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Mission

The University of Maryland Center for Bioinformatics and Computational Biology is a multidisciplinary center dedicated to research on questions arising from the genome revolution. CBCB brings together scientists and engineers from many fields, including computer science, molecular biology, genomics, genetics, mathematics, statistics, and physics, all of whom share a common interest in gaining a better understanding of how life works.

The Center for Bioinformatics and Computational Biology is a joint effort between the College of Chemical and Life Sciences and the College of Mathematical, Computer, and Physical Sciences,and is organized as a center within the University of Maryland Institute for Advanced Computer Studies (UMIACS).

Research Spotlight: Genome Assembly with Short Reads

High-throughput sequencing technologies are providing small research labs with a sequencing capacity similar to what was previously only available at large genome centers. CBCB researchers are supporting this sequencing "revolution" through the development of software tools for the assembly and analysis of the data generated by the new technologies. Click here to find out more about our software and our current research in this area. The recent availability of high-throughput sequencing technologies has "democratized" genome sequencing by providing individual labs with a sequencing capacity similar to what was previously only available at large genome centers. read more »

Scientific Findings

Oct. 9, 2008. Scientists publish the genome of the human malaria parasite Plasmodium vivax, which is responsible for 25–40% of the $approx$ 515 million annual cases of malaria worldwide. The study led by NYU's Jane Carlton included CBCB scientist Steven Salzberg and graduate student Sam Angiuoli as co-authors, and appeared in the journal Nature.

Link to Nature article

Story at ScienceDaily

Sept. 2008. CBCB scientists publish a new method for assembling a bacterial genome from very short "next-gen" sequencing data, and describe its application to a new strain of the bacterium Pseudomonas aeruginosa.

Link to PLoS Computational Biology article

July 2008. A Nature special section on human and avian influenza features this commentary by Steven Salzberg proposing greater openness in the process of designing the flu vaccine each year.

Link to Nature editor's summary
Reprint of article

May 2008. CBCB scientists led a consortium that published the complete genome of the bacterium Xanthomonas oryzae pv. oryzae, which causes bacterial blight in rice. The international collaboration include 35 scientists from the U.S., Japan, India, France, and Ireland.

Link to BMC Genomics article

April 24, 2008. Scientists this week published a description of the papaya tree's genome in the journal Nature, the first transgenic crop ever to have its genome sequenced. The "SunUp" papaya plant includes an artificially inserted virus protein that confers resistance to papaya ringspot virus. The collaboration included CBCB scientists Salzberg, Schatz, Nagarajan, Delcher, and Mount.

Link to Nature article

March 10, 2008. CBCB scientists Schatz, Trapnell, Delcher and Varshney publish MUMmerGPU, a short-read mapping program. MUMmerGPU uses the graphics processing unit (GPU) in a desktop PC to map short reads to a reference genome up to 10-fold faster than conventional CPU-based programs.

Link to BMC Bioinformatics article

November 8, 2007. The Drosophila 12 Genomes Consortium publishes its analysis of 12 species of the fruit fly Drosophila in the journal Nature. The Consortium, led by Prof. Andrew Clark of Cornell University, includes CBCB scientists Delcher, Mount, Salzberg, Schatz, Yorke, and Zimin.

Link to Nature article

September 21, 2007. An international team of researchers, including seven CBCB scientists, reveal the genetic make-up of the parasite Brugia malayi, a tiny worm tha causes elephantiasis and river blindness. The WHO estimates that more than 40 million people have been disfigured by this parasite and over 150 million people are infected, primarily in Southeast Asia and Indonesia. The genome project, published in the September 21 issue of the journal Science, is an important towards discovering vaccines and therapies against this debilitating disease.

Link to Science article

July 27, 2007. CBCB scientists have provided a compelling explanation for a pattern in the position of overlapping and closely spaced genes in prokaryotes. The analysis appears in the journal Molecular Biology and Evolution.

Link to MBE article

June 22, 2007. Genome sequence of mosquito that carries the yellow fever and dengue fever viruses published in Science. Three CBCB scientists - M. Pertea, M. Schatz, and S. Salzberg - contributed to this landmark study.

Link to Science article
Comment: A breakthrough for global public health

May 18, 2007. CBCB scientists publish details of a new computational method for DNA signature discovery in the journal PLoS Computational Biology.

Link to PLoS article

April 17, 2007. CBCB scientists lead a study that discovered 3 new strains of avian influenza ("bird flu") which developed as the flu moved into European countries. The study, which included scientists from 11 different countries as co-authors, appears in the May issue of the journal Emerging Infectious Diseases.

...press release

Link to EID article

March 9, 2007. CBCB researchers have three papers in the current issue of the journal Genome Biology. These include a paper on prediction of transcription terminators, another on the Hawkeye genome assembly visualization tool, and an opinion piece on genome re-annotation.

January 12, 2007. Researchers decode genome of the parasite that causes trichomoniasis, a sexually transmitted diseas that infects 170 million people annually worldwide. The genome analysis of Trichomonas vaginalis, led by Prof. Jane Carlton of NYU in partnership with a team that includes four CBCB scientists, appears in the 12 January issue of Science.

...press release

Link to Science article

...news archive

Job Opportunities

Address and directions

Center for Bioinformatics and Computational Biology
3115 Biomolecular Sciences Building #296
University of Maryland
College Park, MD 20742

Tel: 301.405.5936
Fax: 301.314.1341

Directions

CBCB News & Events

Sept. 24, 2008. CBCB faculty member Mihai Pop receives funding from NIH for a new R01 basic research grant, "Assembly and analysis software for exploring the human microbiome". This award is part of the Human Microbiome Project an NIH Roadmap initiative aimed at characterizing the microbial communities inhabiting the human body.
Sept. 2, 2008. Liliana Florea, who works on sequence alignment and comparative genome analysis, joins CBCB and UMIACS as an Assistant Research Scientist.
Sept. 2008. CBCB scientists receive $445,358 grant from the National Science Foundation. Mihai Pop and Carl Kingsford will develop new algorithms for extracting information on genomic variation from genome assembly graphs. This research will provide the computational infrastructure for analyzing the genomic diversity present in bacterial and viral communities.
Dec. 2007. Steven Salzberg is recognized as one of BioMedCentral's "Hot 100 authors". The Hot 100 list includes authors who have played key roles in supporting open access journals by publishing their research and acting as reviewers.
Dec. 19, 2007. CBCB faculty member Mihai Pop receives funding from the Bill and Melinda Gates Foundation as part of a large project to develop tools for the rapid diagnosis of diarrheal disease in third world countries. The study is led by James Nataro from the University of Maryland School of Medicine (see press release) Dr. Pop's research will focus on new computational methods for uncovering the bacteria causing this disease.
Sept. 16-20, 2007. The 15th Annual Conference on Microbial Genomics was held on the UMD campus in College Park.
Jul. 1, 2007. Carl Kingsford, who works on algorithms for understanding biological data, joins CBCB and the University of Maryland faculty as an Assistant Professor in the Department of Computer Science.
Jun. 8, 2007. Mihai Pop has been invited to give a keynote address at the "Finishing in the Future" conference held in Santa Fe, NM, June 18-20, 2007. The conference is co-organized by Los Alamos National Laboratory and the Joint Genome Institute of the US Department of Energy.
Oct. 23, 2006. Najib El-Sayed, an expert on the genomics of parasitic diseases, joins CBCB and the University of Maryland faculty as an Associate Professor in the Department of Cell Biology and Molecular Genetics.
June 13, 2006. New web interfaces released for three CBCB projects: Insignia, TransTermHP , SeeEse , and Operon .
Mar 29, 2006. Scientific American's podcast includes an interview with the CBCB director calling for open sharing of avian influenza data. See also the Canadian Press news service interview with CBCB Director on this topic, reported on 12 March.
Mar. 8 and Jan. 4, 2006. Science and Society's hosts discuss genomics, influenza, and other topics with Steven Salzberg. Hear the Mar 8 interview or the Jan 4 interview online, or download the podcasts.
Dec. 11, 2005. StudioJ broadcasts an interview on Sirius satellite radio of CBCB Director Salzberg's interview on evolution, intelligent design, and the flu. (Listen to the mp3 recording.)
Nov. 2, 2005. Steven Salzberg published editorial in the Philadelphia Inquirer on the topics of evolution and the influenza virus. (Read the article.)
UMIACS Calendar of Events

...news archive

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