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jsdearbo/README.md

Jake Dearborn

PhD candidate in Molecular Biology working at the intersection of computational biology, regulatory genomics, RNA splicing, and machine learning.

I build sequence-to-function models, RNA-seq / splicing analysis pipelines, and interpretable ML workflows to study how genomic sequence encodes splicing regulation and immune-cell-specific transcript variation.

I am currently seeking roles in:

  • Computational Biology
  • Machine Learning for Genomics / Biology
  • Bioinformatics
  • Scientific ML / Research Engineering

Current focus

  • Alternative splicing regulation in immune systems
  • Fine-tuning genomic foundation models for splicing prediction
  • RNA-seq and splicing label generation pipelines
  • Attribution, motif discovery, and model interpretation
  • Reproducible analysis and training workflows for large genomics datasets

Featured work

  • Personal website — portfolio, project summaries, publications, and CV
  • sequence_to_function_model_tools — tooling for sequence-based regulatory genomics modeling
  • Selected RNA-seq / splicing analysis repositories — pipelines and analysis workflows from transcriptomics projects

Technical areas

ML / Engineering PyTorch · PyTorch Lightning · foundation model fine-tuning · interpretability · HPC / SLURM · reproducible workflows

Computational Biology RNA-seq · scRNA-seq · alternative splicing · STAR · StringTie · rMATS · regulatory genomics

Links

Notes

Most of my current work centers on RNA splicing regulation, immune transcriptomics, and interpretable deep learning for genomics.
If you're hiring in computational biology or ML for biology, feel free to reach out.

Pinned Loading

  1. sequence_to_function_model_tools sequence_to_function_model_tools Public

    Reusable tools for training, fine-tuning, evaluating, and interpreting genomic sequence-to-function models.

    Python

  2. SRA_to_BigWigs SRA_to_BigWigs Public

    Shell workflow for downloading SRA FASTQs, trimming reads, aligning to a reference genome, and generating BigWig tracks.

    Shell

  3. programmed_delayed_splicing programmed_delayed_splicing Public

    Analysis and modeling code for identifying regulatory sequence features associated with delayed splicing in immune genes.

    Python

  4. genomic_model_interpretation genomic_model_interpretation Public

    Utilities for attribution analysis, motif discovery, and visualization of genomic sequence-to-function models.

    Python

  5. variant_effect_prediction variant_effect_prediction Public

    Prototype toolkit for scoring genetic variant effects with genomic sequence-to-function models.

    Python

  6. pabpc1_borzoi_analysis pabpc1_borzoi_analysis Public

    Borzoi attribution and motif-analysis workflows for investigating PABPC1-associated regulatory sequence features.

    Python