Selected Unusual Projects by Members of the Laboratory

“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 be.” — Maya Angelou –

 

Selected Unusual Projects by Current and Former Members or close collaborators of the Laboratory/Group

Simon Kasif: Artificial Tikkun Olam Perspective:

We are fully committed to deploying AI responsibly and safely in the service of social justice, inclusion, fairness, reducing social inequalities and diversity.

Stan Letovsky and his collaborators participate in the very important sharing cancer mutation data project

Jonathan and Hui in Nature  

Alfred Ramirez wins best graduate student paper of the year with his paper in Cell Reports.

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

Andy’s AI2MED company is sold.  Mazal Tov. 

 

COMBREX perspective (Not All Experiments are Created Equal) is deposited in bioarchive (this is an old paper, first submission to Science  October 2011)

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

Many people had this idea, but so far very little movement in this direction.

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

We participate in the “Computation as a Driver for Translational Medicine” in Sicily 

Tarjei Mikkelsen (former intern, another gem)

Precision Medicine Symposium: Patient Driven

Esther (former joint student with Brad Bernstein) in NEJM

Jonathan in Nature Medicine (his work is funded by the DRC BU-Joslin Bioinformatics and Systems Biology Core)

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).

Chris Nogiec paper is selected as Cover in Molecular Metabolism.

Andy McMurry successfully defends his thesis on Distributed Medical Record Data Mining.  Very early work on Federated Medical Health Records. 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

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).

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 

Kasif attends Columbia University Systems Biology Retreat/Advisory Board Meeting: In the picture he is trying to confuse Michael Waterman who is rarely confused.

Kamila Tracks Cancer Heterogeneity and Lineage

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

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

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.

Tarjei in Nature (again)

Andy McMurry releases SHRINE

Chris challenges the Supplements Myths

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

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). 

Lewis Stiller in NY Times

Lewis Stiller in Scientific American

PARALLEL LOGIC PROGRAMMING – FIRST OPERATIONAL SYSTEM (1)

PARALLEL LOGIC PROGRAMMING – FIRST OPERATIONAL SYSTEM (2)