Popular Press, News, Events and Announcements
“Every man must decide whether he will walk in the light of creative altruism or in the darkness of destructive selfishness.” – Martin Luther King, Jr.
“An investment in knowledge pays the best interest” — Ben Franklin
“Educating the mind without educating the heart is no education at all.” ― attributed to Aristotle.
“The only thing that will redeem mankind is cooperation” — Bertrand Russell
“If you’re always trying to be normal, you will never know how amazing you can me.” — Maya Angelou –
Code of Ethics (Boston University)
Selected list of events, news and announcements from group, collaborators and community.
I have a broad view of the “family” we helped create. I will post selected announcements from former lab members, affiliates or close collaborators when they deserve special attention so people can track their progress. I occasionally post some broad announcements that are of interest to people who care about issues that touch us all.
Wisdom from the smartest/bravest people that ever lived on our planet (feel free to distribute).
Petition to Unite in Opposition to the War in Ukraine (feel free to distribute)
List of Events
August 2024 : TM Murali is leading a new center for pandemic prevention.
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.
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).
T. M. Murali is a particularly noteworthy story.
He is an academic grandchild of the legendary computer scientist Don Knuth (through Jeff Vitter).
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.
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.
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).
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). :)
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).
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.
I am hopeful and will try to let Don know about this new center. I know he and his other descendants would be proud. In some ways, its symbolic and perhaps he envisioned this in a few comments about biology he made 30+ years ago. Biological knowledge is deep, magical and essential. But computational sciences are enriched in creative problem solving, rigorous and abstract formalization of difficult problems, theoretical depth and rapid pace of technological developments.
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.
Spring of 2024: we introduced a completely new AI class at Boston University. It’s a first of a kind (at least at BU and perhaps beyond) AI seminar for Biomedical Science and Engineering. All the papers were presented by students and included some of the most radically innovative applications of AI to biomedical science and medicine. The quality of the vast majority of student presentations was way above expectations showcasing the excitement about this area.
We lost Daniel Kahneman. Sad. He inspired us to challenge the dogma (any dogma), come up with radically new ideas and attempt to prove them empirically, thus inspiring others to catalyze new theories across multiple disciplines that included psychology, behavioral economics, mathematical decision theory, AI, cognitive science and beyond. We started an informal discussion with him leading to a possible collaboration. I now must complete this work. It will not be the same quality but at least will honor our attempt to understand something important.
Congratulations to our dear friend and long term collaborators Sir Richard J. Roberts for being selected to the US National Academy of Sciences. Of course, Rich received numerous awards and recognition including a Nobel.
Congratulations to Brian Haas on his paper in Cell Reports Methods. The paper introduces the novel concept of inspectors.
Professor Simon Kasif is on long sabbatical. Expect delays in communication. We continue our efforts to bridge AI, Biology and Medicine. With an emphasis on radical or early innovation. We obviously continue to consult to applied projects in the space of AI, Computational Biology, Bioinformatics, Machine Learning and Biotechnology and advise companies or institutions in a BROAD range of AI2BIOMED.
We lost Bill Russell. I don’t track any specific team in the NBA but I follow players that made a difference, changed the game and/or showcased broader views that touch all of us. Examples include Michael Jordan, Julius Irving, Kareem Abdul-Jabbar, Magic Johnson, Steph Curry and of course Bill Russell.
Most people remember him for his role in 11 championships. Others remember him for his role in changing the game of basketball and his strong stance against racism.
Congratulations to Adam Phillippy for being selected for Time 100 Person of the Year
This work by Adam and his collaborators is just great science: fundamental, ambitious and what a service to the broader community! It also showcases an intellectual transformation manifested by computational scientists co-leading major genomic efforts – not “just” 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. All three are among our closest collaborators and I cannot be more proud of their accomplishments.
But there are so many others including computational scientists or engineers doing deep biology or biotechnology. Not to mention the computational work that enables transformative discovery and invention such as Koonin & Makarova et al and others.
We are seeing a real convergence of biological and computational sciences of remarkable future significance. AI will just make it converge faster and with higher impact. 20+ years ago many speculated that biology would become an “information science”. Many of us felt (even then) that this is not the most ambitious or imaginative vision of the genomic revolution. We were naive but right :)
Our colleague and collaborator Charles DeLisi does not rest on his laurels. He just organized a transformative workshop proposing a focus on synthetic biology for climate change.
Congratulations to Jeff Law, T.M. Murali, Catherine Della Santina and all the collaborators (including multiple people at VT, BU, UCLA, etc) on their publication of drug repositioning targets for covid-19 using interpretable network propagation
Congratulations to Jonathan Dreyfuss and ME Patti at Joslin Diabetes Center at Harvard Med on the Nature Communication paper. This causality effort started many years ago (joint BU/Harvard) but was completed and published with a heroric effort by ME Patti (her lab) and Jonathan Dreyfuss both at Joslin Diabetes Center.
Starting September 2021, the Lab will focus on (AI2BIO2)*, i.e., building the bridge between AI and Biomedical Science. This was the reason we (with Art Delcher) wrote our first paper in Computational biology in 1992. This also means the lab will not accept new PhD students in main-stream Bioinformatics or Computational Biology. These fields have been growing rapidly since 2000 and there are many talented young scientists who can advise students in this space and we are happy to refer students to the many universities who have major strength in main stream bioinformatics area. We will focus on continuing to build bridges between AI and Biomedical Science / Engineering that still require significant experience, breadth and depth that remain rare. Our focus would be on new ideas that have a good chance to innovate in both AI and Biomedical Science / Engineering (rather than just using off the shelf prediction techniques on biological or clinical data).
We will continue consulting and collaborating in both AI and Bioinformatics.
We made two predictions in our 1993-5 papers at Johns Hopkins University that still provide a good foundation and vision for the utility of AI in reasoning about biology and modeling/understanding biological systems.
“To summarize, scientific analysis of data is an important potential application of Artificial Intelligence (AI) research. We believe that the ultimate data analysis system using AI techniques will have a wide range of tools at its disposal and will adaptively choose various methods.
It will be able to generate simulations automatically and verify the model it constructed with the data generated during these simulations. When the model does not fit the observed results the system will try to explain the source of error, conduct additional experiments, and choose a different model by modifying system parameters. If it needs user assistance, it will produce a simple low-dimensional view of the constructed model and the data. This will allow the user to guide the system toward constructing a new model and/or generating the next set of experiments.”
Prediction 1:
“We believe that flexibility, efficiency and direct representation of causality in probabilistic networks are important desirable features that make them very strong candidates as a framework for biological modeling systems.”
This quote is from Delcher, A., S. Kasif, H. Goldberg and W. Xsu, “Protein Secondary-Structure Modeling with Probabilistic Networks”, International Conference on Intelligent Systems and Molecular Biology, pp. 109–117, 1993.
Delcher, A., S. Kasif, H. Goldberg and W. Xsu, “Application of Probabilistic Causal Trees to Analysis of Protein Secondary Structure”, Proceedings of the National Conference on Artificial Intelligence, pp. 316–321, July 1993.
Prediction 2:
Based on Prediction 1, we also proposed a relatively efficient computational framework to implement in-silico directed evolution (synthetic biology) using graphical models. More specifically, the framework must perform mutagenesis (e.g., amino acid substitutions in proteins) and screen for mutations and adaptations that satisfy structural and functional constraints. For each such perturbation (mutation) we must perform an efficient inference in the graphical model to assess the probability a given property of a protein or system was affected by the perturbation. Our novel procedure enables to COMPILE THE GRAPHICAL MODEL using dynamic data structures and subsequently compute the change in a specific property in computational time that is exponentially faster than using standard algorithms. This is described in detail in the paper below.
Delcher, A, A. Grove, S. Kasif and J. Pearl, “Logarithmic Time Queries and Updates in Probabilistic Networks”, Journal of Artificial Intelligence Research, Vol. 4., pp. 37–59, 1996
Brian Haas submits his second thesis chapter for publication.
Brian Haas defends his PhD (co-advised by Aviv Regev and Simon Kasif). Brian is an unusual student (even among the exceptional students the I was fortunate to c0-advise). His H-index is over 73 and he has multiple papers as first author with thousands of citations.
Our dear friend and former colleague Ham Smith retires.
Very sad news. We lost my academic co-mentor Jack Minker at the age of 93. He was a leading scientist, a human rights crusader and a great human being who treated everyone with respect.
My academic sister Terry Gaasterland becomes Mayor
BE700 SPRING 2021 INTRODUCTION LECTURE POSTED
I generally stay away from all politics but this appears to be completely objective news. DOGS ARE MOVING TO THE WHITE HOUSE.
I would propose to make dogs a requirement for a US Presidency in addition to being born in the US :)
Also, I really like this picture, I wonder, however, if we should set an age limit on US President unless it becomes a primarily honorary post. It’s not a political statement, just common sense.
During a Zoom meeting today I learned that Arianna Rosenbluth just died in December at the age of 93. Dr. Arianna Rosenbluth co-pioneered the very famous Metropolis-Hastings algorithm. 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. The paper that documents this work is enclosed.
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.
COVID RESEARCH ANNOUNCEMENT (joint work with many colleagues across the US)
New: Steps towards reproducibility. Tracing computational predictions to their experimental sources with Rich Roberts (in PLoS Biology).
Brian Haas publishes his first thesis chapter in Genome Biology (co-advised by Aviv Regev and Simon Kasif)
New: AI Risks and Solutions: Co-evolving Human and Computer Ethics
New: AI and Network Systems Biology of COVID-19
New: Pooled Testing for COVID-19 – Based on Deep Complexity Theory Instead of Deep Networks – most credit goes to Richard Beigel
Dan Lancour publishes 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
Simon Kasif reviews the (AI2BIO2)* Vision in an MIT Talk — “Should Machines Understand Nature to Pass the Turing Test : Co-evolving AI and Systems/Synthetic Biology
Congratulation to Alfred Ramirez on publishing his paper on Systems Biology of Differentiation in Nature Communications (Joslin Press Release) (Alfred was co-advised by Ron Kahn)
Very Sad News from Hopkins: We lost James Taylor a Bioinformatics Pioneer in Reproducibility
Congratulations to Dan Lancour on Defending his PhD and graduating (co-advised by Lindsay Farrer (Genetics) and Mark Crovella (CS)
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
Congratulations to Brias Haas on publishing his Fusion Transcript Benchmarking paper in Genome Biology
Congratulations to Alfred Ramirez on starting a great job in a Microbiome Start-up
Esther Rheinbay launches a new laboratory at Mass. General and Harvard Medical School
Afred Ramirez defends his PhD (co-advised by Ron Kahn and Simon Kasif )
Title: “Systems Biology of Human Adipocytes: From Genes and Molecular Networks to Heterogeneity and Metabolic Phenotypes”
Kamila Naxerova launches a new laboratory at Mass General Hospital and Harvard Medical School
John Rachlin starts as faculty at Northeastern University
Simon Kasif gives a provocative talk at Tel Aviv University reviewing Network Biology of the Axis of Wellness for Disease Prevention
Title: “Towards a Network Biology Axis of Wellness and Disease Prevention: How to Live Happy and Healthy to 120
Dan Lancour publishes a new paper on Network Based Analysis of Azheimer’s Genetics Data in PLoS Genetics
Simon Kasif gives a talk at CMU introducing Network Biology Axis of Wellness for Disease Prevention
Simon Kasif gives a talk at Hopkins Lieber Brain Development Institute introducing Network Biology of the Axis of Wellness for Disease Prevention
Jonathan and Hui in Nature
Alfred Ramirez wins best graduate student paper of the year with his paper in Cell Reports.
Clark Freifeld directs a graduate program in Health Analytics at Northeastern
Our visitor Nurit Haspel from U. Mass is co-chairing a Bioinformatics meeting in Boston August 2017
Congratulations to Jonathan Dreyfuss. He is joining Joslin Diabetes Center.
July 5th : Great week for former lab affiliates:
Kamila Naxerova in Science following up on a heroic project she started and led in her PhD thesis tracing cancer lineage
Esther Rheinbay in Nature with Gad Getz and other collaborators at the Broad
COMBREX perspective (Not All Experiments are Created Equal) is deposited in bioarchive (this is an old paper, first submission to Science October 2011)
Kasif proposes a course “Humanity 101” as a response to the racist displays at Charlottesville match
Jonathan and Hui in Cell Metabolism
Congratulations to Jonathan, Hui and Alfred for their publication in Nature Communication
Congratulations to Jonathan Dreyfuss for his publication in Nature
Congratulations to Jonathan Dreyfuss for his publication in Journal of Clinical Investigation
Fall 2016 Simon Kasif visits the Johns Hopkins School of Engineering (advisory visit)
Congratulations for Dan Lancour for passing his PhD oral exam
Many people had this idea, but so far very little movement in this direction.
During the break I have compiled a fun collection of quotes. Some from legends, some from friends, some from me.
Our collaborator Ron Kahn Wins the Wolf Prize for Medicine for his contributions to insulin signaling and its role in Diabetes and increasingly other diseases.
Happy 2016 to all !
Thanksgiving is around the corner. Happy Holiday to all!
Reflecting on Paris events (November 2015)
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 response to the plague, i.e., transforming us into better human beings. In plain English making us much, much tougher when needed (both before, during and after any predictable crisis) and more humane when not. I think the two are not inconsistent. I hope our friends in Paris did not die for nothing, and the long term the response (as stated above) will prevent more significant bloodshed, like an immune response to a weakened version of a pathogen.
Finally, here is a thought du jour. I 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.
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.
Our COMBREX paper is accepted in the Annual DB Issue edited by Michael Galperin. The first database paper (to our knowledge) that includes “Knowledge Gaps…”
NAR-02923-Data-E-2015.R1
COMBREX-DB: “An Experiment-Centered Database Of Protein Function: Knowledge, Predictions and Knowledge Gaps” Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian; Kasif, Simon.; Roberts, Rich; Steffen, Martin
Soo Lee in Nature Biotechnology (Soo is at Harvard Medical School now).
Evan Appleton (former undergraduate researcher in the lab) defends his PhD thesis on Synthetic Biology (with Doug Densmore). Well done Evan! Evan just joined Church Lab at Harvard Medical School as a fellow.
Pilot and Feasibility Studies: 2016 Competition:
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.
J. Faith (now at Mount Sinai School of Medicine) in Nature Medicine
Yi-Chien (COMBREX primary developer) defends his PhD thesis
We participate in the “Computation as a Driver for Translational Medicine” in Sicily
Tarjei Mikkelsen (former intern, another gem)
Precision Medicine Symposium: Patient Driven
Kasif is on sabbatical on the Longwood campus of HMS, funded in part by the Iacocca Senior Fellowship and Joslin Diabetes Center
Biomedical Engineering at BU ranks 9.
Esther (former joint student with Brad Bernstein) in NEJM
Jonathan in ELIFE (his work is funded by the DRC BU-Joslin Bioinformatics and Systems Biology Core)
Kasif Receives the Iacocca Senior Fellowship
Daniel Segre (our collaborator and colleague) was promoted to Full Professor. Well Deserved.
Eduardo Coronado and Joseph Mendoza complete their senior project in collaboration with David Sinclair Lab and graduate.
The program for ISMB 2015 in Dublin. We helped organize the Disease Models area.
Andy McMurry submits a final copy of his PhD thesis on Distributed Mining of Electronic Health Records to graduate school !
Manway Liu is heading to GoogleX !
Chris Nogiec paper is selected as Cover in Molecular Metabolism.
Andy McMurry successfully defends his thesis on Distributed Medical Record Data Mining. Andy recently joined a start-up in California and it just went public.
Harvard Medical School announces the formation of a new Medical Informatics Department
Boston University announces a Data Science Hiring Initiative
An important new program at Childrens Hospital (Undiagnosed Diseases).
Michael Molla helps analyze insulin resistance in iPS cells
Paul Erdos — Noga Alon — {Simon Kasif ,Charles Cantor}
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.
Quote from the article:
“If you want to be charitable, you can say there’s just a lack of awareness” about what kind of sharing is permissible, Kohane said. “If 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.”…
Kasif attends Columbia University Systems Biology Retreat : In the picture he is trying to confuse Michael Waterman who is rarely confused.
Kamila Tracks Cancer Heterogeneity and Lineage
Chris Nogiec, Clark Freifeld, Richard Park, Dean Pavlick, Bryan Cosco, Elias Lougacos graduate
Clark Freifeld in Business Week
Clark in BU Engineering News After Receiving the Best Societal Impact Thesis Award
Esther Rheinbay and Mario Suva play Connect Four and Reprogram Cancer Stem Cells
Boston University (BME) and Joslin Diabetes Center open the 2014 Pilot and Feasibility Competition
Simon Kasif and David Heckerman co-chair ISMB 2014 Disease Models
Joslin celebrates Ron Kahn with a symposium
Andrea Califano and Barry Honig start Department of Systems Biology at Columbia
Joslin Diabetes Center and BU establish a joint (BUJRC) Bioinformatics and Systems Biology
Core
BE568: Systems Biology of Human Disease is now a regular approved elective in Biomedical Engineering
Drug Response – A Tool for Understanding the Systems Biology of Type 2 Diabetes
Steven Salzberg gets the much deserved Franklin Award
Boston University starts a new Systems and Synthetic Biology Center
Kamila defends her PhD thesis (well done)
Richard Park (co-advised by Peter Park, Harvard Med. School) is a finalist in the Illumina iDEA Challenge in 2011 with the Genome Browser Richard co-developed in Peter Park’s group.
Sir Richard Roberts on COMBREX
COMBREX (Computational Bridges to Experiments) is a new project that funds biologists to perform experimental determinations on genes predicted to be important by the system that integrates knowledge from many databases, prediction servers and internal algorithms based on Information Gain and Active Learning.
Esther defends her PhD thesis (with Simon and Brad)
Our friend and former collaborator Judea Pearl wins Turing Award
Simon Kasif and Zak Kohane co-chair Disease Models at ISMB 2012
Brandeis hosts a symposium in honor and memory of David Waltz
Chris challenges the Supplements Myths
Jack Minker receives a Human Rights Award
Scott Weiss (former JHU graduate student) breaks Jeopardy
Scott Weiss makes Jeopardy history
Michael Molla in PNAS (with Art Delcher, Charles Cantor, and Shamil Sunyaev)
Kamila in Children’s Hospital News
Martin Steffen in Science Daily
Protein Phosphorylation Cancer Biomarkers
Kasif describes Network Signatures of Disease (Technion)
Kasif describes Biological Network Anomaly and Signatures of Disease (Tufts)
Mesirov, Kasif co-organize RECOMB 2005
Proceedings RECOMB 2005 (all co-organizers)
Roberts, Kasif et al organize a workshop at the American Academy of Microbiology in DC
Very Sad News — Azriel Rosenfed (one of my two PhD thesis mentors) has passed away
DeLisi, Kasif et al launch CAGT
Collaboration network (out of date)
Early Book in Computational Biology
S. Salzberg, D. Searls and S. Kasif, eds, “Computational Methods in Molecular Biology”, Elsevier Publ. 1998. (2nd Printing, February 1999).
Lewis Stiller in Scientific American
PARALLEL LOGIC PROGRAMMING – FIRST OPERATIONAL SYSTEM (1)
PARALLEL LOGIC PROGRAMMING – FIRST OPERATIONAL SYSTEM (2)
