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CBCB faculty Eytan Ruppin's group publishes a paper in Cell Systems on predicting drug side effects

Mon Apr 11, 2016

CBCB faculty Eytan Ruppin's group has published a paper titled "Metabolic Network Prediction of Drug Side Effects" on March 23, 2016 in the journal Cell Systems .

For further information, please see: https://www.cs.umd.edu/article/2016/03/professor-eytan-ruppin-publishes-...

Metabolic Network Prediction of Drug Side Effects" article: http://www.sciencedirect.com/science/article/pii/S2405471216300734

Recent Promotions for CBCB Faculty

Mon Apr 11, 2016

Congratulations to the following mentioned faculty:

Dr. Hector Corrada Bravo has been promoted to Associate Professor. Additionally, Dr. Mihai Pop, Dr. Najib El-Sayed, and Dr. Michael Cummings have been promoted to Professor.

Adam Phillippy quoted in the NY Times

Apr 03, 2016
CBCB alumnus Adam Phillippy, now Head of the Genomics Informatics Section of the Computational within Statistical Genomics Branch at the National Human Genome Research Institute (NIHGRI), was quoted in the NY Times on the challenges involved in the reconstruction of the genome of Aedes aegypti - the mosquito that carries, among other diseases, the Zika virus.
Team of Rival Scientists Comes Together to Fight Zika

CBCB faculty Mihai Pop is mentioned in the Wall Street Journal for sequencing UMD's mascot

Fri Mar 18, 2016

The article can be found here: http://www.wsj.com/article_email/does-your-mascot-have-a-dna-sequence-sc...

A youtube video has been posted that shows Dr. Pop working with UMD freshmen to sequence the genome of the University's mascot, the diamondback terrapin: https://www.youtube.com/watch?v=oBoV5j-oQes&feature=youtu.be

CBCB scientists Mahfuza Sharmin, Hector Corrada Bravo, and Sridhar Hannenhalli publish a paper in BMC Cancer on hypomethylated blocks in colon cancer

Fri Feb 19, 2016
Lead author and CBCB doctoral student Mahfuza Sharmin, and CBCB faculty Hector Corrada Bravo and Sridhar Hannenhalli, have published a paper titled "Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer" on February 11, 2016 in the journal BMC Cancer. In this paper, they found that the classical promoter epigenomic mark - H3K4me3, is highly enriched at Hypomethylated Block (HMB) boundaries, as are insulator protein CTCF bound sites. HMB boundaries harbor distinct combinations of transcription factor (TF) motifs. A Random Forest machine learning model based on TF motifs can accurately distinguish boundaries not only from regions inside and outside HMBs, but surprisingly, from active promoters as well. Interestingly, the distinguishing TFs and their interacting proteins are involved in chromatin modification. Finally, HMB boundaries significantly coincide with the boundaries of Topologically Associating Domains of the chromatin. Their analyses suggest that the overall architecture of HMBs is guided by pre-existing chromatin architecture, and are associated with aberrant activity of promoter-like sequences at the boundary.

"Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer" article: https://bmccancer.biomedcentral.com/articles/10.1186/s12885-016-2128-1

CBCB scientists Senthil Kumar and Sridhar Hannenhalli publish a paper in PLOS Computational Biology on the dynamical model of CRISPR-mediated prokaryote-phage coevolution

Wed Feb 17, 2016
Lead author and CBCB doctoral student Senthil Kumar, CBCB faculty Sridhar Hannenhalli, and Dr. Plotkin of U Penn have published a paper titled “Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution” on November 6, 2015 in the journal PLOS Computational Biology. In this paper, they develop and analyze a dynamical model of CRISPR-mediated prokaryote-phage coevolution that incorporates classical CRISPR kinetics along with the recently discovered infection-induced activation and autoimmunity side effects. Their results indicate that except in limited growth rates, regulated CRISPRs exploit both autoimmunity and target restriction and can therefore be considered a hybrid class that leverages both restriction and suicide mechanisms to limit phage infection.

"Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution” article: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.10...

CBCB faculty Eytan Ruppin’s group publishes a paper in Nature Communications on Non-Alcoholic Fatty Liver Disease

Mon Feb 08, 2016

CBCB faculty Eytan Ruppin’s group has published a paper titled “Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease” on February 3, 2016 in the journal Nature Communications.

For further information, please see: https://www.cs.umd.edu/article/2016/02/researchers-steno-center-eytan-ru...

“Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease” article: http://www.nature.com/ncomms/2016/160203/ncomms9994/full/ncomms9994.html

Jeremy Selengut on Thompson's highly cited researcher list

Thu Jan 14, 2016
Dr. Jeremy Selengut has been selected by Thompson Reuters as one of the most highly cited researchers in the field of Microbiology. The "Highly Cited Researchers 2015" list includes scientists ranking among the 1% most cited in their field.

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