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.

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

“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.

 

List of Events,

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 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.

 

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

 

WEKA LECTURE POSTED

 

 

I generally stay away from all politics but this appears to be completely objective news. DOGS ARE MOVING TO THE WHITE HOUSE. In fact, if it was up to me I would make Dogs a requirement for a US Presidency in addition to being born in the US :)

 

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.

 

We produced a brief summary of Boston University Legacy in Computational, Systems and Synthetic Biology that began with Charles DeLisi coming to BU.

 

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)

 

Jonathan in Nature Medicine (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 !

 

GlaxoSmithKline working with Epidemico  (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).

 

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.

 

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 

 

Clark Freifeld’s company (with John Brownstein), Epidemico is bought by Booz Allen, Congratulations to Clark.

 

Chris’s paper in Molecular Metabolism is out and made cover !  Very impressive work  co-led  by ME Patti at Joslin and her laboratory.

 

Michael Molla in Nature Medicine  (his work is funded by the BU-Joslin Bioinformatics and Systems Biology Core).

 

We announced the 2015 Competition for the Boston University – Joslin Diabetes Center Pilot and Feasibility Awards

Details can be found here:

 

An important new program at Childrens Hospital (Undiagnosed Diseases).

 

Michael Molla helps analyze insulin resistance in iPS cells

 

Our paper with Charles Cantor helps shorten the “Erdos Distance” in the collaboration graph between biologists and mathematicians.

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.

Multinode Graphs 

 

Zak Kohane in the New Yorker

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

 

Zak Kohane (TEDMED)

 

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

Cor

 

BE568: Systems Biology of Human Disease is now a regular approved elective in Biomedical Engineering

 

Esther and Mario Suva (in Brad Bernstein Lab) review histone mutations and their role in driving pediatric glioblastoma (in Cancer Cell)

 

Simon Kasif in AIMBE

 

Simon Kasif and Ron Kahn at

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.

COMBREX NEWS (1)

COMBREX NEWS (2)

COMBREX NEWS (3)

 

Esther defends her PhD thesis (with Simon and Brad)

 

Our friend and former collaborator Judea Pearl  wins Turing Award

 

Tarjei in Nature (again)

 

Andy McMurry releases SHRINE

 

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

 

Manway Liu in BU News

 

I2B2 gets launched

 

Kasif describes Network Signatures of Disease  (Technion)

 

Kasif describes Biological Network Anomaly and Signatures of Disease (Tufts)

 

Kasif talks about “Systems Macro-Biology: From Parts and Genomes to Network Signatures of Disease” as a new paradigm for Disease Staging (Brown University)

 

 

Megon Walker describes the application of Active Learning to Drug Discovery (her PhD thesis starting 2001). 

 

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)

 

Human Genome First Draft

 

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 NY Times

 

Lewis Stiller in Scientific American

 

PARALLEL LOGIC PROGRAMMING – FIRST OPERATIONAL SYSTEM (1)

PARALLEL LOGIC PROGRAMMING – FIRST OPERATIONAL SYSTEM (2)