Archived News

Algorithms find genetic cancer networks:

CCMB Ph.D. students Hsin-Ta Wu and Max Leiserson, working in Ben Raphael's group, use powerful algorithms to assemble the most complete genetic profile yet of acute myeloid leukemia, an aggressive form of blood cancer, in collaboration with researchers at Washington University in St., Louis and The Cancer Genome Atlas (TCGA). Findings are reported in the New England Journal of Medicine.
Full article here 

Translational Seed Award:

Sorin Istrail has received the inaugural Translational Seed Award from OVPR for the project “Development of New Computational and Point of Care Platforms for HIV Drug Resistance” in collaboration with Joe Hogan (Biostatistics), Rami Kantor (Medicine), and Anubhav Tripathi (Engineering).

Introduced this year by OVPR, Translational Seed Awards are intended to advance programs that have promising intellectual property and commercial potential.

The award will be presented at the Teaching Awards Ceremony on May 6, 4pm-6pm, in Pembroke 305.

Congratulations, Sorin!


When the cell's two genomes collide:

Animal cells contain two genomes: one in the nucleus and one in the mitochondria. When mutations occur in each, they can become incompatible, leading to disease. To increase understanding of such illnesses, scientists at Brown University and Indiana University have traced one example in fruit flies down to the individual errant nucleotides and the mechanism by which the flies become sick. Full text here.

Brown Helps Win Genomics Challenge:

A team of researchers led by Brigham and Women’s Hospital in Boston, including members of William Fairbrother’s lab at Brown, has won the national CLARITY genomics contest, organizers announced in San Francisco Nov. 7. Boston Children’s Hospital challenged more than 20 teams to analyze the whole genomes of three families to find the mutations causing a disease in children from each family. Brown News article here. Full text here.

Brown Awarded $1.5M for new Big Data tools:

Eli Upfal and Fabio Vandin of the Computer Science Department, and Ben Raphael of the Computer Science Department and the CCMB at Brown University, from left, are developing Big Data analytical tools that make sense of large datasets and eliminate the noise of data errors. 
Full text here. 

Sohini Ramachandran Interviewed for Nature's "Turning Point".

Full text here. 

Brown University Researchers Develop New Method for Haplotype Assembly with NGS Data:

Researchers from Brown University have developed a method that they say can generate more accurate haplotype assemblies for genome-wide and whole-exome studies than current methods. 
Full text of article available here or  on genomeweb.

Sohini Ramachandran featured in The Scientist as their "Scientist to Watch":

article on her research which can be found on their website here.

Sohini Ramachandran named Pew Scholar - article here

Directory listing here

The Center for Computational Molecular Biology has awarded two Postdoctoral Research Fellowships in the first round of its new Postdoctoral Fellows program.  Rachel Soemedi, PhD (Newcastle University) will take a population genetics approach to studying how sequence variants and disease alleles affect pre-mRNA processing. She will work in a collaborative group that spans the Fairbrother, Ramachandran and Weinreich labs.   Dr. Yevgeny (Eugene) Raynes, PhD (University of Pennsylvania) will use computational analyses of genomic sequence data to model cancer as an asexual evolutionary process. This work will span The Weinreich, Brodsky, Raphael labs.  Both appointments are two year positions that will begin 1 July 2012.

Congratulations to Drs. Soemedi and Raynes.


Max Leiserson awarded National Science Foundation Graduate Research Fellowship:
Max Leiserson was selected for an NSF Graduate Research Fellowship this year. He is currently a Ph.D. student in the CCMB working with Ben Raphael's group. Congratulations Max! 

Sohini Ramachandran wins Sloan Award:
Sohini Ramachandran, assistant professor of biology in the Department of Ecology and Evolutionary Biology department, was one of 126 U.S. and Canadian researchers to receive a research fellowship from the Alfred P. Sloan Foundation this year, the foundation announced on Wednesday. The fellowships are given to early career scientists and scholars whose achievements and potential identify them as rising stars, the next generation of scientific leaders. Besides the recognition, Ramachandran will receive $50,000 to further her research. She said she is honored to receive a research fellowship, noting that her father-in-law, David Mumford, professoremeritus of applied mathematics, received the award early in his academic career. “The freedom of the award gives my research group the opportunity to pursue innovative projects that are difficult to fund traditionally,” Ramachandran said. “This award also recognizes the strong and supportive environment for young faculty at Brown, Ecology and Evolutionary Biology, and our Center for Computational Molecular Biology.” Ramachandran came to Brown in 2010. She earned her doctorate in biological sciences from Stanford University.  

David Rand named AAAS fellow:
David Rand along with fellow professors Barry Connors and Dian Lipscombe have been named fellows of the American Association for the Advancement of Science. They will be officially welcome as fellows at the AAAS Annual Meeting in Vancouver, B.C. on February 18th, 2012. 

HotNet is the heat-seeker of cancer 
This summer, more than a hundred scientists from dozens of research institutions published a landmark paper that identified a single gene responsible for the most prevalent form of ovarian cancer. Their success hinged in no small part on an ingenious algorithm developed by computer scientists at Brown University. (From

Continents influenced human migration, spread of technology
Researchers at Brown University and Stanford University have pieced together ancient human migration in North and South America. Writing in the American Journal of Physical Anthropology, the authors find that technology spread more slowly in the Americas than in Eurasia. Population groups in the Americas have less frequent exchanges than groups that fanned out over  Europe and Asia. (From

CCMB's Ben Raphael Promoted to Associate Professor