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I just heard that NSF started a new large center for pandemic prevention and our own T.M. Murali is the PI. Murali was a postdoctoral fellow and research scientist at BU.<\/p>\n
So much talent passed through our labs (and hopefully became enhanced by the high risk and ambitious environment that emphasized leading with new ideas (early innovation).<\/p>\n
T. M. Murali is a particularly noteworthy story.
\nHe is an academic grandchild of the legendary computer scientist Don Knuth (through Jeff Vitter).<\/p>\n
Obviously, I had nothing to do with this important new center (I am neither a co-PI, nor a consultant). Murali and the whole team deserve ALL the credit and applause.<\/p>\n
It’s true that Murali was part of a broad effort to formalize and produce efficient solutions for network propagation based gene function prediction that we co-pioneered at BU (in several papers 2002-2006). He led one of the main projects. This area became a mini-field and was popularized in numerous excellent papers by leaders in computational biology.<\/p>\n
Influenced intellectually, by my old friend and collaborator Rich Roberts, we also started formulating and implementing various methods for grounding AI predictions (facts and gold standard matter!). Murali, co-led one of these efforts published in Nature Biotechnology 2006. We continued doing this more broadly in our COMBREX project that involved more than 100 scientists (both biologists and computational scientists).<\/p>\n
We were ahead of our time, as ML – grounding (in facts and gold standard truths) became a major emphasis in AI safety these days because of the hallucinations produced by language models! We started doing it in 2003 (using network and other ideas). :)<\/p>\n
During the pandemic, I was honored to be part of a “ML grounding” paper (other senior authors were Murali and Mark Crovella). The paper was focused on drug targets for COVID. But following on our broad ” provenance and tracing predictions to experimental facts” vision, we formulated provenance in the important context of network prediction of drug targets for COVID. Murali and his team carried the heavy load. But one of our own BME undergraduates Catherine Della Santina was also an important contributor to this effort (she is now at MIT).<\/p>\n
This new center led by Murali, is a significant intellectual, conceptual and logistic opportunity for innovation in this important space. We all saw the impact of COVID on the world. Please feel free to contact Murali for collaborations that I know he would genuinely appreciate.<\/p>\n
I am proud of NSF taking a risk on this center and of course T.M. Murali for leading this project. According to Murali we, in Boston, deserve some credit and I would like to attribute it to the incredible environment at that time at BU in this area that I personally was lucky to join myself with many friends such as Rich Roberts, Charles Delisi, Charles Cantor, Jim Collins, Tim Gardner, Mark Crovella and many adjuncts (such as Jill Mesirov and Stan Letovsky). Last but not least, numerous exceptional students and postdocs that continue to distinguish us here and elsewhere. Bravo to Murali and all others.<\/p>\n
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This work by Adam and his collaborators is just great science: fundamental, ambitious and what a service to the broader community!\u00a0 It also showcases an intellectual transformation manifested by computational scientists co-leading major genomic efforts – not \u201cjust\u201d method development. It follows decades of computational scientists such as Charles Delisi starting the human genome project, Aviv Regev co-leading the human Cell Atlas (and more) and Tarjei Mikkelsen co-leading the first draft of the Chimp Genome paper.\u00a0 All three are among our closest collaborators and I cannot be more proud of their accomplishments.<\/p>\n
But there are so many others including computational scientists or engineers doing deep biology or biotechnology.\u00a0 Not to mention the computational work that enables transformative discovery and invention such as Koonin\u00a0 & Makarova et al and others.<\/p>\n
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BE700 SPRING 2021 INTRODUCTION LECTURE POSTED<\/a><\/p>\n <\/p>\n WEKA LECTURE POSTED<\/a><\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n <\/p>\n We produced a brief summary of Boston University Legacy in Computational, Systems and Synthetic Biology that began with Charles DeLisi coming to BU.<\/a><\/p>\n <\/p>\n Our COMBREX paper is accepted in the Annual DB Issue edited by Michael Galperin. \u00a0The first database paper (to our knowledge) that includes “Knowledge Gaps…”<\/strong><\/p>\n NAR-02923-Data-E-2015.R1<\/span> <\/p>\n Soo Lee in Nature Biotechnology (Soo is at Harvard Medical School now).<\/a><\/p>\n <\/p>\n Evan Appleton (former undergraduate researcher in the lab) defends his PhD thesis on Synthetic Biology (with Doug Densmore). \u00a0Well done Evan! Evan just joined Church Lab at Harvard Medical School as a fellow.<\/p>\n <\/p>\n J. Faith (now at Mount Sinai School of Medicine) in Nature Medicine<\/a><\/p>\n <\/p>\n Yi-Chien (COMBREX primary developer) defends his PhD thesis<\/p>\n <\/p>\n We participate in the “Computation as a Driver for Translational Medicine” in Sicily\u00a0<\/a><\/p>\n <\/p>\n Tarjei Mikkelsen (former intern, another gem)<\/a><\/p>\n <\/p>\n Precision Medicine Symposium: Patient Driven<\/a><\/p>\n <\/p>\n Kasif is on sabbatical on the Longwood campus of HMS, funded in part by the Iacocca Senior Fellowship and Joslin Diabetes Center<\/a><\/p>\n <\/p>\n Biomedical Engineering at BU ranks 9.<\/a><\/p>\n <\/p>\n Esther (former joint student with Brad Bernstein) in NEJM<\/a><\/p>\n <\/p>\n Jonathan in ELIFE \u00a0(his work is funded by the DRC BU-Joslin Bioinformatics and Systems Biology Core)<\/span><\/a><\/p>\n <\/p>\n Jonathan in Nature Medicine (his work is funded by the DRC BU-Joslin Bioinformatics and Systems Biology Core)<\/a><\/p>\n <\/p>\n Kasif Receives the Iacocca Senior Fellowship<\/a><\/p>\n <\/p>\n Daniel Segre (our collaborator and colleague) was promoted to Full Professor. Well Deserved.<\/a><\/p>\n <\/p>\n Eduardo Coronado and Joseph Mendoza complete their senior project in collaboration with David Sinclair Lab<\/a> and graduate.<\/p>\n <\/p>\n The program for ISMB 2015 in Dublin. We helped organize the Disease Models area.<\/a><\/p>\n <\/p>\n Andy McMurry submits a final copy of his PhD thesis on Distributed Mining of Electronic Health Records to graduate school !<\/p>\n <\/p>\n GlaxoSmithKline working with Epidemico \u00a0(John Brownstein and Clark Freifeld) and their software is acknowledged with a Best Practice Award — Clark’s thesis work (Twitter mining for Drug Side Effects).<\/a><\/p>\n <\/p>\n Owen White (former Glimmer collaborators at TIGR) receives the Ben Franklin Award for Sharing Data activities — not related to our joint work with him Art Delcher and Steven Salzberg.<\/a><\/p>\n <\/p>\n Manway Liu is heading to GoogleX !<\/p>\n <\/p>\n Chris Nogiec paper is selected as Cover in Molecular Metabolism.<\/a><\/p>\n <\/p>\n Andy McMurry successfully defends his thesis on Distributed Medical Record Data Mining. \u00a0Andy recently joined a start-up in California and it just went public.<\/p>\n <\/p>\n Harvard Medical School announces the formation of a new Medical Informatics Department<\/a><\/p>\n <\/p>\n Boston University announces a Data Science Hiring Initiative\u00a0<\/a><\/p>\n <\/p>\n Clark Freifeld’s company (with John Brownstein), Epidemico is bought by Booz Allen, Congratulations to Clark.<\/a><\/p>\n <\/p>\n Chris’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>\n Michael Molla in Nature Medicine \u00a0(his work is funded by the BU-Joslin Bioinformatics and Systems Biology Core).<\/a><\/p>\n <\/p>\n We announced the 2015 Competition for the Boston University – Joslin Diabetes Center Pilot and Feasibility Awards<\/a><\/p>\n Details can be found here:<\/a><\/p>\n <\/p>\n An important new program at Childrens Hospital (Undiagnosed Diseases).<\/a><\/p>\n <\/p>\n Michael Molla helps analyze insulin resistance in iPS cells<\/a><\/p>\n <\/p>\n Our paper with Charles Cantor helps shorten the “Erdos Distance” in the collaboration graph between biologists and mathematicians.<\/a><\/p>\n Paul Erdos — Noga Alon — {Simon Kasif ,Charles Cantor}<\/p>\n 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 Multinode Graphs\u00a0<\/a><\/p>\n <\/p>\n Zak Kohane in the New Yorker<\/a><\/p>\n Quote from the article: <\/p>\nI generally stay away from all politics but this appears to be completely objective news. DOGS ARE MOVING TO THE WHITE HOUSE. <\/a><\/h3>\n
I would propose to make dogs a requirement for a US Presidency in addition to being born in the US :)<\/a><\/h3>\n
Also, I really like this picture, I wonder, however,\u00a0 if we should set an age limit on US President unless it becomes a primarily honorary post.\u00a0 \u00a0It’s not a political statement, just common sense.\u00a0\u00a0<\/a><\/h3>\n
During a Zoom meeting today I learned that Arianna Rosenbluth<\/a> just died in December at the age of 93.\u00a0 \u00a0Dr. Arianna Rosenbluth co-pioneered the very famous Metropolis-Hastings algorithm. \u00a0<\/a>I routinely cover Gibbs Sampling in my class and refer to the Metropolis-Hastings algorithm which is related. Dr. Rosenbluth co-developed and was the first to implement it.\u00a0 The paper<\/a> that documents this work is enclosed.<\/h3>\n
AI is playing an increasing role in Drug Discovery. I am reminded of the early leadership by Megan Walker (PhD thesis with us 2001-2006). Megan presented some of her thesis work in this symposium.<\/a><\/h3>\n
COVID RESEARCH ANNOUNCEMENT\u00a0 (joint work with many colleagues across the US)<\/a><\/h3>\n
New:\u00a0 Steps towards reproducibility. Tracing computational predictions to their experimental sources with Rich Roberts (in PLoS Biology).\u00a0<\/a><\/h3>\n
Brian Haas publishes his first thesis chapter\u00a0 in Genome Biology (co-advised by Aviv Regev and Simon Kasif)<\/a><\/h3>\n
New:\u00a0 AI Risks and Solutions: Co-evolving Human and Computer Ethics<\/a><\/h3>\n
New: AI and Network Systems Biology of COVID-19<\/a><\/h3>\n
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New: Pooled Testing for COVID-19 – Based on Deep Complexity Theory Instead of Deep Networks – most credit goes to Richard Beigel<\/a><\/h3>\n
Dan Lancour publishes\u00a0 analysis of Brain Atlas Data to suggest new Alzheimer’s risk genotypes (joint work with Lindsay Farrer (genetics), Jose Dupuis (BioStat), Mark Crovella (CS) and AD consortium<\/a><\/h3>\n
Simon Kasif reviews the (AI2BIO2)* Vision in an MIT Talk — “Should Machines Understand Nature to Pass the Turing Test : <\/a>Co-evolving AI and Systems\/Synthetic Biology<\/span><\/h3>\n
Congratulation to Alfred Ramirez on publishing his paper on Systems Biology of Differentiation in Nature Communications\u00a0 (Joslin Press Release) (Alfred was co-advised by Ron Kahn)<\/a><\/h3>\n
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Very Sad News from Hopkins: We lost James Taylor a Bioinformatics Pioneer in Reproducibility<\/a><\/h3>\n
Congratulations to Dan Lancour on Defending his PhD and graduating (co-advised by Lindsay Farrer (Genetics) and Mark Crovella (CS)<\/h3>\n
Simon Kasif gives a provocative talk at Tel Aviv University reviewing the COMBREX PROJECT and the (AI2BIO2)* Vision : Not All Experimental Questions are born equal\u00a0<\/a><\/h3>\n
Congratulations to Brias Haas on publishing his Fusion Transcript Benchmarking paper in Genome Biology<\/a><\/h3>\n
Congratulations to Alfred Ramirez on starting a great job in a Microbiome Start-up<\/h3>\n
Esther Rheinbay launches a new laboratory at Mass. General and Harvard Medical School<\/a><\/h3>\n
Afred Ramirez defends his PhD (co-advised by Ron Kahn and Simon Kasif )<\/a><\/h3>\n
Title: \u201cSystems Biology of Human Adipocytes: From Genes and Molecular Networks to Heterogeneity and Metabolic Phenotypes\u201d<\/span><\/h3>\n
Kamila Naxerova launches a new laboratory at Mass General Hospital and Harvard Medical School<\/a><\/h3>\n
John Rachlin starts as faculty at Northeastern University<\/a><\/h3>\n
Simon Kasif gives a provocative talk at Tel Aviv University reviewing\u00a0Network Biology of the Axis of Wellness for Disease Prevention\u00a0<\/a><\/h3>\n
Title:\u00a0\u00a0\u00a0“Towards a Network Biology Axis of Wellness and Disease Prevention:\u00a0\u00a0How to Live Happy and Healthy to 120<\/a><\/h3>\n
Dan Lancour publishes a new paper on Network Based Analysis of Azheimer’s Genetics Data\u00a0 in PLoS Genetics\u00a0<\/a><\/h3>\n
Simon Kasif gives a talk at CMU introducing Network Biology Axis of Wellness for Disease Prevention<\/h3>\n
Simon Kasif gives a\u00a0 talk at Hopkins Lieber Brain Development Institute introducing Network Biology of the Axis of Wellness for Disease Prevention<\/a><\/h3>\n
Jonathan and Hui in Nature\u00a0\u00a0<\/a><\/h3>\n
Alfred Ramirez wins best graduate student paper of the year with his paper in Cell Reports.<\/a><\/h3>\n
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Clark Freifeld directs a graduate program in Health Analytics at Northeastern<\/a><\/h3>\n
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Our visitor Nurit Haspel from U. Mass is co-chairing a Bioinformatics meeting in Boston August 2017<\/a><\/h3>\n
Congratulations to Jonathan Dreyfuss. He is joining Joslin \u00a0Diabetes Center.<\/h3>\n
July 5th : Great week for former lab affiliates:<\/h3>\n
Kamila Naxerova in Science following up on a heroic project she started and led in her PhD thesis tracing cancer lineage<\/a><\/h3>\n
Esther Rheinbay in Nature with Gad Getz and other collaborators at the Broad<\/a><\/h3>\n
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
Kasif proposes a course “Humanity 101” as a response to the racist displays at Charlottesville match<\/a><\/h4>\n
Jonathan and Hui in Cell Metabolism\u00a0<\/a><\/h3>\n
Congratulations to Jonathan, Hui and Alfred \u00a0for their publication in Nature Communication\u00a0<\/a><\/h3>\n
Congratulations to Jonathan Dreyfuss for his publication in Nature<\/a><\/h3>\n
Congratulations to Jonathan Dreyfuss for his publication in Journal of Clinical Investigation<\/h3>\n
Fall 2016 Simon Kasif visits the Johns Hopkins School of Engineering (advisory visit)<\/h3>\n
Congratulations for Dan Lancour for passing his PhD oral exam<\/h3>\n
Many people had this idea, but so far very little movement in this direction.<\/a><\/h3>\n
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During the break I have compiled a fun collection of quotes. Some from legends, some from friends, some from me.<\/a><\/h3>\n
Our collaborator Ron Kahn Wins the Wolf Prize for Medicine for his contributions to insulin signaling and\u00a0its role in Diabetes and increasingly other diseases.<\/a><\/h3>\n
Happy 2016 to all !<\/h2>\n
Thanksgiving is around the corner. \u00a0Happy Holiday to all!<\/h3>\n
Reflecting on Paris events (November 2015)<\/h3>\n
My heart goes out to our fellow Parisians, both scientists and non-scientists. I hope the response of the world to this crazy atrocity would be similar to the Renaissance\u00a0<\/span>response to the plague, i.e., \u00a0transforming us\u00a0into better human beings. In plain English making us much, much tougher\u00a0<\/span>when needed (both before, during and after any predictable crisis) and more humane when not.\u00a0I think the two are not inconsistent.\u00a0I hope our friends in Paris did not die for nothing, and the long term the response\u00a0<\/span>(as stated above) will prevent more significant bloodshed, like an\u00a0immune response to a weakened version of a pathogen.<\/h3>\n
Finally, here is a thought du jour.\u00a0I don’t believe (like many including the terrorists in Paris did) that there is one “right” and many “wrongs”… on the contrary there are many “right-s” and only one wrong. What happened in Paris was wrong.<\/h3>\n
I am booking my next flight on Air France. I think it’s one of the many “right-s” that we can take a stand on now. There are many more.<\/h3>\n
\nCOMBREX-DB: “An Experiment-Centered Database Of Protein Function: Knowledge, Predictions and Knowledge Gaps”\u00a0<\/span>Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian; Kasif, Simon.; Roberts, Rich; Steffen, Martin<\/span>
\n<\/span><\/p>\nPilot and Feasibility Studies: 2016 Competition:<\/a><\/h3>\n
Letter of Intent deadline for Boston University and Neighboring Institutions Applicants is on Monday, November 2nd, 2015. The letters of intent can be uploaded at http:\/\/pandf.joslinresearch.org\/bu\/ using the template available at this site. Please distribute to relevant colleagues.<\/a><\/h3>\n
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\n\u201cIf you want to be charitable, you can say there\u2019s just a lack of awareness\u201d about what kind of sharing is permissible,\u00a0Kohane\u00a0said. \u201cIf you want to be uncharitable, you can say that researchers use that concern about privacy as a shield by which they can actually hide their more selfish motivations.\u201d…<\/p>\n