{"id":11964,"date":"2023-07-06T12:40:52","date_gmt":"2023-07-06T10:40:52","guid":{"rendered":"https:\/\/new.sano.science\/?post_type=people&p=11964"},"modified":"2026-07-21T16:17:24","modified_gmt":"2026-07-21T14:17:24","slug":"jakub-jonczyk","status":"publish","type":"people","link":"https:\/\/sano.science\/people\/jakub-jonczyk\/","title":{"rendered":"Jakub Jo\u0144czyk"},"excerpt":{"rendered":"

PostDoc in Clinical Data Science<\/p>\n","protected":false},"featured_media":11965,"template":"","people_teams":[24],"class_list":["post-11964","people","type-people","status-publish","has-post-thumbnail","hentry","people_teams-alumni"],"yoast_head":"\nJakub Jo\u0144czyk - 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\/jakub-jonczyk\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Jakub Jo\u0144czyk\" \/>\n<meta property=\"og:description\" content=\"PostDoc in Clinical Data Science\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sano.science\/people\/jakub-jonczyk\/\" \/>\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=\"2026-07-21T14:17:24+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sano.science\/wp-content\/uploads\/2023\/07\/jakub_jonczyk.png\" \/>\n\t<meta property=\"og:image:width\" content=\"350\" \/>\n\t<meta property=\"og:image:height\" content=\"350\" \/>\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\\\/jakub-jonczyk\\\/\",\"url\":\"https:\\\/\\\/sano.science\\\/people\\\/jakub-jonczyk\\\/\",\"name\":\"Jakub Jo\u0144czyk - 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His doctoral research concerns the application of molecular modeling in drug design, specifically in designing multitarget ligands for future Alzheimer\u2019s treatment. After that Jakub spent one year as a assistant professor with the Medicinal Chemistry Department at Jagiellonian University teaching and expanding his research with machine learning techniques. At Sano, he joined the Clinical Data Science Team for his PostDoc training. He aims to build his computational knowledge to advance his career as a medical chemistry. He is excited is collaborate with a vibrant interdiscplanary team of computer scientists, biologists, pharmacologist to provide a better response to the needs of patients and medical professionals around the world.<\/p>\n","email":"","social_media":[{"icon":{"ID":11994,"id":11994,"title":"linkedin","filename":"linkedin.svg","filesize":914,"url":"https:\/\/sano.science\/wp-content\/uploads\/2023\/05\/linkedin.svg","link":"https:\/\/sano.science\/people\/maciej-malawski\/linkedin-2\/","alt":"","author":"5","description":"","caption":"","name":"linkedin-2","status":"inherit","uploaded_to":531,"date":"2023-07-06 11:24:13","modified":"2023-07-06 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Schoolar"}],"tabs":false,"quote":"","position_with_team":{"text_before_link":"","link_text":"","text_after_link":"","link":""},"publications":[{"ID":32176,"post_author":"8","post_date":"2026-07-21 16:15:23","post_date_gmt":"2026-07-21 14:15:23","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-XIhDT7\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Interpreting machine learning models trained on molecular data remains challenging, particularly at the level of individual atoms. Although many attribution methods can indicate which atoms influence a prediction, the field still lacks standardized benchmarks for determining whether these explanations are chemically and structurally meaningful.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-w7fPSA\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">To address this gap, this work introduces a controlled benchmark based on rule-derived pharmacophore annotations. Predefined geometric constraints describe the spatial arrangement of functional features within a molecule and provide reference atom sets against which model explanations can be evaluated.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-pY3VG2\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">The benchmark is accompanied by PharmacoScore, a metric that quantifies how closely atom-level attributions align with these pharmacophore-derived references. The framework was used to compare explanation methods across several model families, ranging from fragment-based approaches to distance-aware transformers that explicitly encode interatomic geometry.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-IljwbN\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Distance-aware transformers consistently achieved higher PharmacoScore values, indicating that the atoms emphasized by their explanations more closely reflected the expected spatial relationships. Together, the benchmark and PharmacoScore provide a unified framework for systematically evaluating and comparing atom-level explainability methods in molecular machine learning.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-2gqUdL\",\"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-gJa0es\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Autors<\/strong>: Adam Su\u0142ek, Jakub Klimczak, Jakub Jo\u0144czyk, Tomasz Kosciolek, Tomasz Danel, Barbara Pucelik<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-RtIONs\",\"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_6a5f7e6dca8e9\",\"name\":\"acf\/button\",\"data\":{\"title\":\"Read the article\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S187775032600164X\",\"_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-RtIONs\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:image {\"id\":32193,\"sizeSlug\":\"large\",\"linkDestination\":\"none\",\"epAnimationGeneratedClass\":\"edplus_anim-eHjexA\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<figure class=\"wp-block-image size-large eplus-wrapper\"><img src=\"https:\/\/sano.science\/wp-content\/uploads\/2026\/07\/FIRST-TEAM-FENG-FNP-Foundation-for-Polish-Science-1024x88.png\" alt=\"\" class=\"wp-image-32193\"\/><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-RtIONs\",\"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-BZNiNt\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">This publication is one of the outcomes of the FIRST TEAM FENG project\u00a0<a href=\"https:\/\/www.linkedin.com\/company\/foundation-for-polish-science\/\" target=\"_blank\" rel=\"noreferrer noopener\">FNP Foundation for Polish Science<\/a>, under which\u00a0<a href=\"https:\/\/www.linkedin.com\/company\/lukasiewicz-krakow-institute-of-technology\/\" target=\"_blank\" rel=\"noreferrer noopener\">\u0141ukasiewicz \u2013 Krakow Institute of Technology<\/a>\u00a0is developing\u00a0new approaches\u00a0to the identification and evaluation of therapeutic candidates in hormone-dependent breast cancer.\u00a0<\/p>\n<!-- \/wp:paragraph -->","post_title":"Benchmarking\u00a0atom-level\u00a0explainability\u00a0against\u00a0pharmacophore-computed\u00a0labels\u00a0in\u00a0molecular\u00a0machine\u00a0learning","post_excerpt":"In: Journal of Computational Science, 2026","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"benchmarking-atom-level-explainability-against-pharmacophore-computed-labels-in-molecular-machine-learning","to_ping":"","pinged":"","post_modified":"2026-07-22 11:36:50","post_modified_gmt":"2026-07-22 09:36:50","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=32176","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":21508,"post_author":"8","post_date":"2025-02-17 17:40:47","post_date_gmt":"2025-02-17 16:40:47","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-5nKxVv\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Dr. Dawid Panek, Dr. Anna Pasieka, Dr. <a href=\"https:\/\/sano.science\/people\/jakub-jonczyk\/\">Jakub Jo\u0144czyk<\/a>, Milena Gawli\u0144ska, Dr. Paula Zar\u0119ba, Dr. Agata Siwek, Dr. Ma\u0142gorzata Wolak, Dr. Barbara Mordyl, Dr. Monika G\u0142uch-Lutwin, Dr. Gniewomir Latacz, Dr. Xavier Brazzolotto, Dr. Fabien Chantegreil, Dr. Florian Nachon, Prof.\u2005Dr. Jana Zdarova Karasova, Dr. Jaroslav Pejchal, Dr. Martin Mzik, Dr. Vit Sestak, Lukas Prchal, Dr. Jitka Odvarkova, Dr. Ondrej Soukup, Prof.\u2005Dr. Jan Korabecny, Dr. Ales Sorf, Dr. Marie Hamsikova, Dr. Lucie Zemanova, Dr. Lubica Muckova, Dr. Nela V\u00e1nova, Pola Dryja, Prof.\u2005Dr. Kinga Sa\u0142at, Dr. Georg H\u00f6fner, Prof.\u2005Dr. Klaus Wanner, Dr. Anna Wi\u0119ckowska, Prof.\u2005Dr. Barbara Malawska<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-V2l7ci\",\"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-7dFj5s\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Progressive cognitive decline characterizing Alzheimer's disease (AD) includes memory impairments and various behavioral and psychological symptoms of dementia (BPSD). Treatments traditionally target the predominantly affected cholinergic neurons to boost neurotransmission. However, dysfunctions in additional neurotransmitters such as \u03b3-aminobutyric acid (GABA) also significantly influence AD\u2019s clinical manifestations. This research introduces compound 6, developed through a blend of crystallography and computational analytics, serving as a dual regulator of GABAergic and cholinergic transmission. It effectively inhibits BuChE (IC50=0.21\u2005\u03bcM) and GABA transporters 1 (IC50=10.96\u2005\u03bcM) and 3 (IC50=7.76\u2005\u03bcM), with a robust profile suitable for drug development. Compound 6's efficacy in improving memory retention and mitigating symptoms of anxiety and depression was confirmed through in vivo tests, showing it to be safe and orally bioavailable. Offering a novel, multi-targeted therapeutic strategy, compound 6 holds potential for managing cognitive deficits and BPSD in Alzheimer\u2019s disease.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-V2l7ci\",\"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-p5dL3M\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>DOI<\/strong>: 10.1002\/anie.202420510<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-V2l7ci\",\"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_67b35e96c50b1\",\"name\":\"acf\/button\",\"data\":{\"title\":\"READ HERE\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/anie.202420510\",\"_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":"Multifunctional, Fluorene-Based Modulator of Cholinergic and GABAergic Neurotransmission as a Novel Drug Candidate for Palliative Treatment of Alzheimer's Disease","post_excerpt":"In: Angewandte Chemie International Edition, 2024","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"multifunctional-fluorene-based-modulator-of-cholinergic-and-gabaergic-neurotransmission-as-a-novel-drug-candidate-for-palliative-treatment-of-alzheimers-disease","to_ping":"","pinged":"","post_modified":"2025-02-17 17:51:45","post_modified_gmt":"2025-02-17 16:51:45","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=21508","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"}]},"_links":{"self":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/11964","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":4,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/11964\/revisions"}],"predecessor-version":[{"id":32189,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/11964\/revisions\/32189"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media\/11965"}],"wp:attachment":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media?parent=11964"}],"wp:term":[{"taxonomy":"people_teams","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people_teams?post=11964"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}