{"id":344,"date":"2022-09-15T11:26:25","date_gmt":"2022-09-15T15:26:25","guid":{"rendered":"https:\/\/health.uconn.edu\/blinov-lab\/?page_id=344"},"modified":"2025-01-23T10:11:07","modified_gmt":"2025-01-23T15:11:07","slug":"lab-and-alumni","status":"publish","type":"page","link":"https:\/\/health.uconn.edu\/blinov-lab\/lab-and-alumni\/","title":{"rendered":"Lab and alumni"},"content":{"rendered":"<div id=\"pl-206\" class=\"panel-layout\">\n<div id=\"pg-206-0\" class=\"panel-grid panel-no-style\">\n<div id=\"pgc-206-0-0\" class=\"panel-grid-cell\" data-weight=\"1\">\n<div id=\"panel-206-0-0-0\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce panel-first-child\" data-index=\"0\" data-style=\"{&quot;background_image_attachment&quot;:false,&quot;background_display&quot;:&quot;tile&quot;,&quot;accordion&quot;:&quot;&quot;}\">\n<h3 class=\"widget-title\">Current Lab members<\/h3>\n<div class=\"textwidget\">\n<ul>\n<li><strong>Dan Vasilescu<\/strong>, programmer working on VCell software\n<ul>\n<li>Shaikh, B., Smith, L. P., <strong>Vasilescu, D.<\/strong>, &#8230;, <strong>Blinov, M. L<\/strong>., Sauro, H., Moraru, I. I., Karr, J. R. (<strong>2022<\/strong>). BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic acids research, 50(W1), W108\u2013W114. https:\/\/doi.org\/10.1093\/nar\/gkac331<\/li>\n<li><strong>Blinov, M. L.<\/strong>, Schaff, J. C., <strong>Vasilescu, D.<\/strong>, Moraru, I. I., Bloom, J. E., &amp; Loew, L. M. (<strong>2017<\/strong>). Compartmental and Spatial Rule-Based Modeling with Virtual Cell. Biophysical journal, 113(7), 1365\u20131372. https:\/\/doi.org\/10.1016\/j.bpj.2017.08.022<\/li>\n<li>Schaff, J. C., <strong>Vasilescu, D<\/strong>., Moraru, I. I., Loew, L. M., &amp; <strong>Blinov, M. L<\/strong>. (<strong>2016<\/strong>). Rule-based modeling with Virtual Cell. Bioinformatics (Oxford, England), 32(18), 2880\u20132882. https:\/\/doi.org\/10.1093\/bioinformatics\/btw353<\/li>\n<li><strong>Blinov, M. L.<\/strong>, Schaff, J. C., Ruebenacker, O., Wei, X., <strong>Vasilescu, D<\/strong>., Gao, F., Morgan, F., Ye, L., Lakshminarayana, A., Moraru, I. I., &amp; Loew, L. M. (<strong>2014<\/strong>). Pathway Commons at virtual cell: use of pathway data for mathematical modeling. Bioinformatics (Oxford, England), 30(2), 292\u2013294.<\/li>\n<\/ul>\n<\/li>\n<li>Logan Drescher, programmer working on VCell software<\/li>\n<\/ul>\n<h3 class=\"widget-title\">Alumni<\/h3>\n<div class=\"textwidget\">\n<h3 class=\"widget-title\">PostDocs<\/h3>\n<div class=\"textwidget\">\n<ul>\n<li><strong>Cibele Falkenberg<\/strong>\n<ul>\n<li><strong>Falkenberg, C. V.<\/strong>, Carson, J. H., &amp; <strong>Blinov, M. L.<\/strong> (<strong>2017<\/strong>). Multivalent Molecules as Modulators of RNA Granule Size and Composition. Biophysical journal, 113(2), 235\u2013245. https:\/\/doi.org\/10.1016\/j.bpj.2017.01.031<\/li>\n<li><strong>Falkenberg, C. V.<\/strong>, <strong>Blinov, M. L<\/strong>., &amp; Loew, L. M. (<strong>2013<\/strong>). Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. Biophysical journal, 105(11), 2451\u20132460. https:\/\/doi.org\/10.1016\/j.bpj.2013.10.016.<\/li>\n<\/ul>\n<\/li>\n<li><strong>Oliver Ruebenacker<\/strong>\n<ul>\n<li><strong>Blinov, M. L<\/strong>., Schaff, J. C., <strong>Ruebenacker, O<\/strong>., Wei, X., Vasilescu, D., Gao, F., Morgan, F., Ye, L., Lakshminarayana, A., Moraru, I. I., &amp; Loew, L. M. (<strong>2014<\/strong>). Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. Bioinformatics (Oxford, England), 30(2), 292\u2013294.<\/li>\n<li><strong>Ruebenacker, O<\/strong>., &amp; <strong>Blinov, M.<\/strong> (<strong>2011<\/strong>). Using views of Systems Biology Cloud: application for model building. Theory in biosciences = Theorie in den Biowissenschaften, 130(1), 45\u201354. https:\/\/doi.org\/10.1007\/s12064-010-0108-6.<\/li>\n<li><strong>Blinov, M. L.<\/strong>, <strong>Ruebenacker, O<\/strong>., Schaff, J. C., &amp; Moraru, I. I. (<strong>2010<\/strong>). Modeling without borders: creating and annotating VCell Models using the web. In International Symposium on Bioinformatics Research and Applications (pp. 3-17). Springer, Berlin, Heidelberg.<\/li>\n<li><strong>Ruebenacker, O.<\/strong>, Moraru, I. I., Schaff, J. C., &amp; <strong>Blinov, M. L<\/strong>. (<strong>2009<\/strong>). Integrating BioPAX pathway knowledge with SBML models. IET systems biology, 3(5), 317\u2013328. https:\/\/doi.org\/10.1049\/iet-syb.2009.0007<\/li>\n<li><strong>Blinov, M. L.<\/strong>, <strong>Ruebenacker, O.<\/strong>, &amp; Moraru, I. I. (<strong>2008<\/strong>). Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation. IET systems biology, 2(5), 363\u2013368. https:\/\/doi.org\/10.1049\/iet-syb:20080092<\/li>\n<li><strong>Ruebenacker, O.<\/strong>, Moraru, I. I., Schaff, J. C., &amp; <strong>Blinov, M. L.<\/strong> (<strong>2007<\/strong>). Kinetic Modeling using BioPAX ontology. Proceedings. IEEE International Conference on Bioinformatics and Biomedicine, 2007, 339\u2013348. https:\/\/doi.org\/10.1109\/BIBM.2007.55<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<h3 class=\"widget-title\">Graduate Students<\/h3>\n<div class=\"textwidget\">\n<ul>\n<li>Aniruddha Chattaraj\n<ul>\n<li><span><strong>Chattaraj, A.<\/strong>, Nalagandla, I., Loew, L. M., &amp; <strong>Blinov, M. L.<\/strong> (<strong>2023<\/strong>). MolClustPy: a Python package to characterize multivalent biomolecular clusters.\u00a0<\/span><i>Bioinformatics<\/i><span>,\u00a0<\/span><i>39<\/i><span>(6), btad385. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37326981\/\">PMID: 37326981\/<\/a><\/span><\/li>\n<li><strong>Chattaraj, A.<\/strong>, <strong>Blinov, M. L<\/strong>., &amp; Loew, L. M. (<strong>2021<\/strong>). The solubility product extends the buffering concept to heterotypic biomolecular condensates. <em>eLife<\/em>, 10, e67176. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34236318\/\">PMID: 34236318<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<h3 class=\"widget-title\">Undergraduate Students<\/h3>\n<div class=\"textwidget\">\n<ul>\n<li>Noah Liguori-Bills\n<ul>\n<li><span><strong>Liguori-Bills, N<\/strong>., &amp; <strong>Blinov, M. L<\/strong>. (<strong>2024<\/strong>). bnglViz: Online visualization of rule-based models.\u00a0<\/span><i>Bioinformatics<\/i><span>, btae351. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38814806\/\">PMID: 38814806\/<\/a><\/span><\/li>\n<li><a href=\"http:\/\/modelbricks.org\/\">http:\/\/modelbricks.org\/<\/a><\/li>\n<li><a href=\"http:\/\/bnglViz.github.io\">http:\/\/bnglViz.github.io<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Nathan Schaumburger, Joel Pally\n<ul>\n<li><span><strong>Schaumburger, N.<\/strong>, <strong>Pally, J.<\/strong>, Moraru, I. I., Kositsawat, J., Kuchel, G. A., &amp; <strong>Blinov, M. L.<\/strong> (<strong>2023<\/strong>). Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes.\u00a0<\/span><i>Frontiers in Network Physiology<\/i><span>,\u00a0<\/span><i>3<\/i><span>, 1079070. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37216041\">PMID: 37216041<\/a><\/span><\/li>\n<\/ul>\n<\/li>\n<li>John Albanese\n<ul>\n<li>Rougny, A., Tour\u00e9, V., <strong>Albanese, J.<\/strong>, Waltemath, D., Shirshov, D., Sorokin, A., Bader, G. D., <strong>Blinov, M. L.<\/strong>, &amp; Mazein, A. (<strong>2021<\/strong>). SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. <em>Briefings in bioinformatics<\/em>, 22(5), bbab049. https:\/\/doi.org\/10.1093\/bib\/bbab049<\/li>\n<\/ul>\n<\/li>\n<li>James Green\n<ul>\n<li>Vasilescu,D., <strong>Greene,J<\/strong>., Schaff, J.C., Moraru, I.I., <strong>Blinov, M.L.<\/strong> (<strong>2018<\/strong>) Molecular Process Diagram: a precise, scalable and compact visualization of rule-based models bioRxiv 503359; https:\/\/doi.org\/10.1101\/503359<\/li>\n<\/ul>\n<\/li>\n<li>Daniel Fryer\n<ul>\n<li><a href=\"http:\/\/findingyourinnermodeler.org\/\" class=\"broken_link\">http:\/\/findingyourinnermodeler.org\/<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Maria Heredia Chavez\n<ul>\n<li><a href=\"http:\/\/modelbricks.org\/\">http:\/\/modelbricks.org\/<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Keeyan Goreshi<\/li>\n<li>Raman Allawirdi<\/li>\n<li>Kevin Reid<\/li>\n<li>Mitchell Clough<\/li>\n<li>Thomas Vecca<\/li>\n<li>Tyler McLoughlin<\/li>\n<li>Dhruv Vig<\/li>\n<li>Xiaozhou Liu<\/li>\n<li>Max Win<\/li>\n<li>Ritika Sahni<\/li>\n<\/ul>\n<h3 class=\"widget-title\">High School Students<\/h3>\n<div class=\"textwidget\">\n<ul>\n<li>Ricky Paul<\/li>\n<li>Bushrah Khan<\/li>\n<li>Zaiba Khan<\/li>\n<li>Arundeep Singh<\/li>\n<li>Nathan Schaumburger<\/li>\n<li>Laurie Yousman<\/li>\n<li>Tanya Miller<\/li>\n<li>Summer Xu<\/li>\n<li>Patrick Demkowitz<\/li>\n<li>Thomas Vecca<\/li>\n<li>Joel Pally\n<ul><\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Current Lab members Dan Vasilescu, programmer working on VCell software Shaikh, B., Smith, L. P., Vasilescu, D., &#8230;, Blinov, M. L., Sauro, H., Moraru, I. I., Karr, J. R. (2022). BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic acids research, 50(W1), W108\u2013W114. https:\/\/doi.org\/10.1093\/nar\/gkac331 Blinov, M. L., Schaff, J. C., [&hellip;]<\/p>\n","protected":false},"author":398,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"publishpress_future_action":{"enabled":false,"date":"2026-05-01 23:15:26","action":"change-status","newStatus":"draft","terms":[],"taxonomy":""},"_links":{"self":[{"href":"https:\/\/health.uconn.edu\/blinov-lab\/wp-json\/wp\/v2\/pages\/344"}],"collection":[{"href":"https:\/\/health.uconn.edu\/blinov-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/health.uconn.edu\/blinov-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/blinov-lab\/wp-json\/wp\/v2\/users\/398"}],"replies":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/blinov-lab\/wp-json\/wp\/v2\/comments?post=344"}],"version-history":[{"count":16,"href":"https:\/\/health.uconn.edu\/blinov-lab\/wp-json\/wp\/v2\/pages\/344\/revisions"}],"predecessor-version":[{"id":391,"href":"https:\/\/health.uconn.edu\/blinov-lab\/wp-json\/wp\/v2\/pages\/344\/revisions\/391"}],"wp:attachment":[{"href":"https:\/\/health.uconn.edu\/blinov-lab\/wp-json\/wp\/v2\/media?parent=344"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}