Harvard Chan Bioinformatics Core (HBC): 2024 Highlights
As we wrap up another eventful year, we’re excited to share some of the key developments and highlights from the Bioinformatics Core in 2024, which was marked by new collaborations, team members, and initiatives to better serve our community.
Welcome and Welcome Back!
We were delighted to welcome four new members to our team this year. A special mention of Lorena Pantano, who rejoined us after five years in the biotech industry. As Director of Platforms, Lorena is spearheading our shift to nf-core and Nextflow pipelines to modernize our automated, scalable tools and ensure reproducibility in high throughput sequencing data analysis. Her insight and expertise in genomic and data visualization are valuable assets to our core’s mission.
This work prompted a major transition for the core, as we announced the retirement of bcbio, an open-source platform for automated analysis that we launched in 2011 and which had begun to show its age. While bcbio continues to be used globally and was cited in 82 publications this year, we are focusing our efforts on transitioning our community to newer nf-core pipelines that are more efficient and easier to deploy and monitor. It’s a bittersweet farewell as we look toward these new horizons.
Also joining us were Upendra Bhattarai, bringing expertise in genome assembly and transcriptomics, Alex Bartlett with a focus on non-coding RNA analysis and Nextflow development, and Elizabeth Partan, specializing in cancer genetics and biostatistics. We were thrilled to announce two internal promotions. Meeta Mistry is now the Associate Director of the core, leading the training program with creativity and drive, and James Billingsley was promoted to Senior Research Scientist, continuing his impactful work within the HU Center for AIDS Research.
Growing Our Training Program
Our training team successfully launched several new workshops and modules. We introduced “Differential Expression of Single Cell RNA-seq“, “Peak Analysis“, and “Variant Analysis”; a new module focused on R Shiny app development; and a series entitled “Big Data? Big Computer! The Skill Set You Need to Succeed”, which was met with great interest with nearly 100 attending across Harvard. We established a collaboration with the DFCI Department of Data Science, offering a workshop focused on single cell RNA-seq data pre-processing led by Jeremy Simon, and co-hosted our Fall Seminar Series on Novel Applications in Single Cell Omics with the DF/HCC Cancer Data Sciences Program to enrich our offerings with advanced topics. We’re thrilled to have received commendations from the NIH for our open-source training materials, a testament to the hard work and dedication of our team.
Enabling Research
Along with ongoing demand for bulk and single cell transcriptomic analysis, we saw an increase in requests for spatial transcriptomics support, including projects using Stereo-seq, Xenium, Visium HD and Merscope platforms. Our core received 217 requests for bioinformatics support this year, including 59 requests for grant support. Core members coauthored 18 publications spanning diverse research areas including bioinformatics tools, developmental biology, environmental health, immunology, cancer research, stem cell maturation, and neurological studies. We are grateful for the opportunities to learn and collaborate within such an inspiring environment and look forward to what the coming year holds.
Building Community
We continued to engage with researchers in Harvard’s vibrant bioinformatics ecosystem and beyond. The core hosted three popular Bioinformatics Community Breakfasts to connect with experimentalists, other core facilities, and bioinformaticians across campus. We took advantage of opportunities to present our work at ISMB, the Nextflow Summit, and EMBL-EBI’s Managing a Bioinformatics Core workshop, and returned from these meetings with new ideas and knowledge.
Many thanks and congratulations to our team members for their fantastic work and to our collaborators for involving us in their exciting projects. Wishing you all a wonderful holiday season and a happy new year!
Warm regards,
The Harvard Chan Bioinformatics Core Team
