{"id":88899,"date":"2025-02-27T09:22:10","date_gmt":"2025-02-27T08:22:10","guid":{"rendered":"https:\/\/port.lukasiewicz.gov.pl\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/researches\/"},"modified":"2025-12-15T11:38:47","modified_gmt":"2025-12-15T10:38:47","slug":"researches","status":"publish","type":"page","link":"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/researches\/","title":{"rendered":"Researches"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"88899\" class=\"elementor elementor-88899 elementor-64724\" data-elementor-post-type=\"page\">\n\t\t\t\t<div class=\"elementor-element elementor-element-ea288c0 e-flex e-con-boxed e-con e-parent\" data-id=\"ea288c0\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t<div class=\"elementor-element elementor-element-f9d32c3 e-con-full e-flex e-con e-child\" data-id=\"f9d32c3\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t<div class=\"elementor-element elementor-element-ee4f416 elementor-widget elementor-widget-heading\" data-id=\"ee4f416\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">Quantitative Virology Research Group<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7d10b69 elementor-nav-menu--dropdown-none elementor-widget elementor-widget-nav-menu\" data-id=\"7d10b69\" data-element_type=\"widget\" data-e-type=\"widget\" data-settings=\"{&quot;layout&quot;:&quot;horizontal&quot;,&quot;submenu_icon&quot;:{&quot;value&quot;:&quot;&lt;svg aria-hidden=\\&quot;true\\&quot; class=\\&quot;e-font-icon-svg e-fas-caret-down\\&quot; viewBox=\\&quot;0 0 320 512\\&quot; 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href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/researches\/\" class=\"elementor-item\">Researches<\/a><\/li>\n<li class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-91148\"><a href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/projects\/\" class=\"elementor-item\">Projects<\/a><\/li>\n<li class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-91149\"><a href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/publications\/\" class=\"elementor-item\">Publications<\/a><\/li>\n<li class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-91167\"><a href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/contact\/\" class=\"elementor-item\">Contact<\/a><\/li>\n<\/ul>\t\t\t<\/nav>\n\t\t\t\t\t\t<nav class=\"elementor-nav-menu--dropdown elementor-nav-menu__container\" aria-hidden=\"true\">\n\t\t\t\t<ul id=\"menu-2-7d10b69\" class=\"elementor-nav-menu\"><li class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-91150\"><a href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/\" class=\"elementor-item\" tabindex=\"-1\">About Us<\/a><\/li>\n<li class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-91166\"><a href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/researches\/\" class=\"elementor-item\" tabindex=\"-1\">Researches<\/a><\/li>\n<li class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-91148\"><a href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/projects\/\" class=\"elementor-item\" tabindex=\"-1\">Projects<\/a><\/li>\n<li class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-91149\"><a href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/publications\/\" class=\"elementor-item\" tabindex=\"-1\">Publications<\/a><\/li>\n<li class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-91167\"><a href=\"https:\/\/port.lukasiewicz.gov.pl\/en\/rd-centers\/population-diagnostics-center\/quantitative-virology-research-group\/contact\/\" class=\"elementor-item\" tabindex=\"-1\">Contact<\/a><\/li>\n<\/ul>\t\t\t<\/nav>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-48f4cca elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"48f4cca\" data-element_type=\"section\" data-e-type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-20c14194\" data-id=\"20c14194\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-36312d00 elementor-widget elementor-widget-heading\" data-id=\"36312d00\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Research topics<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c37a1a1 elementor-widget__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"c37a1a1\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>One of the main goals of our laboratory is to study the establishment of HIV latency in connection with stochastic HIV transcription and the functional host genome. Using quantitative genomic approaches and machine learning\u2013based methods developed in our lab, we aim to deepen our understanding of how single-virus-level variability in HIV genome integrity and transcription influences the configuration of HIV reservoirs. Our research directions include the following:  <\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-eff5df0 elementor-widget elementor-widget-heading\" data-id=\"eff5df0\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">1. The Role of HIV Antisense Transcripts (ASTs) in Latency Establishment<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-ef2a015 e-grid e-con-boxed e-con e-parent\" data-id=\"ef2a015\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-249b7d3 elementor-widget elementor-widget-text-editor\" data-id=\"249b7d3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p data-start=\"729\" data-end=\"1148\">Although the existence of HIV antisense transcripts (ASTs) and their encoded proteins was first suggested by computational analyses in 1988, the underlying mechanisms remain poorly understood. <strong data-start=\"938\" data-end=\"950\">In vitro<\/strong> studies have shown that HIV antisense RNAs may promote the initiation and maintenance of HIV latency; however, <strong data-start=\"1052\" data-end=\"1063\">in vivo<\/strong> evidence is limited and contradictory, leaving their role in pathogenesis uncertain. <\/p><p data-start=\"1150\" data-end=\"1477\">Our goal is to characterize the potential threshold ratio between sense and antisense HIV transcription by defining distinct HIV transcriptional phenotypes. We achieve this using barcode-labeled HIV constructs and cell clones, each exhibiting a unique HIV transcriptional profile. <\/p><p><strong data-start=\"2189\" data-end=\"2214\">Related publication:<\/strong><br data-start=\"2214\" data-end=\"2217\">Wi\u0119cek, K. i in. 2025. <em data-start=\"2240\" data-end=\"2292\">Computational and Structural Biotechnology Journal<\/em> DOI:10.1016\/j.csbj.2025.08.003 <\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4cab425 elementor-widget elementor-widget-image\" data-id=\"4cab425\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t<figure class=\"wp-caption\">\n\t\t\t\t\t\t\t\t\t\t<img alt=\"\" fetchpriority=\"high\" decoding=\"async\" width=\"939\" height=\"463\" src=\"https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-1.webp\" class=\"attachment-full size-full wp-image-86904\" alt=\"\" srcset=\"https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-1.webp 939w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-1-300x148.webp 300w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-1-768x379.webp 768w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-1-24x12.webp 24w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-1-36x18.webp 36w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-1-48x24.webp 48w\" sizes=\"(max-width: 939px) 100vw, 939px\" \/>\t\t\t\t\t\t\t\t\t\t\t<figcaption class=\"widget-image-caption wp-caption-text\">Figure 1. The contribution of HIV asRNA to stochastic fluctuations in HIV gene expression. We propose that stochastic HIV transcription may occur at two main levels: (1) the chromosomal landscape and (2) the HIV integration site (A, B). We observed a minimal degree of heritability of such fluctuations and identified proviral integration sites near genomic repeat regions associated with strong H3K27ac and H3K4me3 signals. In both cases, similar temporal patterns of sense and antisense transcript expression were observed (C), suggesting that stochastic HIV transcription phenotypes are determined by independent production of both transcript types rather than their ratio.      <\/figcaption>\n\t\t\t\t\t\t\t\t\t\t<\/figure>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9524354 elementor-widget elementor-widget-heading\" data-id=\"9524354\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">2. Distinct Task-Induced Topology of Functional Genomic Networks in HIV Reservoirs<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-87e6597 e-grid e-con-boxed e-con e-parent\" data-id=\"87e6597\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-f6cc082 elementor-widget elementor-widget-text-editor\" data-id=\"f6cc082\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p data-start=\"2383\" data-end=\"2878\">Our approach to HIV reservoirs assumes that they can be represented as task-induced topological properties of networks composed of gene communities targeted by HIV. These communities form immunological signatures.<br>The frequency of HIV integration within these networks can serve as an indicator for identifying specific immune cell types and soluble proinflammatory factors, facilitating precise tuning of the reservoir microenvironment.   <\/p><p data-start=\"2880\" data-end=\"3351\">To better understand the heterogeneity and functional implications of HIV reservoirs, we were among the first to apply a convergent approach to characterize their composition. Using graph theory\u2013based tools, we observed distinct topological features in networks enriched for immunological signatures containing genes with intact and defective proviruses, comparing ART-treated individuals with elite controllers. <\/p><p data-start=\"3353\" data-end=\"3979\">A key variable\u2014the rich factor\u2014plays a decisive role in classifying distinct topological network properties.<br>Host gene expression improves classification accuracy between elite controllers and ART-treated patients. Using Markov Chain Monte Carlo modeling, we simulated various graph networks and discovered an internal barrier separating elite controllers from non-controllers. Our research represents an important example of using genomic and mathematical approaches to unravel the complexity of HIV reservoirs.   <\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-cc79ffc elementor-widget elementor-widget-image\" data-id=\"cc79ffc\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t<figure class=\"wp-caption\">\n\t\t\t\t\t\t\t\t\t\t<img alt=\"\" decoding=\"async\" width=\"988\" height=\"559\" src=\"https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/04\/Fig_1.jpg\" class=\"attachment-full size-full wp-image-67222\" alt=\"\" srcset=\"https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/04\/Fig_1.jpg 988w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/04\/Fig_1-300x170.jpg 300w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/04\/Fig_1-768x435.jpg 768w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/04\/Fig_1-24x14.jpg 24w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/04\/Fig_1-36x20.jpg 36w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/04\/Fig_1-48x27.jpg 48w\" sizes=\"(max-width: 988px) 100vw, 988px\" \/>\t\t\t\t\t\t\t\t\t\t\t<figcaption class=\"widget-image-caption wp-caption-text\">Figure 2. Topology of HIV reservoir networks in ART-treated patients versus elite controllers. Compared with elite controllers, the network architecture of ART-treated patients shows three major features: (1) weaker signature enrichment, (2) higher assortativity, and (3) increased connectivity between adjacent nodes. These results suggest that the networks in ART-treated patients are more cohesive and structured.   <\/figcaption>\n\t\t\t\t\t\t\t\t\t\t<\/figure>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d50e622 elementor-widget elementor-widget-text-editor\" data-id=\"d50e622\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><strong data-start=\"2189\" data-end=\"2214\">Related publications:<\/strong><\/p><p><span data-contrast=\"auto\">Chen, H.-C. 2023. <\/span><b><i><span data-contrast=\"auto\">Vaccines <\/span><\/i><\/b><span data-contrast=\"auto\">DOI:<\/span><a href=\"https:\/\/10.0.13.62\/vaccines11020402\"><span data-contrast=\"none\">10.3390\/vaccines11020402<\/span><\/a><span data-ccp-props=\"{}\"> <\/span><\/p><p><span data-contrast=\"auto\">Wi\u0119cek, K., and Chen, H.-C. 2023. <\/span><b><i><span data-contrast=\"auto\">iScience<\/span><\/i><\/b><span data-contrast=\"auto\"> DOI:<\/span><a href=\"https:\/\/10.0.3.248\/j.isci.2023.108342\"><span data-contrast=\"none\">10.1016\/j.isci.2023.108342<\/span><\/a><span data-ccp-props=\"{}\"> <\/span><\/p><p><span data-contrast=\"auto\">Wi\u015bniewski, et al. 2024.  <\/span><b><i><span data-contrast=\"auto\">iScience<\/span><\/i><\/b><span data-contrast=\"auto\"> DOI:<\/span><a href=\"https:\/\/10.0.3.248\/j.isci.2024.11122\"><span data-contrast=\"none\">10.1016\/j.isci.2024.11122<\/span><\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-48f3b1f elementor-widget__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"48f3b1f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p data-start=\"4465\" data-end=\"4637\">We also study zoonotic viral infections, analyzing the relationship between intra-host tropism of coronavirus variants and host domestication. <\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b2ad75a elementor-widget elementor-widget-heading\" data-id=\"b2ad75a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3. Identification of Potential Genetic Markers of SARS-CoV-2 Resulting from Host Domestication<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-ff03382 e-grid e-con-boxed e-con e-parent\" data-id=\"ff03382\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-5bf77bf elementor-widget elementor-widget-text-editor\" data-id=\"5bf77bf\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p data-start=\"4748\" data-end=\"5024\">We developed a k-mer\u2013based pipeline, called PORT-EK (<strong data-start=\"4799\" data-end=\"4867\">Pathogen Origin Recognition Tool using Enriched K-mers<\/strong>), designed to identify genomic regions enriched in specific hosts by comparing metagenomes of isolates between two host species.Opracowali\u015bmy pipeline oparty na k-merach, nazwany Pathogen Origin Recognition Tool using Enriched K-mers (PORT-EK), s\u0142u\u017c\u0105cy do identyfikacji region\u00f3w genomowych wzbogaconych u odpowiednich gospodarzy po por\u00f3wnaniu metagenom\u00f3w izolat\u00f3w mi\u0119dzy dwoma gatunkami gospodarzy.<\/p><p data-start=\"5026\" data-end=\"5424\">Using PORT-EK, we identified thousands of enriched k-mers in North American white-tailed deer and betacoronaviruses compared to human isolates. We further demonstrated distinct coverage landscapes of enriched k-mers in deer and bats and discovered 144 enriched k-mer mutations derived from comparisons between bat and human viral metagenomes. <\/p><p data-start=\"5426\" data-end=\"5833\">We also observed that the third codon position is particularly susceptible to mutations, leading to a high frequency of synonymous amino acid substitutions that preserve the same physicochemical properties as the original residues. Importantly, we can classify and predict host species identity based on the number of enriched k-mers. <\/p><p><strong data-start=\"2189\" data-end=\"2214\">Related publication:<\/strong><br>Wi\u015bniewski and Chen. 2024. iMetaOmics DOI:10.1002\/imo2.70019<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5a7ff9f elementor-widget elementor-widget-image\" data-id=\"5a7ff9f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t<figure class=\"wp-caption\">\n\t\t\t\t\t\t\t\t\t\t<img alt=\"\" decoding=\"async\" width=\"580\" height=\"447\" src=\"https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-3.webp\" class=\"attachment-large size-large wp-image-86906\" alt=\"\" srcset=\"https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-3.webp 628w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-3-300x231.webp 300w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-3-24x18.webp 24w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-3-36x28.webp 36w, https:\/\/port.lukasiewicz.gov.pl\/wp-content\/uploads\/sites\/35\/2025\/09\/fig-3-48x37.webp 48w\" sizes=\"(max-width: 580px) 100vw, 580px\" \/>\t\t\t\t\t\t\t\t\t\t\t<figcaption class=\"widget-image-caption wp-caption-text\">Figure 3. Schematic design of PORT-EK and identification of enriched k-mers. (A) Analytical workflow of PORT-EK, which consists of four steps: (1) k-mer matrix preparation, (2) k-mer filtering and selection, (3) identification of host-specific mutations, and (4) host classification. (B) Funnel chart illustrating the filtering strategies used to select enriched k-mers. Details are described in the main text.      <\/figcaption>\n\t\t\t\t\t\t\t\t\t\t<\/figure>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-28dff98 elementor-hidden-desktop elementor-hidden-tablet elementor-hidden-mobile elementor-widget elementor-widget-text-editor\" data-id=\"28dff98\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><span class=\"TextRun SCXW242574241 BCX8\" lang=\"PL-PL\" xml:lang=\"PL-PL\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW242574241 BCX8\">Wi\u015bniewski and Chen. 2024.  <\/span><\/span><em><strong><span class=\"TextRun SCXW242574241 BCX8\" lang=\"PL-PL\" data-contrast=\"auto\"><span class=\"NormalTextRun SpellingErrorV2Themed SCXW242574241 BCX8\">BioRxiv<\/span><\/span><\/strong><\/em><a href=\"http:\/\/DOI:10.1101\/2024.07.27.605454\"><span class=\"TextRun SCXW242574241 BCX8\" lang=\"PL-PL\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW242574241 BCX8\"> DOI:10.1101\/2024.07.27.605454<\/span><\/span><\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Quantitative Virology Research Group Research topics One of the main goals of our laboratory is to study the establishment of HIV latency in connection with stochastic HIV transcription and the functional host genome. Using quantitative genomic approaches and machine learning\u2013based methods developed in our lab, we aim to deepen our understanding of how single-virus-level variability [&hellip;]<\/p>\n","protected":false},"author":218,"featured_media":0,"parent":88895,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","inline_featured_image":false,"footnotes":""},"class_list":["post-88899","page","type-page","status-publish","hentry"],"acf":[],"publishpress_future_action":{"enabled":false,"date":"2026-04-12 13:21:03","action":"change-status","newStatus":"draft","terms":[],"taxonomy":"translation_priority","extraData":[]},"publishpress_future_workflow_manual_trigger":{"enabledWorkflows":[]},"_links":{"self":[{"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/pages\/88899","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/users\/218"}],"replies":[{"embeddable":true,"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/comments?post=88899"}],"version-history":[{"count":5,"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/pages\/88899\/revisions"}],"predecessor-version":[{"id":91165,"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/pages\/88899\/revisions\/91165"}],"up":[{"embeddable":true,"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/pages\/88895"}],"wp:attachment":[{"href":"https:\/\/port.lukasiewicz.gov.pl\/en\/wp-json\/wp\/v2\/media?parent=88899"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}