. . . .

The HSPH Center for Health Bioinformatics

The Harvard School of Public Health is taking a leading role in interdisciplinary research involving the computational analysis of complex relationships between genes and their environment as well as basic biological and quantitative sciences. The CHB is integral to the development and application of computational biology methods at the School, providing support in all aspects of data storage and management, data analysis (sequencing, array, biological context), and methods development. It works closely with the Research Computing Group at the Faculty of Arts and Sciences who provide world-class computational support. As part of the Center for Stem Cell Bioinformatics CHB extends its services to members of the HSCI community.

The team

The Center is led by Winston Hide, an Associate Professor of Bioinformatics and Computational Biology in the Department of Biostatistics at Harvard School of Public Health where he drives development of public health bioinformatics addressing genomic approaches to public health in the developed and developing worlds. He founded and directed the South African National Bioinformatics Institute (SANBI) near Cape Town. With over 20 years of experience in computational biology, his expertise addresses integration of ‘omics data to deliver clinical translation. He uses standardized approaches to disease gene discovery in stem cells and cancer stem cells, host response to pathogens, and complex diseases.

Oliver Hofmann is a Senior Research Scientist in the Department of Biostatistics at HSPH, an Affiliated Faculty member of the HSCI and the Associate Director of the Center. He has worked in a molecular biology wetlab environment before switching to natural language processing, database development and curation as part of his PhD thesis, eventually branching out to sequence clustering and pattern recognition as a visiting researcher at deCODE Genetics. His work as a postdoctoral fellow at the South African National Bioinformatics Institute focused on data integration (eVOC ontology), second-generation sequencing analysis and network analysis.

His current research focuses on stem cell biology and integrating heterogeneous data sources to provide biological context to results obtained from high throughput experiments. He can be found on Twitter and blogs about workshops and conferences. Oliver has a PhD in Biochemistry from the University of Cologne, Germany.

Brad Chapman has spent more than 10 years answering biological questions with computational approaches after switching over from a background in wet-lab research. He combines automated high-throughput analysis pipelines with custom visualization and processing tools. By utilizing a wide variety of languages, he strives to maximize code re-use while maintaining the flexibility to answer highly-specific collaborative questions.

Brad is involved in the open source community as a member of the Biopython and CloudBioLinux projects, as well as contributing regularly to freely available GitHub and Bitbucket repositories. He posts about his research on BCBio and can be found on Twitter as chapmanb. He has a PhD in plant biology from the University of Georgia.

Shannan Ho Sui is a Research Scientist in the Department of Biostatistics at the Harvard School of Public Health and an Affiliated Faculty member of the HSCI. Her expertise includes data integration, next generation sequence analysis, transcriptional gene regulation, stem cell biology, pathogen bioinformatics, and anti-infective drug discovery. She developed the oPOSSUM system, a web-based analysis platform for identifying putative transcriptional regulators from gene expression data, and led the development of the HSCI Stem Cell Discovery Engine to facilitate molecular comparisons of stem cell experiments. Her current research focuses on analytical approaches for stem cell data integration and identifying cell population specific markers during differentiation. This has resulted in her playing a key role in the creation of the HSCI Stem Cell Commons – an initiative to promote open exchange of stem cell data and analysis tools. Shannan has a PhD in Genetics from the University of British Columbia.

John Hutchinson is a research associate in the Department of Biostatistics at the Harvard School of Public Health and coordinating the bioinformatics consulting efforts for the Harvard Stem Cell Institute. He has a background in academia, and transitioned from the wet lab to computational approaches during his postdoctoral training. He has pursued research in fields ranging from breast cancer biology to the role of epigenetics in allele-specific transcription. He enjoys to adapting standard technologies and public data to novel uses, most recently adapting Affymetrix SNP6.0 arrays to detect allele-specific methylation.

His work at the Whitehead Institute, Massachusetts General Hospital and Brigham and Women’s Hospital familiarized him with many members of the research community in Boston. His background as both a molecular biologist and bioinformatician serve him well in translating basic biological questions into practical bioinformatic approaches.

Rory Kirchner is a visiting research fellow with a background in engineering combined with five years of research in RNA-Seq in neurobiology at MIT, providing him with the skillset to tackle novel biomedical problems with different quantitative approaches.

Meeta Mistry is a research associate in the Department of Biostatistics at the Harvard School of Public Health. Her training began in Biochemistry, however postgraduate interests in computational approaches fostered the transition to Bioinformatics. During her graduate career she has pursued various areas of research including the identification of bacterial drug targets, implementing metrics for functional similarity, and cancer proteomics. Her expertise includes complex statistical analysis of large-scale datasets pertaining to postmortem human brain, meta-analysis and genomics of neuropsychiatry. She also has a passion for teaching bioinformatics with experience at the highschool, graduate and postgraduate level. Her current role involves both bioinformatics consulting and training efforts. Meeta has a PhD in Bioinformatics from the University of British Columbia.

The Center is supported by Rachel Boschetto (Grants manager) and Meagan Plante (Project manager).

Collaborations

CHB collaborates with bioinformatics cores and research groups to provide you with an optimal service. We work closely with our colleagues in the Department of Biostatistics and the Program in Quantitative Genomics. The CHB is a member of the Environmental Statistics and Bioinformatics Core at the Harvard NIEHS Center for Environmental Health and the Genetics & Bioinformatics Consulting group for Harvard Catalyst. It provides dedicated support to the Harvard NeuroDiscovery Center and the Harvard Medical School community through the Tools and Technology group.

Additional partners include the Center for Cancer Computational Biology (DFCI), the Bioinformatics & Research Computing group (Whitehead) and the Galaxy team. All computational resources are located at the FAS Research Computing Center.

Stay in touch

Join the BioBioComp Google Group to discuss and learn more about bioinformatics, computational biology and related events in the community.