{"id":1687,"date":"2019-12-19T00:21:18","date_gmt":"2019-12-19T00:21:18","guid":{"rendered":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?p=1687"},"modified":"2019-12-24T14:46:45","modified_gmt":"2019-12-24T14:46:45","slug":"congratulations-to-kristina-for-her-bioinformatics-paper-acceptance","status":"publish","type":"post","link":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?p=1687","title":{"rendered":"Congratulations to Kristina for her Bioinformatics paper acceptance"},"content":{"rendered":"<p><a href=\"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/04\/IMG_7766_sm2.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-1378 alignleft\" src=\"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/04\/IMG_7766_sm2-300x255.jpg\" alt=\"\" width=\"171\" height=\"146\" srcset=\"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/04\/IMG_7766_sm2-300x255.jpg 300w, https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/04\/IMG_7766_sm2-768x653.jpg 768w, https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/04\/IMG_7766_sm2-177x150.jpg 177w, https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/04\/IMG_7766_sm2-150x127.jpg 150w, https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/04\/IMG_7766_sm2.jpg 998w\" sizes=\"auto, (max-width: 171px) 100vw, 171px\" \/><\/a>We reached an important milestone today. \u00a0Kristina got a major part of her thesis work accepted for publication in the journal <em>Bioinformatics<\/em>. The paper describes a new method, <em>single sample Network Perturbation Assessment\u00a0<\/em>(<em>ssNPA<\/em>), which learns a gene expression network (in the form of a directed graph) from a set of reference samples. Then for every query sample, it evaluates which network neighborhoods are perturbed and by how much.\u00a0 The resulting perturbation features can be used to subsequently cluster the non-reference samples.<\/p>\n<p>The title of the paper is \u201cCausal network perturbations for instance-specific analysis of single cell and disease samples\u201d and it will soon be published on the journal\u2019s web site.<\/p>\n<p>A pre-print of this paper can be found on bioRxiv (<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/637710v1\" target=\"_blank\" rel=\"noopener\">here<\/a>). [Uploaded on May 16, 2019]\n<p>The code for ssNPA and the datasets used in the paper can be found <a href=\"http:\/\/www.benoslab.pitt.edu\/Software\/ssnpa\/\" target=\"_blank\" rel=\"noopener\">here<\/a>.<\/p>\n<p><strong>Congratulations Kristina!<\/strong><\/p>\n[UPDATE 24-Dec-2019] The paper is now published at the\u00a0<em>Bioinformatics<\/em> web site. (<a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btz949\/5686385\" target=\"_blank\" rel=\"noopener\">here)<\/a><\/p>\n<p><a href=\"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/01\/figure1_20191118-e1576714512825.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-1684 aligncenter\" src=\"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/wp-content\/uploads\/2019\/01\/figure1_20191118-300x169.jpg\" alt=\"\" width=\"300\" height=\"169\" \/><\/a> <\/p>\n","protected":false},"excerpt":{"rendered":"<p>We reached an important milestone today. \u00a0Kristina got a major part of her thesis work accepted for publication in the journal Bioinformatics. The paper describes a new method, single sample Network Perturbation Assessment\u00a0(ssNPA), which learns a gene expression network (in the form of a directed graph) from a set of &#8230;<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?p=1687\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":3,"featured_media":1684,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3],"tags":[],"class_list":["post-1687","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-news"],"_links":{"self":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/posts\/1687","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1687"}],"version-history":[{"count":5,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/posts\/1687\/revisions"}],"predecessor-version":[{"id":1717,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/posts\/1687\/revisions\/1717"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/media\/1684"}],"wp:attachment":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1687"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1687"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1687"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}