Harvard Chan Bioinformatics Core 2021 Year-End Update

Harvard Bioinformatics Core

Happy holidays from the Harvard Chan Bioinformatics Core. We hope our annual newsletter finds you well as we continue to navigate our Covid-informed lives, communities, society and world. Some of us recently returned to the office, and pending a better understanding of the Covid omicron variant, we hope to see more Core members in the office in the new year. 

We are excited to announce the arrival of two new colleagues. Will Gammerdinger joined the training team in August after a post-doc at the Institute of Science and Technology, Austria where he studied the evolution of sexual conflict in Cyprinids. Amélie Julé joined last month following a post-doc at Boston Children’s Hospital, and comes to us with expertise in genetics and immunology. We are thrilled to have them on the team. After nine, seven and two years at the Core respectively, Rory Kirchner, Mary Piper and Joon Yoon accepted positions in industry. We thank each of them for their countless contributions and commitment to the Core, and wish them all the best in their new roles.

Our team of 13 provides bioinformatics consulting and training to investigators at the Harvard Chan School and across the Harvard community, with a focus on applications of high throughput sequencing (HTS). Through individual collaborations and ongoing relationships with Harvard Catalyst, the Harvard Chan-NIEHS Center for Environmental Health, the Harvard Center for AIDS Research (CFAR), the Dana Farber/Harvard Cancer Center (DFHCC), the Harvard Stem Cell Institute (HSCI),and Harvard Medical School (HMS), we supported 51 grant applications and 226 consult requests this year. We continued to see high demand for single cell and bulk transcriptomics support, and saw increases in requests for ATAC-seq and CUT&RUN analyses to interrogate mechanisms of gene regulation. We were excited to explore methods for long read sequence (both PacBio and Nanopore) analysis,  integration of multi-omics data (CITE-seq, scRNA/ATAC-seq, TCR/BCR profiling)  and interactive data visualization using the R-Shiny framework. We co-authored 20 and were acknowledged in 9 publications across a broad range of science, including studies of face transplant rejection, cancer, cold-induced brown/beige fat, effects of environmental exposures, clinical studies of liver disease, and more. With funding from long-time collaborators, AstraZeneca, we continued to maintain and develop the core’s open source bcbio-nextgen platform for automated HTS analysis, with a focus on cancer genomics. We released a new version that contains major updates and pipeline improvements, as well as the addition of new tools (e.g. PureCN for copy number calling). We also saw double the number of acknowledgements of bcbio-nextgen as measured by Google Scholar. Many thanks and congratulations to our team members for their fantastic work! 

The training team offered 19 workshops (all online) in 2021, and trained 666 researchers on basic data skills and HTS data analysis. This includes four workshops specifically for researchers at HSPH, marking the start of our new collaboration with the Research Platforms team to expand bioinformatics capacity at the  school. These workshops involved a close collaboration with Harvard’s FAS Research Computing “RC” group to make high performance computing more accessible to School researchers. The training materials for all these workshops are freely available. 

We once again offered 11 short, free workshops throughout the year as part of the “Current Topics in Bioinformatics” series. This series is free and open to all Harvard affiliates, and remains very popular. For the fall semester, we collaborated with the Cancer Data Sciences program at DFHCC to offer three workshops highlighting tools for single-cell analysis developed at Harvard. Last, but not least, as part of a collaboration with Harvard Catalyst, we launched a new set of video tutorials for learning R. We are excited about this learning resource that focuses on the fundamentals of R, and we hope it will help meet our community’s growing need for R skills.

We feel fortunate to be a part of the Harvard Chan community and to work with wonderful collaborators across Harvard. It has been a year of compelling science with many opportunities to grow and learn despite ongoing challenges. Wishing you all the best for 2022!