David R. Kelley

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Teaching an old dog new cells

  Nature Methods · 2026-05-25

• Sequence design for three-dimensional genome folding using Akita Semifreddo

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-30

• A PyTorch implementation of the AkitaV2 deep learning model for predicting contact matrices from DNA sequences.

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

• A PyTorch implementation of the AkitaV2 deep learning model for predicting contact matrices from DNA sequences.

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

• Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts

  Genome biology · 2026-01-30 · 1 citations

• Baskerville Release (with Transfer scripts)

  Zenodo (CERN European Organization for Nuclear Research) · 2025-12-25

• Baskerville Release (with Transfer scripts)

  Zenodo (CERN European Organization for Nuclear Research) · 2025-12-25 · 1 citations

• Predicting dynamic expression patterns in budding yeast with a fungal DNA language modelPreprint

  Research Square · 2025-10-14 · 1 citations

• Predicting dynamic expression patterns in budding yeast with a fungal DNA language modelPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-21

• Borzoi-informed fine mapping improves causal variant prioritization in complex trait GWASPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-14 · 2 citations

• Predicting cell type-specific coverage profiles from DNA sequencePreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-11 · 2 citations

• Parameter-Efficient Fine-Tuning of a Supervised Regulatory Sequence ModelPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-30 · 9 citations

• Rewriting regulatory DNA to dissect and reprogram gene expression

  Cell · 2025-04-16 · 22 citations

• Shift augmentation improves DNA convolutional neural network indel effect predictionsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-11 · 2 citations

• Selective State Space Models Outperform Transformers at Predicting RNA-Seq Read CoveragePreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-17 · 4 citations

• Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2

  PLoS Computational Biology · 2025-02-04 · 7 citations

• Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation

  Nature Genetics · 2025-01-08 · 172 citations

• How to build the virtual cell with artificial intelligence: Priorities and opportunities

  Cell · 2024-12-01 · 288 citations

• Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2Preprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-08-04 · 1 citations