The Bioinformatics Core Facility in the MGH Molecular Biology Department offers computational and analytic resources to all members of the department and on a consulting basis to researchers outside the department. The Bioinformatics group offers state of the art data processing and analysis in all areas of computational biology, including sequence analysis, gene expression, custom software applications, machine learning, classification, and other algorithms necessary to advance fundamental biomedical research.
We collaborate with researchers on projects in all stages of discovery, from initial development and grant writing to experimental analysis. As both biologists and computer scientists, we enjoy talking through your research questions and providing additional insights into your data. Our analysis techniques incorporate existing algorithms into custom pipelines and visualization frameworks, ranging from unique commandline scripts and programmers toolkits to web-based display environments.
The Bioinformatics Core provides informatics services and data anlysis in many areas. One area of focus is support for the Illumina Genome Analyzer II high throughput sequencer available to the department. The team has extensive expertise in gene and genome sequencing and sequence analysis, working with sequence data produced by all major sequencing platforms from ABI sequencing platforms to the range of "next generation" sequencing methods such as Illumina and 454.
Joint leadership of the Bioinformatics and Sequencing cores ensures tight integration of sequencing with downstream informatics analysis. Our work spans the full range of biological applications including genome resequencing, small RNA discovery, RIP-seq, ChIP-seq and mRNA-seq on organisms as diverse as mice, plants and bacteria.
The informatics group is supported by extensive computational infrastructure at MGH and Partners, including an on-site data center and systems team, a compute farm with over 200 CPUs, 32 terabytes of high-performance memory, a high speed data network, and licenses to commercially available analysis software applications.
Mark Borowsky leads the Molecular Biology bioinformatics team and co-directs the Illumina sequencing core. His ten years in computational biology include experience in gene expression analysis, comparative genomics, genome sequencing, annotation, and machine learning. His current research focus is genomic analysis of drug resistant Mycobacterium tuberculosis. Prior to MGH, Mark worked at the Broad Institute from 2003-2008 and at Incyte Corporation from 1999-2003. Mark earned a bachelors degree in Biochemistry and Molecular Biology at Harvard, a Ph.D. in biology at MIT, and did postdoctoral work on the bacterial pathogen Listeria monocytogenes at University of California at Berkeley.
Toshiro Ohsumi develops fast, memory efficient algorithms for sequencing alignment, ChIP-seq, polymorphism detection, and other data- processing applications for next-generation sequencer data, primarily in C++0x. His current research focus is on developing a C++0x framework for common sequence tasks and develop new algorithms for polymorphism detection and ChIP-Seq binding location prediction. Prior to MGH, Toshiro has worked at the Broad Institute as a computational biologist and Colgate University as an assistant professor of computer science. Toshiro earned a B.A. in mathematics and physics (University of California at Santa Cruz), a M.A. in applied mathematics (University of California at Irvine), and a Ph.D. in computer science (Rensselaer Polytechnic Institute) on efficiently solving time-dependent partial differential equations in moving domains arising in simulating formation and healing of artificial and natural [biphasic] tissue.
Brad's background in wet-lab research is now applied to answering computational problems. He uses scripting languages to tie data presentation and visualization with high-throughput analyses. Brad is also involved in the open source community as a member of Biopython and regularly contributes other open source code to GitHub and Bitbucket. Brad has a PhD in plant biology from the University of Georgia.
John shares time between the Molecular Biology Department and a collaborative large-scale effort to understand inflammation following injury. As a long time member of the MGH research community, he combines expert database administration experience with his programming and biology knowledge to provide custom analysis pipelines.
Please contact Mark Borowsky (borowsky at molbio.mgh.harvard.edu) to discuss your research goals.