{"id":2712,"date":"2022-07-25T17:36:08","date_gmt":"2022-07-25T21:36:08","guid":{"rendered":"https:\/\/sites.bu.edu\/phenogeno\/?page_id=2712"},"modified":"2024-05-21T16:32:12","modified_gmt":"2024-05-21T20:32:12","slug":"selected-projects-led-by-students-working-with-us","status":"publish","type":"page","link":"https:\/\/sites.bu.edu\/phenogeno\/selected-projects-led-by-students-working-with-us\/","title":{"rendered":"Selected Unusual Projects by Members of the Laboratory"},"content":{"rendered":"<h3 dir=\"ltr\">&#8220;The only thing that will redeem mankind is cooperation&#8221; &#8212; Bertrand Russell<\/h3>\n<h3>&#8220;If you&#8217;re always trying to be normal, you will never know how amazing you can be.&#8221; &#8212; Maya Angelou &#8211;<\/h3>\n<p>&nbsp;<\/p>\n<h3>Selected Unusual Projects by Current and Former Members or close collaborators of the Laboratory\/Group<\/h3>\n<h2 style=\"text-align: center;\"><a href=\"https:\/\/arxiv.org\/abs\/2010.12015\">Simon Kasif: Artificial Tikkun Olam Perspective: <\/a><\/h2>\n<h2 style=\"text-align: center;\"><a href=\"https:\/\/arxiv.org\/abs\/2010.12015\">We are fully committed to deploying AI responsibly and safely in the service of social justice, inclusion, fairness, reducing social inequalities and diversity.<\/a><\/h2>\n<h3><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27633797\/\">Stan Letovsky and his collaborators participate in the very important sharing cancer mutation data project<\/a><\/h3>\n<h3><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28199304\">Jonathan and Hui in Nature\u00a0\u00a0<\/a><\/h3>\n<h3>Alfred Ramirez wins best graduate student paper of the year with <a href=\"http:\/\/www.cell.com\/cell-reports\/fulltext\/S2211-1247(17)31717-5\">his paper in Cell Reports.<\/a><\/h3>\n<h3><a href=\"http:\/\/science.sciencemag.org\/content\/357\/6346\/35\">Kamila Naxerova in Science following up on a heroic project she started and led in her PhD thesis tracing cancer lineage<\/a><\/h3>\n<h3><a href=\"https:\/\/www.nature.com\/nature\/journal\/v547\/n7661\/full\/nature22992.html\">Esther Rheinbay in Nature with Gad Getz and other collaborators at the Broad<\/a><\/h3>\n<h3><\/h3>\n<h3><a href=\"https:\/\/www.bloomberg.com\/press-releases\/2020-07-28\/ciox-health-acquires-biomedical-natural-language-processing-pioneer-medal-inc\">Andy&#8217;s AI2MED company is sold. \u00a0Mazal Tov.\u00a0<\/a><\/h3>\n<p>&nbsp;<\/p>\n<h3><a href=\"http:\/\/www.biorxiv.org\/content\/early\/2017\/06\/25\/155150\">COMBREX perspective (Not All Experiments are Created Equal) is deposited in bioarchive (this is an old paper, first submission to Science\u00a0 October 2011)<\/a><\/h3>\n<h3><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28380379\">Jonathan and Hui in Cell Metabolism\u00a0<\/a><\/h3>\n<h3><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5378997\/\">Congratulations to Jonathan, Hui and Alfred \u00a0for their publication in Nature Communication\u00a0<\/a><\/h3>\n<h3><a href=\"http:\/\/www.nature.com\/nature\/journal\/v542\/n7642\/full\/nature21365.html#affil-auth\">Congratulations to Jonathan Dreyfuss for his publication in Nature<\/a><\/h3>\n<h3><a href=\"http:\/\/www.slideshare.net\/sjcockell\/reproducibility-the-myths-and-truths-of-pipeline-bioinformatics\" target=\"_blank\" rel=\"noopener noreferrer\">Many people had this idea, but so far very little movement in this direction.<\/a><\/h3>\n<h3><strong>Our COMBREX paper is accepted in the Annual DB Issue edited by Michael Galperin. \u00a0The first database paper (to our knowledge) that includes <span style=\"color: #ff0000;\">&#8220;Knowledge Gaps&#8230;&#8221;<\/span><\/strong><\/h3>\n<h3><span style=\"line-height: 1.5;\"><span>NAR-02923-Data-E-2015.R1<\/span><br \/>\n<span>COMBREX-DB: &#8220;An Experiment-Centered Database Of Protein Function: Knowledge, Predictions and <span style=\"color: #ff0000;\">Knowledge Gaps<\/span>&#8221;\u00a0<\/span><span>Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian; Kasif, Simon.; Roberts, Rich; Steffen, Martin<\/span><br \/>\n<\/span><\/h3>\n<p><a href=\"http:\/\/www.isn.cnr.it\/wp-content\/uploads\/locandina.pdf\" target=\"_blank\" style=\"line-height: 1.5;\" rel=\"noopener noreferrer\">We participate in the &#8220;Computation as a Driver for Translational Medicine&#8221; in Sicily\u00a0<\/a><\/p>\n<p><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26186193\" target=\"_blank\" rel=\"noopener noreferrer\">Tarjei Mikkelsen (former intern, another gem)<\/a><\/p>\n<p><a href=\"http:\/\/www.pic-sure.org\/events\/precision-medicine-2015-patient-driven\" target=\"_blank\" rel=\"noopener noreferrer\">Precision Medicine Symposium: Patient Driven<\/a><\/p>\n<p><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26061751\" target=\"_blank\" rel=\"noopener noreferrer\">Esther (former joint student with Brad Bernstein) in NEJM<\/a><\/p>\n<p><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26076036\" target=\"_blank\" rel=\"noopener noreferrer\">Jonathan in Nature Medicine (his work is funded by the DRC BU-Joslin Bioinformatics and Systems Biology Core)<\/a><\/p>\n<p>Andy McMurry submits a final copy of his PhD thesis on Distributed Mining of Electronic Health Records to graduate school !<\/p>\n<p><a href=\"http:\/\/www.bio-itworld.com\/2015\/4\/22\/2015-bio-it-world-best-practices-awards-winners-announced.html\" target=\"_blank\" rel=\"noopener noreferrer\">GlaxoSmithKline working with Epidemico \u00a0(John Brownstein and Clark Freifeld) and their software is acknowledged with a Best Practice Award &#8212; Clark&#8217;s thesis work (Twitter mining for Drug Side Effects).<\/a><\/p>\n<p><a href=\"https:\/\/sites.bu.edu\/phenogeno\/?attachment_id=619\" target=\"_blank\" rel=\"noopener noreferrer\">Chris Nogiec paper is selected as Cover in Molecular Metabolism.<\/a><\/p>\n<p>Andy McMurry successfully defends his thesis on Distributed Medical Record Data Mining. \u00a0Very early work on Federated Medical Health Records. Andy recently joined a start-up in California and it just went public.<\/p>\n<p><a href=\"http:\/\/hms.harvard.edu\/news\/new-department-biomedical-informatics\" target=\"_blank\" rel=\"noopener noreferrer\">Harvard Medical School announces the formation of a new Medical Informatics Department<\/a><\/p>\n<p><a href=\"http:\/\/www.washingtonpost.com\/business\/capitalbusiness\/booz-allen-buys-boston-health-analytics-start-up-epidemico\/2014\/10\/29\/0e55061a-5ed3-11e4-91f7-5d89b5e8c251_story.html\" target=\"_blank\" rel=\"noopener noreferrer\">Clark Freifeld&#8217;s company (with John Brownstein), Epidemico is bought by Booz Allen, Congratulations to Clark.<\/a><\/p>\n<p><a href=\"http:\/\/www.molmetab.com\/article\/S2212-8778(14)00225-7\/abstract?rss=yes\" target=\"_blank\" rel=\"noopener noreferrer\">Chris&#8217;s paper in Molecular Metabolism is out and made cover ! \u00a0Very impressive work \u00a0co-led \u00a0by ME Patti at Joslin and her laboratory.<\/a><\/p>\n<p><a href=\"http:\/\/www.nature.com\/nm\/journal\/v19\/n5\/full\/nm.3112.html\" target=\"_blank\" rel=\"noopener noreferrer\">Michael Molla in Nature Medicine \u00a0(his work is funded by the BU-Joslin Bioinformatics and Systems Biology Core).<\/a><\/p>\n<p><a href=\"http:\/\/diabetes.diabetesjournals.org\/content\/63\/12\/4130.long\" target=\"_blank\" rel=\"noopener noreferrer\">Michael Molla helps analyze insulin resistance in iPS cells<\/a><\/p>\n<p><a href=\"https:\/\/sites.bu.edu\/phenogeno\/?attachment_id=587\" title=\"Erdos and the Genome\" target=\"_blank\" rel=\"noopener noreferrer\">Our paper with Charles Cantor helps shorten the &#8220;Erdos Distance&#8221; in the collaboration graph between biologists and mathematicians.<\/a><\/p>\n<p>Paul Erdos &#8212; Noga Alon &#8212; {Simon Kasif ,Charles Cantor}<\/p>\n<p>Our paper (link below) has two parts, one developed by Vera Asodi during her graduate work with Noga Alon and one developed by John Rachlin during his graduate work with Simon Kasif, Charles Cantor and Shanqua Teng.<\/p>\n<p><a href=\"https:\/\/sites.bu.edu\/phenogeno\/?attachment_id=314\" title=\"multinode graphs\" target=\"_blank\" rel=\"noopener noreferrer\">Multinode Graphs\u00a0<\/a><\/p>\n<p><a href=\"http:\/\/systemsbiology.columbia.edu\/news\/department-of-systems-biology-holds-annual-magnet-retreat\" target=\"_blank\" rel=\"noopener noreferrer\">Kasif attends Columbia University Systems Biology Retreat\/Advisory Board Meeting<\/a>: In the picture he is trying to confuse Michael Waterman who is rarely confused.<\/p>\n<p><a href=\"http:\/\/blog.pnas.org\/?p=1684\" target=\"_blank\" rel=\"noopener noreferrer\">Kamila Tracks Cancer Heterogeneity and Lineage<\/a><\/p>\n<p><a target=\"_blank\" href=\"http:\/\/www.businessweek.com\/articles\/2014-05-15\/searching-social-media-for-drug-side-effects\" rel=\"noopener noreferrer\">Clark Freifeld in Business Week<\/a><\/p>\n<p><a href=\"http:\/\/www.bu.edu\/bme\/2014\/05\/30\/tweet-your-reaction\/\" target=\"_blank\" rel=\"noopener noreferrer\">Clark in BU Engineering News After Receiving the Best Societal Impact Thesis Award\u00a0<\/a><\/p>\n<p><a target=\"_blank\" href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867414004218\" rel=\"noopener noreferrer\">Esther Rheinbay and Mario Suva play Connect Four and Reprogram Cancer Stem Cells<\/a><\/p>\n<p><a href=\"http:\/\/www.cell.com\/cancer-cell\/abstract\/S1535-6108(12)00084-0\" target=\"_blank\" rel=\"noopener noreferrer\">Esther and Mario Suva (in Brad Bernstein Lab) review histone mutations and their role in driving pediatric glioblastoma (in Cancer Cell)<\/a><\/p>\n<p><span>Richard Park (co-advised by Peter Park, Harvard Med. School) \u00a0is a finalist in the Illumina iDEA Challenge in 2011 with the Genome Browser Richard co-developed in Peter Park&#8217;s group.<\/span><\/p>\n<p><a href=\"http:\/\/www.nature.com\/nature\/journal\/v447\/n7141\/full\/7141xia.html\">Tarjei in Nature (again)<\/a><\/p>\n<p><a target=\"_blank\" href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0055811\" rel=\"noopener noreferrer\">Andy McMurry releases SHRINE<\/a><\/p>\n<p><a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0068751\" target=\"_blank\" rel=\"noopener noreferrer\">Chris challenges the Supplements Myths<\/a><\/p>\n<p><a href=\"http:\/\/selinker.livejournal.com\/42816.html\" target=\"_blank\" rel=\"noopener noreferrer\">Scott Weiss (former JHU graduate student) breaks Jeopardy\u00a0<\/a><\/p>\n<p><a href=\"https:\/\/thetartan.org\/2007\/3\/26\/news\/jeopardy\" target=\"_blank\" rel=\"noopener noreferrer\">Scott Weiss makes Jeopardy history<\/a><\/p>\n<p><a href=\"https:\/\/www.bu.edu\/eng\/2009\/10\/27\/bme-researchers-help-advance-novel-personal-genotyping-technique\/\">Michael Molla\u00a0 in PNAS (with Art Delcher, Charles Cantor, and Shamil Sunyaev)\u00a0<\/a><\/p>\n<p><a target=\"_blank\" href=\"https:\/\/static1.squarespace.com\/static\/568e93cfa976af0914263f2c\/t\/5923066d5016e1f3fb3f08a1\/1495467630674\/CHBcancerbigpic.pdf\" rel=\"noopener noreferrer\">Kamila in Children&#8217;s Hospital News<\/a><\/p>\n<p><a target=\"_blank\" href=\"http:\/\/www.sciencedaily.com\/releases\/2009\/11\/091124204327.htm\" rel=\"noopener noreferrer\">Martin Steffen in Science Daily<\/a><\/p>\n<p><a href=\"\/phenogeno\/files\/2020\/12\/phosphoIMG_8689.jpg\">Protein Phosphorylation Cancer Biomarkers<\/a><\/p>\n<p><a target=\"_blank\" href=\"https:\/\/www.bu.edu\/eng\/2007\/09\/13\/looking-at-the-big-picture-brings-diabetes-findings-into-focus\/\" rel=\"noopener noreferrer\">Manway Liu in BU News<\/a><\/p>\n<p><a href=\"http:\/\/www.cs.technion.ac.il\/events\/2008\/393\/\">Kasif describes Network Signatures of Disease\u00a0 (Technion)<\/a><\/p>\n<p><a href=\"http:\/\/bcb.cs.tufts.edu\/abstracts\/kasif.html\">Kasif describes Biological Network Anomaly and Signatures of Disease (Tufts)<\/a><\/p>\n<p><a href=\"https:\/\/www.brown.edu\/Research\/Istrail_Lab\/CCMB\/events_seminar_0809.htm\">Kasif talks about &#8220;Systems Macro-Biology: From Parts and Genomes to Network Signatures of Disease&#8221; as a new paradigm for Disease Staging (Brown University)<\/a><\/p>\n<p><a href=\"https:\/\/slideplayer.com\/slide\/5218597\/\">Megon Walker describes the application of Active Learning to Drug Discovery (her PhD thesis starting 2001).\u00a0<\/a><\/p>\n<p><a target=\"_blank\" href=\"http:\/\/www.nytimes.com\/1991\/10\/30\/us\/computer-is-pushed-to-edge-to-solve-old-chess-problem.html\" rel=\"noopener noreferrer\">Lewis Stiller in NY Times<\/a><\/p>\n<p><a href=\"\/phenogeno\/files\/2015\/03\/scientificamerican1191-38.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">Lewis Stiller in Scientific American<\/a><\/p>\n<p><a target=\"_blank\" href=\"https:\/\/groups.google.com\/forum\/#!topic\/mod.ai\/9QmsOAnJIJo\" rel=\"noopener noreferrer\">PARALLEL LOGIC PROGRAMMING &#8211; FIRST OPERATIONAL SYSTEM (1)<\/a><\/p>\n<p><a target=\"_blank\" href=\"http:\/\/citeseerx.ist.psu.edu\/viewdoc\/download?doi=10.1.1.74.8440&amp;rep=rep1&amp;type=pdf\" rel=\"noopener noreferrer\">PARALLEL LOGIC PROGRAMMING &#8211; FIRST OPERATIONAL SYSTEM (2)<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>&#8220;The only thing that will redeem mankind is cooperation&#8221; &#8212; Bertrand Russell &#8220;If you&#8217;re always trying to be normal, you will never know how amazing you can be.&#8221; &#8212; Maya Angelou &#8211; &nbsp; Selected Unusual Projects by Current and Former Members or close collaborators of the Laboratory\/Group Simon Kasif: Artificial Tikkun Olam Perspective: We are [&hellip;]<\/p>\n","protected":false},"author":8782,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/2712"}],"collection":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/users\/8782"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/comments?post=2712"}],"version-history":[{"count":17,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/2712\/revisions"}],"predecessor-version":[{"id":2857,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/2712\/revisions\/2857"}],"wp:attachment":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/media?parent=2712"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}