/people\/lukasz-szydlowski\/\">Lukasz M. Szydlowski<\/a>, Alper A. Bulbul, Anna C. Simpson, Deniz E. Kaya, Nitin K. Singh, Ugur O. Sezerman, Pawe\u0142 P. \u0141abaj, <a href=\"https:\/\/sano.science\/people\/tomasz-kosciolek\/\">Tomasz Kosciolek<\/a> & Kasthuri Venkateswaran <\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-DDc0wF\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>DOI:<\/strong> https:\/\/doi.org\/10.1186\/s40168-024-01916-8<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-vUaWby\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Link to article<\/strong>: https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-024-01916-8<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-lJDuvK\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Keywords<\/strong>: functional annotation, international space station, extremophiles<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-olQC3k\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_6780f5dda81cc\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-024-01916-8\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-olQC3k\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:video {\"id\":19104,\"epAnimationGeneratedClass\":\"edplus_anim-SmK5nk\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<figure class=\"wp-block-video eplus-wrapper\"><video controls src=\"https:\/\/sano.science\/wp-content\/uploads\/2024\/10\/adaptation_of_bacterial_species_from_the_international_space_station_to_life_in_space-720p.mp4\"><\/video><\/figure>\n<!-- \/wp:video -->","post_title":"Adaptation to space conditions of novel bacterial species isolated from the International Space Station revealed by functional gene annotations and comparative genome analysis","post_excerpt":"Journal paper in: microbiomejournal.biomedcentral.com, 2024","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"adaptation-to-space-conditions-of-novel-bacterial-species-isolated-from-the-international-space-station-revealed-by-functional-gene-annotations-and-comparative-genome-analysis","to_ping":"","pinged":"","post_modified":"2025-01-10 13:45:10","post_modified_gmt":"2025-01-10 12:45:10","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=19114","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":20647,"post_author":"8","post_date":"2025-01-10 11:17:24","post_date_gmt":"2025-01-10 10:17:24","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-qKj7lS\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\" id=\"h-pawel-szczerbiak-lukasz-m-szydlowski-witold-wydmanski-p-douglas-renfrew-julia-koehler-leman-tomasz-kosciolek\">Pawe\u0142 Szczerbiak, Lukasz M. Szydlowski, Witold Wydma\u0144ski, P. Douglas Renfrew, Julia Koehler Leman, Tomasz Kosciolek<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-BU3oJP\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-ydGv10\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Advances in protein structure prediction have resulted in a remarkable rise in high-quality 3D models, emphasizing the need for effective computational methods to handle and explore this structural data. Our study explores structural clusters derived from the AlphaFold Protein Structure Database (AFDB), a high-quality subset of ESMAtlas, and the Microbiome Immunity Project (MIP). We generate a unified low-dimensional representation of the protein structure space, revealing that while each database occupies distinct regions, they share significant overlap in functional profiles. Key biological functions cluster within specific regions, indicating a common functional landscape across diverse datasets. To support data exploration, we developed an open-access web server. These findings provide a foundation for further research into protein sequence-structure-function relationships, including taxonomic classification, environmental influences, and functional specificity.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-BU3oJP\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-b6JXoH\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>DOI<\/strong>: https:\/\/doi.org\/10.1101\/2024.08.14.607935<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-nv0xgb\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Keywords<\/strong>: protein structure prediction3D modelsAlphaFold Protein Structure Database (AFDB)ESMAtlasMicrobiome Immunity Project (MIP)structural clusterslow-dimensional representationfunctional profilesbiological functionsopen-access web serverprotein sequence-structure-function relationships<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-BU3oJP\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_6780f1729ec59\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.08.14.607935v2\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Large protein databases reveal structural complementarity and functional locality","post_excerpt":"Journal paper in: www.biorxiv.org\/content, 2024","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"large-protein-databases-reveal-structural-complementarity-and-functional-locality","to_ping":"","pinged":"","post_modified":"2025-01-10 13:44:35","post_modified_gmt":"2025-01-10 12:44:35","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=20647","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":20713,"post_author":"8","post_date":"2025-01-10 13:29:47","post_date_gmt":"2025-01-10 12:29:47","post_content":"<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-8PQu2K\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\" id=\"h-zuzanna-karwowska-oliver-aasmets-estonian-biobank-research-team-tomasz-kosciolek-elin-org\">Zuzanna Karwowska, Oliver Aasmets, Estonian Biobank research team, Tomasz Kosciolek, Elin Org<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"50px\",\"epAnimationGeneratedClass\":\"edplus_anim-UZJmFC\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:50px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-kOAyOm\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">The effective classification of host phenotypes through microbiome data is essential for the progression of microbiome-centered treatments, where machine learning serves as a pivotal tool. The inherent complexity of the gut microbiome, coupled with issues like data sparsity, compositionality, and variability across populations, poses substantial challenges. Although transforming microbiome data can mitigate some of these difficulties, its application in machine learning endeavors remains largely underinvestigated.<br>In our study, we examined more than 8500 samples across 24 shotgun metagenomic datasets, discovering that it is feasible to differentiate between healthy and diseased states using microbiome data, with minimal reliance on specific algorithms or data transformations. We found that presence-absence data transformations were as effective as those based on abundance, and that accurate classification could be achieved using only a limited set of predictive features. Despite similar levels of classification accuracy across different transformations, the key features identified varied significantly, underscoring the importance of reevaluating the detection of biomarkers through machine learning.<br>Our results demonstrate that while microbiome data transformations have a substantial impact on feature selection, they do not significantly alter classification accuracy. This indicates that although the classification process is stable across various transformations, careful consideration is necessary in the selection of features for biomarker discovery using machine learning. This study not only contributes valuable insights into the application of machine learning to microbiome data but also points to crucial areas for future research.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-HPXIta\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-H79dq1\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>DOI<\/strong>: 10.1186\/s40168-024-01996-6<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-HPXIta\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_6781125f36ffb\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC11699698\/\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Effects of data transformation and model selection on feature importance in microbiome classification data","post_excerpt":"Journal paper in: Springer Nature - BioMed Central, 2025","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"effects-of-data-transformation-and-model-selection-on-feature-importance-in-microbiome-classification-data","to_ping":"","pinged":"","post_modified":"2025-02-21 12:40:24","post_modified_gmt":"2025-02-21 11:40:24","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=20713","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":20702,"post_author":"8","post_date":"2025-01-10 13:11:05","post_date_gmt":"2025-01-10 12:11:05","post_content":"<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-sMidxN\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:heading {\"epAnimationGeneratedClass\":\"edplus_anim-WNUP7L\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<h2 class=\"wp-block-heading eplus-wrapper\" id=\"h-stefanie-duller-simone-vrbancic-lukasz-szydlowski-alexander-mahnert-marcus-blohs-michael-predl-christina-kumpitsch-verena-zrim-christoph-hogenauer-tomasz-kosciolek-ruth-a-schmitz-anna-eberhard-melanie-dragovan-laura-schmidberger-tamara-zurabischvili-viktoria-weinberger-adrian-mathias-moser-dagmar-kolb-dominique-pernitsch-rokhsareh-mohammadzadeh-torben-kuhnast-thomas-rattei-christine-moissl-eichinger\">Stefanie Duller,\u00a0Simone Vrbancic,\u00a0 \u0141ukasz Szyd\u0142owski,\u00a0 Alexander Mahnert,\u00a0 Marcus Blohs,\u00a0 Michael Predl,\u00a0Christina Kumpitsch,\u00a0 Verena Zrim,\u00a0Christoph H\u00f6genauer,\u00a0Tomasz Kosciolek,\u00a0 Ruth A. Schmitz,\u00a0Anna Eberhard,\u00a0Melanie Dragovan,\u00a0Laura Schmidberger,\u00a0Tamara Zurabischvili, Viktoria Weinberger,\u00a0Adrian Mathias Moser,\u00a0Dagmar Kolb,\u00a0Dominique Pernitsch,\u00a0Rokhsareh Mohammadzadeh,\u00a0 Torben K\u00fchnast, Thomas Rattei,Christine Moissl-Eichinger\u00a0<\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-sMidxN\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-YKq6IE\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Archaea play a crucial role in the human microbiome, yet their study in the gastrointestinal tract (GIT) remains limited due to a lack of cultured strains. This study introduces a method for enriching and isolating methanogenic archaea from human fecal samples using methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and Nanopore sequencing. The approach also involves analyzing co-cultured bacteria, comparative genomics, functional analysis, and protein structure-based function prediction. Stable archaeal cultures were established from 14 of 16 fecal samples, yielding nine previously uncultivated strains, eight of which were absent from a recent archaeome genome catalog. Genomic comparisons of <em>Methanobrevibacter smithii<\/em> and <em>Candidatus Methanobrevibacter intestini<\/em> revealed traits potentially linked to gastrointestinal diseases. This work expands available archaeal strains for GIT research and provides new insights into the adaptability of <em>Candidatus Methanobrevibacter intestini<\/em> in the human microbiome.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-sMidxN\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-TTVH8d\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>DOI<\/strong>: 10.1038\/s41467-024-52037-7<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-UXPFFS\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Keywords<\/strong>: ArchaeaGastrointestinal tract (GIT)Human microbiomeMethanogenic archaeaMethane breath testingFACSNanopore sequencing<em>Methanobrevibacter smithii<\/em><em>Candidatus Methanobrevibacter intestini<\/em>Comparative genomicsFunctional analysisMicrobiome adaptability<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"40px\",\"epAnimationGeneratedClass\":\"edplus_anim-sMidxN\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_67810de554642\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.nature.com\/articles\/s41467-024-52037-7\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->","post_title":"Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome","post_excerpt":"Journal paper in: www.nature.com, 2024","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"targeted-isolation-of-methanobrevibacter-strains-from-fecal-samples-expands-the-cultivated-human-archaeome","to_ping":"","pinged":"","post_modified":"2025-02-03 15:35:48","post_modified_gmt":"2025-02-03 14:35:48","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=20702","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"}],"position_with_team":{"text_before_link":"Research Team Leader of","link_text":"Structural and Functional Genomics Group","text_after_link":"","link":"https:\/\/sano.science\/research-teams\/structural-and-functional-genomics-group\/"}},"_links":{"self":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12707","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people"}],"about":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/types\/people"}],"version-history":[{"count":19,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12707\/revisions"}],"predecessor-version":[{"id":29341,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/12707\/revisions\/29341"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media\/28732"}],"wp:attachment":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media?parent=12707"}],"wp:term":[{"taxonomy":"people_teams","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people_teams?post=12707"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}