All News
CBCB faculty Eytan Ruppin’s group publish a paper in eLife on phenotype-based cell-specific metabolic modeling
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.pdfCBCB researchers Keith Hughitt, Lee Mendelowitz, and Joseph Paulson create an interactive tool that compares country data on women’s empowerment and stunting
CBCB faculty Eytan Ruppin’s group publish a paper in Molecular Systems Biology on computational study of Warburg effect
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
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
“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
CBCB faculty Najib El Sayed, Mihai Pop, and Jeremy Selengut are considered "Highly Cited" by Thompson Reuters
Emily Jones Awarded National Science Foundation Graduate Research Fellowship
Emily Jones Awarded National Science Foundation Graduate Research Fellowship. story here
New video highlights health informatics initiative
CBCB scientists are involved in a new University of Maryland initiative, the Center for Health-related Informatics and Bioimaging (CHIB). This new Center will foster stronger ties between the College Park and Baltimore campuses of our University by supporting inter-disciplinary biomedical research activities. CHIB is featured in a new video: http://vimeo.com/79494983
CBCB researchers publish software for microbiome association statistics
CBCB researchers Héctor Corrada Bravo, Joseph Paulson, and Mihai Pop together with their colleague O. Colin Stine from the University of Maryland School of Medicine publish a new statistical package for performing differential analysis in metagenomic data. The new package, metagenomeSeq, implemented as part of the Bioconductor package, appeared today in as advanced online publication in the journal Nature Methods. This package addresses several challenges specific to metagenomic data, including the high level of sparsity due to insufficient sequence coverage, and provides accurate and robust estimates of the differential abundance of organisms across microbiome samples.
The article additional information is available at http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2658.html, and the software package can be downloaded from http://www.bioconductor.org/packages/2.13/bioc/html/metagenomeSeq.html
Pages
