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
June 5, 2009.   CBCB graduate student Michael Schatz, in collaboration with researchers from the USDA Bee Lab, Columbia University, and 454 Life Sciences, published the draft genome sequence of the honey bee fungal pathogen Nosema ceranae. This fungus is belived to be an agent in honey bee colony collapse disorder, and the genome sequence will aid in understanding this disease and the development of treatments.
Link to PLoS Pathogens article (open access)
May 14, 2009.  CBCB scientist Rita Colwell and colleagues publish a review of the new scientific discipline of microbial oceanography - the study of the ocean as "a habitat for the evolution and regulation of microbial-based processes and their ecological consequences" - in the journal Nature.
Link to Nature article
April 24, 2009.  CBCB scientists, jointly with scientists from the USDA, publish the genome of the domestic cow, Bos taurus.  The cow genome contains 2.86 billion bases spread across 30 chromosomes.  The new paper, in the journal Genome Biology, describes how the genome was assembled and presents in greater detail than previously how the cow genome can be mapped onto the human genome.  In addition, a Bowtie index is now available for rapid mapping of short reads to the new Bos taurus genome.
Link to Genome Biology article (open access)
April 10, 2009.  CBCB scientists publish a paper in PLoS Computational Biology describing a new statistical method for comparing metagenomic data-sets in a clinical setting. Their method, Metastats, allows scientists to compare two treatment populations (e.g. sick and healthy patients), each comprised of multiple samples, in order to determine individual features (organisms, genes, or pathways) that explain the difference between the two populations.
Link to PLoS Computational Biology article (open access)
Link to metastats web portal and source code
April 8, 2009.  Mike Schatz, a graduate student in Computer Science, and a member of the CBCB, publishes a paper in the journal Bioinformatics describing the use of Cloud Computing (highly-parallel computing infrastructure available through the internet) to speed up sequence alignment algorithms. His program CloudBurst, available open-source from http://cloudburst-bio.sourceforge.net can achieve speed-ups of up to 100-fold over current alignment programs.
Link to Bioinformatics article (open access)
Link to other research on high-performance computing within the CBCB
March 4, 2009.  CBCB scientists publish a paper  in Genome Biology describing Bowtie, a new and extremely fast system for aligning short DNA sequences to the human genome or to other large genomes.  Bowtie's innovative use of the Burrows-Wheeler Transform allows it to run many times faster than other leading short-read aligners, and its remarkably small memory footprint allows users to run it on a standard desktop or laptop computer.
Link to Genome Biology article (open access)
January 2009.   The 2009 database issue of the journal Nucleic Acids Research features two CBCB databases: OperonDB - a database of predicted operons in microbial genomes; and ARDB - a database of antibiotic resistance genes.
Oct. 9, 2008.  Scientists publish the genome of the human malaria parasite Plasmodium vivax, which is responsible for 25–40% of the approx515 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.
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.

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.

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.

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

  • April 2009.   Mihai Pop and Steven Salzberg receive a basic research grant from the National Science Foundation to study the application of massively-parallel computation (a paradigm termed Cloud Computing) to the analysis of next generation sequencing data. Their project titled "Algorithms for the analysis of data from massively-parallel genome sequencing" is funded under the NSF Cluster Exploratory (CluE) initiative that supports data-intensive research using computational resources provided by IBM and Google.

    Link to NSF press release
    Link to UM press release
    Link to interview with Mihai Pop, the PI of this study

  • Jan. 2009.  Steven Salzberg and Jim Yorke (Mathematics and IPST) receive $906,098 basic research grant from the US Department of Agriculture for a project titled, "Assembly and Annotation of Agricultural Genomes."  This research will support re-assembly of the cow genome, and assembly and annotation of species such as turkey, water buffalo, and pig.
...news archive