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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
CBCB involved in new Tobacco Center of Regulatory Science (TCORS)
The University of Maryland has been awarded by the Federal Drug Administration and the National Institutes of Health an approximately $19 million dollar award to create a new University of Maryland Tobacco Center of Regulatory Science (UM TCORS). This Center will be one of 14 centers nationwide that will provide the FDA with scientific support for its regulation of tobacco products. CBCB faculty Mihai Pop together with UMIACS director Amitabh Varshney will help manage and analyze the vast amounts of data generated in this project by their colleagues in the UM School of Public Health, UM School of Medicine, George Mason University, and Battelle.
For more information about this project see:
Zia Khan and colleagues publish Science paper on the evolution of protein expression
CBCB faculty Zia Khan is the first author on a new study appearing in the journal Science. Prof. Khan's work, performed in his prior position at the University of Chicago, demonstrates that protein levels are more strongly conserved during evolution than the levels of the transcripts from which these proteins are translated. While this observation makes sense - proteins are the workhorse in cells and their levels must be tightly controlled - Prof. Khan's work is the first to disentangle the experimental noise from biological signal, thereby conclusively demonstrating this effect. A more detailed perspective on this study, written by Christine Vogel appeared in the same Science issue under the title Protein Expression Under Pressure .
Eytan Ruppin Named CBCB Director
Dr. Ruppin will become Director in July 2014. He is currently a professor in the Schools of Computer Science and Medicine at Tel-Aviv University.
Zia Khan Joins CBCB Faculty
Zia Khan will be joining as an Assistant Professor in the Department of Computer Science, UMIACS, and the Center for Bioinformatics and Computational Biology (CBCB) in December of 2013. Read more
CBCB Announces Illumina Support for Summer Internship Program
The Center for Bioinformatics and Computational Biology (CBCB) today announced that Illumina will provide financial support to its summer internship program (http://www.cbcb.umd.edu/summer-internships).
The goal of the summer internship program is to provide hands-on research experience in bioinformatics to talented undergraduate students as part of ongoing research projects within the CBCB. The program involves full-time research in addition to the expectation for students to participate in broader research activities at CBCB. At the conclusion of the summer internship, each student prepares a report outlining the results of the project and gives a presentation at the center’s “Research in Progress” series describing their work, thus additionally helping students improve their presentation skills.
We are especially proud to announce that one of our interns from 2013 – Emily Jones, won the prestigious NSF Graduate Research Fellowship award, based on her summer project, which was in part supported by Illumina. See (https://www.cs.umd.edu/article/2014/04/emily-jones-and-matt-mccutchen-aw...) for the full story.
“We are thrilled to have Illumina’s conitued support for this important program,” said Dr. Sridhar Hannenhalli, Director of the CBCB summer internship program. “Not only will this provide unique exposure to the field of bioinformatics to talented undergraduates, it will also excite them about the unique career opportunities in this important field. We hope to expand this partnership in future.” added Dr. Hannenhalli.
CBCB develops three new packages for the Bioconductor project
The Center for Bioinformatics and Computational Biology (CBCB) has developed three new packages for the Bioconductor project, a premier open-source software system for bioinformatics and computational biology.
'metagenomeSeq' contains tools for finding associations between microbial communities and clinical outcomes in large metagenomic surveys. It was developed as a collaboration between Mihai Pop's and Hector Corrada Bravo's labs at CBCB.
The other two packages - 'antiProfiles' for creating accurate and robust gene expression signatures in cancer and 'bumphunter' for the discovery of spatial genomic features from high-throughput data - were developed by Hector Corrada Bravo in collaboration with the Johns Hopkins University School of Public Health.
Hector Corrada Bravo and collaborators released healthvis this week. healthvis.org
Hector Corrada Bravo and collaborators released healthvis this week. The latest version of the Bioconductor project, the premier open-source software system for Bioinformatics and Computational Biology tools, was released in April. This version includes three new packages developed at CBCB. metagenomeSeq contains tools for finding associations between microbial communities and clinical outcomes in large metagenomic surveys and was developed as a collaboration of the Pop and Corrada Bravo labs at CBCB. The other two packages are 'antiProfiles' for creating accurate and robust gene expression signatures in cancer and 'bumphunter' for the discovery of spatial genomic features from high-throughput data. The latter two were developed by the Corrada Bravo lab in collaboration with the Johns Hopkins School of Public Health. View at:
http://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html
http://bioconductor.org/packages/release/bioc/html/antiProfiles.html
http://bioconductor.org/packages/release/bioc/html/bumphunter.html
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