Harvard Chan Bioinformatics Core – 2016 Summary

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The Harvard Chan Bioinformatics Core had another productive year under the leadership of Shannan Ho Sui. We were excited to recruit Dr. Victor Barrera from Madrid with his expertise in epigenetics and pipeline automation, and to celebrate the promotion of Dr. John Hutchinson from a Research Associate to Research Scientist. We continued to provide bioinformatics consulting services to Harvard-affiliated investigators through individual collaborations as well as through our ongoing relationships with Harvard Catalyst, the Harvard Stem Cell Institute (HSCI), Harvard Medical School Tools and Technology (TnT), the Harvard NeuroDiscovery Center (HNDC), the National Institutes for Environmental Health Sciences (NIEHS), and the Center for AIDS Research (CFAR). This year, our consultants collaborated on 13 papers published in Nature, Molecular Cell, Science Immunology, Environmental Health Perspectives, Cancer Research, Genome Research, Blood, Cell, Stem Cell Reports, the Journal of Virology, Nucleic Acids Research and PLoS Computational Biology. We supported several grant applications including three R01 awards and a K01 award.

Our training team continued to offer our popular short courses and in-depth workshops focused on empowering researchers to perform their own analyses. These included four introductory Unix and two introductory R workshops, and three two-month long workshops focused on best practices in next generation sequence analysis for RNA-seq, ChIP-seq and variant calling. We were involved in three Catalyst workshops including the week-long Flagship ‘Omics course. This year, we hosted our first intern from the Human Heredity and Health in Africa (H3Africa) Initiative, Shaun Aron, who spent three months working in Dr. Liming Liang’s group exploring the complex historical events that have shaped the evolutionary history of Ghanaian genomes.

The core continued development of the bcbio platform (https://bcbio-nextgen.readthedocs.io) with Harvard and industry partners. Bcbio is a python toolkit that provides best-practice pipelines for fully automated high throughput sequence analysis for germline and cancer variant calling, structural variation, RNA-seq, small RNA-seq and ChIP-seq analysis. This year, we improved our quality control reporting and implemented a single cell analysis pipeline in collaboration with the new InDrop Single Cell Core at HMS (Dr. Allon Klein and Dr. Sarah Boswell). We are currently expanding bcbio to also include a module for digital gene expression (DGE) analysis in collaboration with the Laboratory of Systems Pharmacology and ICCB at HMS.