Jesus Gonzalez Ferrer

PhD candidate at UC Santa Cruz

Graduate Researcher · Braingeneers, UC Santa Cruz

I work in the Braingeneers group with David Haussler and Mohammed Mostajo-Radji, and part-time at Genentech in the AIBT group. Previously M.Sc. in Computational Biology (Universidad Politécnica de Madrid) and B.Sc. in Biotechnology (Universidad Miguel Hernández).

Jesus Gonzalez Ferrer

I am a PhD candidate in Bioinformatics & Bioengineering at UC Santa Cruz, working in the Braingeneers group with David Haussler and Mohammed Mostajo-Radji. Before Santa Cruz, I completed an M.Sc. in Computational Biology at the Universidad Politécnica de Madrid and a B.Sc. in Biotechnology at the Universidad Miguel Hernández.

My work sits at the intersection of genomics, neuroscience and deep learning. I build computational tools for single-cell data — including SIMS, a deep-learning label-transfer method for scRNA-seq — and develop models for neural electrophysiology, from variational autoencoders for spike data to studying protosequences and cell-fate plasticity in human cortical organoids. Broadly, I want to use machine learning to understand how the brain develops and computes.

Selected News

  1. 2026

    Paper Our work on preconfigured neuronal firing sequences in human brain organoids is out in Nature Neuroscience.

    Nature Neuroscience
  2. 2026

    Preprint New preprint: CytoVerse runs single-cell AI foundation models entirely in the browser, searching 20M+ reference cells while keeping data private.

    bioRxivGitHub
  3. 2025

    Preprint Released HIPPIE, a multimodal deep-learning model for the electrophysiological classification of neurons.

    PaperGitHub
  4. 2025

    Paper A perspective on automated, explainable high-throughput perturbation analysis in single cells is out in Patterns.

    Patterns
  5. 2025

    Paper Our study of the fate plasticity of interneuron specification was published in iScience.

    iScience
  6. 2024

    Paper SIMS, our deep-learning label-transfer tool for single-cell RNA-seq, was published in Cell Genomics.

    Cell GenomicsGitHub

Selected Publications

Full list on Google Scholar. (*) denotes equal contribution.

  1. Neuroscience

    Preconfigured neuronal firing sequences in human brain organoids

    van der Molen, T., Spaeth, A., Chini, M., Hernandez, S., Kaurala, G. A., Gonzalez-Ferrer, J., et al.

    Nature Neuroscience, 29(1), 123–135, 2026.

    Paper
  2. GenomicsDeep Learning

    SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis

    Gonzalez-Ferrer, J., Lehrer, J., O'Farrell, A., Paten, B., Teodorescu, M., Haussler, D., … & Mostajo-Radji, M. A.

    Cell Genomics, 4(6), 2024.

    PaperGitHub
  3. NeuroscienceDeep Learning

    HIPPIE: A multimodal deep learning model for electrophysiological classification of neurons

    Gonzalez-Ferrer, J., Lehrer, J., Schweiger, H. E., Geng, J., Hernandez, S., … & Mostajo-Radji, M. A.

    bioRxiv, 2025.

    PaperGitHub
  4. GenomicsDeep Learning

    Toward automated and explainable high-throughput perturbation analysis in single cells

    Gonzalez-Ferrer, J. & Mostajo-Radji, M. A.

    Patterns, 6(4), 2025.

    Paper
  5. NeuroscienceGenomics

    Fate plasticity of interneuron specification

    Mostajo-Radji, M. A., Leon, W. R. M., Breevoort, A., Gonzalez-Ferrer, J., … & Pollen, A. A.

    iScience, 28(4), 2025.

    Paper
  6. GenomicsTools

    CytoVerse: Single-cell AI foundation models in the browser

    Currie, R., Gonzalez-Ferrer, J., Mostajo-Radji, M. A. & Haussler, D.

    bioRxiv, 2026.

    PreprintGitHub
  7. Tools

    Internet-enabled lab-on-a-chip technology for education

    Sano, T., Sampad, M. J. N., Gonzalez-Ferrer, J., et al.

    Scientific Reports, 14, 14364, 2024.

    Paper

Writing

Notes on neuroscience, genomics and ML on The Brainformatician.

All posts →