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CBCB alumni win prestigious Sloan Fellowship

Wed Feb 25, 2015

Our former colleagues Michael Schatz and Cole Trapnell have been awarded the prestigious Sloan Fellowship (a full list of recipients is available here: http://www.sloan.org/fellowships/2015-sloan-research-fellows/). Many congratulations to both for this well deserved honor.

CBCB faculty Zia Khan publishes a paper in Science on the impact of regulatory variation from RNA to protein

Tue Jan 06, 2015

CBCB faculty Zia Khan and collaborators have published a paper titled “Impact of regulatory variation from RNA to protein” on December 18, 2014 in the journal Science.

In this study, Dr. Khan and collaborators mapped genetic variants that are associated with changes in gene expression, ribosome occupancy, and protein abundance in human cell lines. This is the first study to map the impact of genetic variation on three distinct regulatory layers, transcriptional, translational, and post-translational, from RNA to protein.

The study provides two main findings: (1) genetic variation that impacts gene expression tends to have attenuated or buffered affects on protein abundance (2) a new class of functional genetic variation that acts post-translationally to alter protein abundance with little affect on gene expression or protein translation. The study is the first of its kind and provides an important resource for the broader scientific community.

“Impact of regulatory variation from RNA to protein” article: http://www.sciencemag.org/content/early/2014/12/17/science.1260793.abstract

CBCB faculty Eytan Ruppin’s group publish a paper in eLife on phenotype-based cell-specific metabolic modeling

Mon Dec 01, 2014

CBCB faculty Eytan Ruppin’s group has published a paper titled “Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer” on November 21, 2014 in the journal eLife.

Utilizing molecular data to derive functional physiological models tailored for specific cancer cells can facilitate the use of individually tailored therapies. To this end, they present an approach termed PRIME for generating cell-specific genome-scale metabolic models (GSMMs) based on molecular and phenotypic data. They built >280 models of normal and cancer cell-lines that successfully predict metabolic phenotypes in an individual manner. They utilize this set of cell-specific models to predict drug targets that selectively inhibit cancerous but not normal cell proliferation. The top predicted target, MLYCD, was experimentally validated and the metabolic effects of MLYCD depletion were investigated. Furthermore, they tested cell-specific predicted responses to the inhibition of metabolic enzymes, and successfully inferred the prognosis of cancer patients based on their PRIME-derived individual GSMMs. These results lay a computational basis and a counterpart experimental proof of concept for future personalized metabolic modeling applications, enhancing the search for novel selective anticancer therapies.

“Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer” article: http://www.cs.tau.ac.il/~ruppin/prime.pdf

CBCB researchers Keith Hughitt, Lee Mendelowitz, and Joseph Paulson create an interactive tool that compares country data on women’s empowerment and stunting

Tue Nov 25, 2014

CBCB researchers Keith Hughitt, Lee Mendelowitz, and Joseph Paulson volunteered for a visualization hackathon for a D.C. non-profit called Bread for the World. They cleaned up some data and prepared a visualization of the relationship/correlation between malnutrition and women's empowerment throughout the world. Data shows that countries that empower women tend to have lower rates of stunting, which is a measure of chronic undernutrition. Their work was published in Bread for the World’s annual hunger report.

For their interactive tool that compares country data on women’s empowerment and stunting, please see: http://hungerreport.org/2015/empowerment-to-improve-nutrition/

Bread for the World’s annual hunger report: http://hungerreport.org/2015/

CBCB faculty Eytan Ruppin’s group publish a paper in Molecular Systems Biology on computational study of Warburg effect

Sep 04, 2014

CBCB faculty Eytan Ruppin's group has published a paper, led by Keren Yizhak, titled “A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration” on July 30, 2014 in the journal Molecular Systems Biology. This article presents a computational analysis of the Warburg effect, which is a key alteration characterizing the metabolism of many cancers. They show that gene knockouts reverting the Warburg effect can inhibit cancer migration and hence the likelihood of spreading metastasis. Their predictions were further tested and corroborated by their experimental collaborators from Leiden (van de Water) and Cambridge (Frezza).

“A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration” article: http://onlinelibrary.wiley.com/doi/10.15252/msb.20134993/pdf

CBCB scientists Héctor Corrada Bravo and Florin Chelaru publish a paper on Epiviz, a web-based tool for interactive visual analytics of genomics data, in Nature Methods

Thu Sep 04, 2014

CBCB faculty Héctor Corrada Bravo and CBCB doctoral student Florin Chelaru, along with undergraduate research assistants, have developed a new, web-based tool that enables researchers to quickly and easily visualize and compare large amounts of genomic information resulting from high-throughput sequencing experiments. They have described the free tool, called Epiviz, in their published paper titled “Epiviz: interactive visual analytics for functional genomics data” on Aug. 3, 2014 in the journal Nature Methods.

Next-generation sequencing has revolutionized functional genomics. These techniques are key to understanding the molecular mechanisms underlying cell function in healthy and diseased individuals and the development of diseases like cancer. Data from multiple experiments need to be integrated, but the growing number of data sets causes a thorough comparison and analysis of results to be challenging. In Corrada Bravo and Chelaru’s paper, Epiviz is shown to be capable of visualizing and analyzing DNA methylation and gene expression data in colon cancer.

“Epiviz: interactive visual analytics for functional genomics data” article: http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3038.html

For Florin Chelaru’s discussion on Epiviz and his research in bioinformatics and genomic research, please see: http://www.cs.umd.edu/article/2014/08/florin-chelaru-epiviz-research-and...

For more information, please see: http://cmns.umd.edu/news-events/features/2376

CBCB faculty Eytan Ruppin’s group publish a paper in Cell on predicting cancer-specific vulnerability

Wed Sep 03, 2014

CBCB faculty Eytan Ruppin's group has published a paper, led by Livnat Jerby, titled “Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality” on Aug. 1, 2014, in the journal Cell. This article describes their development of a computational pipeline that identifies synthetic lethal interactions by analyzing large cohorts of genetic and molecular data of clinical cancer samples. With their experimental collaborators from the Beatson (Gottlieb) and the Broad (Clemons) institutes, they show that synthetic lethality networks can be used to successfully predict the response of cancer cells to various drugs and other treatments, as well as to predict clinical prognosis.

“Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality” article: http://ac.els-cdn.com/S0092867414009775/1-s2.0-S0092867414009775-main.pd...

CBCB scientists Mihai Pop, Joseph Paulson, Irina Astrovskaya, and Héctor Corrada Bravo publish a study on diarrhea in low income countries

Jun 27, 2014

CBCB scientists Mihai Pop, Joseph Paulson, Irina Astrovskaya, and Héctor Corrada Bravo, together with colleagues from the University of Maryland School of Medicine, publish in the journal Genome Biology the results of a large-scale study on diarrheal disease in low-income studies. The study, led by Mihai Pop from the CBCB and Colin Stine from UMSOM, has characterized the gut microbiota in 992 children with diarrhea and diarrhea-free controls from four low-income countries (The Gambia, Mali, Kenya, and Bangladesh). This study identifies new organisms that may be implicated in diarrheal disease as well as the existence of several bacterial groups that may protect children from diarrhea. Further information is available in the UM Press release and on the project's website.

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

CBCB faculty Najib El Sayed, Mihai Pop, and Jeremy Selengut are considered "Highly Cited" by Thompson Reuters

Jun 24, 2014

CBCB faculty Najib El Sayed, Mihai Pop, and Jeremy Selengut, appear on this year's list of Highly Cited researchers published by Thompson Reuters. The list, available at highlycited.com, comprises researchers who appear in the top 1% of their discipline in terms of citations to their papers published between 2002 and 2012. For more information see the press release at Science Watch .

Emily Jones Awarded National Science Foundation Graduate Research Fellowship

Mon Apr 07, 2014

Emily Jones Awarded National Science Foundation Graduate Research Fellowship. story here

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