Harvard Chan Bioinformatics Core: Year-End Update 2022

hbc logoWarm holiday greetings from the Harvard Chan Bioinformatics Core (HCBC). We are excited to report what our team has been up to in 2022!

Personnel changes: We are thrilled that Dr. Emma Berdan has joined our team from the University of Gothenberg, Sweden as a Research Scientist. Emma’s research focuses on evolutionary genomics, and she brings with her extensive expertise in transcriptomics, variant analysis, and methods for linking phenotype with genotype. We bid farewell to Dr. John Hutchinson and Dr. Preetida Bhetariya with deep thanks for their many contributions to the core and across Harvard. John is now a Principal Scientist at the Altius Institute and Preeti joined the Dana Farber Cancer Institute as a Bioinformatics Scientist. We wish them well in their new positions!

Research output: Our team of 12 provides bioinformatics consulting and education to investigators at the Harvard Chan School and across the Harvard community, focusing on applications of high throughput sequencing (HTS). The HCBC works with investigators on bioinformatics analyses, grant preparation, study design, publications, functional analysis and other bioinformatic project needs, and runs a bioinformatics training initiative for the Harvard community. Our core received 270 inquiries this year, including 58 requests for grant support (21%). We continued to see high demand for transcriptomics analysis (bulk, single cell and small RNA-seq), methods that interrogate chromatin biology (ChIP-seq, CUT&RUN and ATAC-seq), and variant analysis from whole genomes, exomes and panels. This year saw an increase in requests for multi-omics data integration and spatial transcriptomics analysis. Our team co-authored or was acknowledged in 28 publications in 2022, across a broad range of science including immunology, fibrosis, cancer, cardiovascular disease, Parkinson’s, and stem cell research.

Training updates: The HCBC teaching team offered 23 training workshops on Zoom in 2022 and hopes to return to in-person training in 2023. Workshops included five 1/2 day sessions as part of the popular Current Topics in Bioinformatics series, which averaged 88 Harvard-wide registrants per workshop. The teaching team offered a new chromatin biology workshop, expanding the ChIP-seq workshop to include CUT&RUN and ATAC-seq. We will continue to develop training materials as methods are tested and validated to make them accessible to the community. HCBC training materials are freely available and designed for self-learning.

Infrastructure: We continued to maintain and develop the core’s open source bcbio-nextgen platform for automated HTS analysis. According to Google Scholar, bcbio-nextgen was cited in 111  publications from around the world in 2022. We’re honored, once again, to receive a Chan Zuckerberg Initiative (CZI) grant from the CZI Essential Open Source Software for Science program. This grant will enable us to provide community support and ongoing maintenance of bcbio-nextgen’s pipelines.

In the coming year, we will continue our work as part of the Longwood Medical Area data management working group (LMA-DMWG) to ensure compliance with NIH’s new Data Management and Sharing Policy.

Many thanks and congratulations to our team members for their fantastic work! We feel fortunate to be a part of the Biostatistics community at the Harvard Chan School, and to work with wonderful collaborators across Harvard in a year of compelling science with many opportunities to grow and learn. Wishing you all the best for 2023!