Pablo Eduardo Garcia-Nieto

Staff Data Scientist in Life Scientist at Biohub

Ph.D. Computational Biology. Stanford University

My work sits at the intersection of large-scale omics data, tool development, and scientific partnerships, translating advanced computational methods into tools and programs that help researchers move faster.

Some highlights of my career include:

Scaling single-cell biology at the Biohub. Technical lead for the Billion Cells Project, supporting labs generating millions of single-cell transcriptomic profiles.
AI-driven drug discovery at insitro. Worked with wet-lab teams to refine experimental strategies and integrate computational insights into decision-making for clinical programs.
Building tools for the single-cell community. _Led the development of products within the CELLxGENE ecosystem, my team’s work enbabled the development of the first transformer-based models in transcriptomics (scGPT, Geneformer and Universal Cell Embeddings).

I obtained my Ph.D in molecular and computational biology from Stanford University, in the labs of Hunter Fraser and Ashby Morrison. My research focused on understanding the somatic mutation landscape in the human body and the molecular mechanisms underlying DNA damage and mutagenesis in a cohort of >500 human donors. My publication in the journal Genome Biology was selected as the top discovery of 2019 from the journal’s collection “Tweanty years with Genome Biology”

selected publications

bioRxiv

CZ CELL×GENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data

CZI Single-Cell Biology Program, Shibla Abdulla, Brian Aevermann, and 51 more authors

bioRxiv, 2023

DOI Bib HTML

@article{cellxgene2023,
  title = {{CZ} {CELL}×{GENE} Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data},
  author = {Program, CZI Single-Cell Biology and Abdulla, Shibla and Aevermann, Brian and Assis, Pedro and Badajoz, Seve and Bell, Sidney M. and Bezzi, Emanuele and Cakir, Batuhan and Chaffer, Jim and Chambers, Signe and Cherry, J. Michael and Chi, Tiffany and Chien, Jennifer and Dorman, Leah and Garcia-Nieto, Pablo and Gloria, Nayib and Hastie, Mim and Hegeman, Daniel and Hilton, Jason and Huang, Timmy and Infeld, Amanda and Istrate, Ana-Maria and Jelic, Ivana and Katsuya, Kuni and Kim, Yang Joon and Liang, Karen and Lin, Mike and Lombardo, Maximilian and Marshall, Bailey and Martin, Bruce and McDade, Fran and Megill, Colin and Patel, Nikhil and Predeus, Alexander and Raymor, Brian and Robatmili, Behnam and Rogers, Dave and Rutherford, Erica and Sadgat, Dana and Shin, Andrew and Small, Corinn and Smith, Trent and Sridharan, Prathap and Tarashansky, Alexander and Tavares, Norbert and Thomas, Harley and Tolopko, Andrew and Urisko, Meghan and Yan, Joyce and Yeretssian, Garabet and Zamanian, Jennifer and Mani, Arathi and Cool, Jonah and Carr, Ambrose},
  journal = {bioRxiv},
  year = {2023},
  doi = {10.1101/2023.10.30.563174},
}

Genome Biol

The somatic mutation landscape of the human body

Pablo E. Garcia-Nieto, Ashby J. Morrison, and Hunter B. Fraser

Genome Biology, 2019

Bib HTML

@article{garciani2019somatic,
  title = {The somatic mutation landscape of the human body},
  author = {Garcia-Nieto, Pablo E. and Morrison, Ashby J. and Fraser, Hunter B.},
  journal = {Genome Biology},
  year = {2019},
}

EMBO J

Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis

Pablo E. Garcia-Nieto, Erin K. Schwartz, Devin A. King, and 4 more authors

The EMBO Journal, 2017

Bib HTML

@article{garciani2017carcinogen,
  title = {Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis},
  author = {Garcia-Nieto, Pablo E. and Schwartz, Erin K. and King, Devin A. and Paulsen, Jonas and Collas, Philippe and Herrera, Rafael E. and Morrison, Ashby J.},
  journal = {The EMBO Journal},
  year = {2017},
}