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Director, Bioinformatics Platform · Harvard Chan School
Lorena Pantano
I build tools and platforms that turn complex genomic data into clear insights. 13+ years spanning biotech, pharma, and academia — from RNA biology to AI-driven target discovery.
Podcast Host
Women in Bioinformatics
Nextflow Maintainer
Portfolio
Featured Work
Open-source tools, platforms, and dashboards built for research and personal use.
Single-Cell RNA-Seq Analysis Reports
Code templates and training materials for single-cell RNA-seq downstream analysis
Spatial Transcriptomics Analysis Reports
Template repository for spatial single-cell transcriptomics data analysis workflows
Experience
Career Journey
Director, Bioinformatics Platform
Harvard Chan Bioinformatics Core- Lead and manage bioinformatics products to keep genomic, transcriptomic, and omics analysis platforms reliable, efficient, and scalable.
- Guide and mentor bioinformaticians, fostering collaboration and innovation.
- Consult with researchers and external collaborators to align platforms with bioinformatics needs.
- Oversee quality assurance and documentation to ensure analysis accuracy and reproducibility.
Director, Head of Computational Biology
NextRNA Therapeutics- Shaped company strategy for genomics data and sequencing assays as member of executive leadership.
- Directed in-silico target discovery and validation, integrating NGS technologies with advanced visualizations.
- Built an RNA structure and RNA–protein interaction AI engine using SHAPE-Seq and eCLIP-Seq data.
- Managed cloud infrastructure to ensure reproducibility and scalability.
Principal Scientist, Computational Biology
Axcella Health- Led R&D pipelines and visualization platforms for multi-omics data.
- Applied machine learning to understand population stratification in pre-clinical studies.
- Built cloud bioinformatics infrastructure for reproducibility and scale.
Senior Computational Biologist
eGenesis Bio- Managed internal NGS teams using Oxford Nanopore and Illumina platforms.
- Researched epigenetic marks to improve transgene expression with machine learning.
- Built QA/QC genomic platforms and multi-omics pipelines.
Research Scientist
Harvard Chan School- Led bioinformatics for a cross-organ fibrosis collaboration with Boehringer Ingelheim.
- Developed scalable, reproducible platforms for NGS data (small RNA-seq, RNA-seq, ChIP-seq, WGS).
Research Associate
Harvard Chan School- Built tools for NGS analysis (small RNA-seq, scRNA-seq, ChIP-seq, WGS) in bcbio-nextgen and Bioconductor.
- Developed visualization and integration of multi-omics data.
Post-doctoral Fellow
Institute of Biotechnology and Biomedicine- Identified de novo transcripts associated with inversions in the HapMap population.
- Performed expression quantitative trait loci analyses of inversions.
Post-doctoral Fellow
Institute of Predictive and Personalized Medicine of Cancer- Characterized small RNAs in human sperm samples.
Writing
View all posts
Posts
From R Shiny to Production: How We Built a Clinical Calculator for a Nature Medicine Paper
How we rebuilt PANGEA-SMM's R Shiny prototype into a production React + R Plumber web app — deployed on Netlify and GCP — for a Nature Medicine publication.
What the Cancer Data Isn't Telling You
Cancer charts show similar numbers for colon and breast cancer. But adding one variable—sex—reveals a completely different story about who is actually affected.
Multi-Lab Genomics Data Sharing with IGV, S3, and GitHub Actions
How to build collaborative research infrastructure using IGV, format conversion, and GitHub Actions automation—without a dedicated development team.
Why I Built My Own Running Dashboard
Fitness apps show weekly summaries but miss the real story. I built a dashboard to track months of running data and discovered what actually drives progress.
Systematic Paper Reviews with Claude Custom Commands
Custom AI commands ensure consistent scientific paper reviews. Learn to automate any repeated workflow while maintaining quality and thoroughness through systematic evaluation.
Bringing IGV webapp to Your Cloud Workspace in Seqera
Run IGV directly in your cloud workspace with automatic track discovery. Eliminate downloads and view genomic data where it lives. Open source proof of concept for Seqera Platform users.
Talks
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Speaking
2025
Unified, community-developed analysis guidelines and templates for multi-omics data interpretability
Biomedical research generates complex, large-scale data that presents challenges in manipulation, storage, distribution, and analysis, particularly for non-comp…
2025
Lorena Pantano: Unified, community-developed analysis guidelines and templates for multi-omics data interpretability
As part of the panel discussion 'Managing Data Analyses with Nextflow and nf-core in Bioinformatics Core Facilities,' I presented our current project, bcbio-rep…
2024
BaWIB X BWCB joint meetup! Leveraging Mentorship Through Career Hurdles
I had the privilege of participating in a panel discussion with [Boahemaa Adu-Oppong](https://www.linkedin.com/in/badu-oppong/?lipi=urn%3Ali%3Apage%3Ad_flagship…
2024
Lorena Pantano: Transitioning through the nf-core era at the Harvard Chan Bioinformatics Core
The Harvard Chan Bioinformatics Core is dedicated to fostering collaboration within the Life Sciences, aiming to expedite research endeavors using innovative an…
2021
Women in Life Sciences: How do we Close the Gender Gap in Leadership?
With a global push in recent years to encourage young women toward careers in STEM, the life sciences have benefited enormously from more inclusive priorities a…
2021
Inside a Bioinformatics Startup – with NextRNA Therapeutics
In this podcast, Rob Lalonde of Seqera Labs speaks with Lorena Pantano, head of Computational Biology at NextRNA, a firm leading the next revolution in RNA-dire…
2019
miRNA variants (isomiRs): real molecules or sequencing artifacts?
Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. In the last year, a few papers have poin…
2018
MiRNA Wars: The isomiRs menance
BIG
MicroRNAs (miRNAs) are small RNA molecules (~22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing techno…
2018
miRTOP: An open source community project for the development of a unified format file for miRNA data
Bioinformatics Open Source Conference 2018
MicroRNAs (miRNAs) are small RNA molecules (20-27 nt long) that are involved in eukaryotic gene regulation. They regulate targeted genes by RNA complementarity…
2016
Characterization of the small RNA transcriptome using the bcbio-nextgen python framework
Bioinformatics Open Source Conference 2016
The study of small RNA helps us understand some of the complexity of gene regulation of a cell. Of the different types of small RNAs, the most important in mamm…
Publications
Research Papers
35+ peer-reviewed publications in bioinformatics, genomics, and computational biology. View full list on Google Scholar →