David Kelley
@drkbio.bsky.social
Making sophisticated guesses at how DNA will behave.
Excited to share our new paper on predicting gene expression in yeast! We introduce "Shorkie," a supervised ML model that builds off a self-supervised foundation to interpret regulatory DNA.
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
Predicting dynamic expression patterns in budding yeast with a fungal DNA language model
Predicting gene expression from DNA sequence remains challenging due to complex regulatory codes. We introduce a masked DNA language model pretrained on 165 fungal genomes closely related to budding y...
www.biorxiv.org
October 13, 2025 at 11:06 PM
Excited to share our new paper on predicting gene expression in yeast! We introduce "Shorkie," a supervised ML model that builds off a self-supervised foundation to interpret regulatory DNA.
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
The poster abstract deadline for the @keystonesymposia.bsky.social AI in Molecular Biology meeting in Santa Fe is coming up on August 21st, so get your submissions in!
www.keystonesymposia.org/conferences/...
www.keystonesymposia.org/conferences/...
AI in Molecular Biology | Keystone Symposia
Join us at the Keystone Symposia on AI in Molecular Biology, September 2025, in Santa Fe, with field leaders!
www.keystonesymposia.org
August 4, 2025 at 11:50 AM
The poster abstract deadline for the @keystonesymposia.bsky.social AI in Molecular Biology meeting in Santa Fe is coming up on August 21st, so get your submissions in!
www.keystonesymposia.org/conferences/...
www.keystonesymposia.org/conferences/...
We’re excited to share a follow-up Borzoi training run and an analysis of the capabilities that emerged. www.biorxiv.org/content/10.1...
Predicting cell type-specific coverage profiles from DNA sequence
Predicting expression profiles from RNA-seq experiments provides a powerful approach for universal sequence-based variant effect prediction, enabling researchers to score variants that affect total ge...
www.biorxiv.org
July 23, 2025 at 4:22 PM
We’re excited to share a follow-up Borzoi training run and an analysis of the capabilities that emerged. www.biorxiv.org/content/10.1...
I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...
Borzoi-informed fine mapping improves causal variant prioritization in complex trait GWAS
Genome-wide association studies (GWAS) have identified thousands of trait-associated loci. Prioritizing causal variants within these loci is critical for characterizing trait biology. Statistical fine...
www.biorxiv.org
July 21, 2025 at 2:51 PM
I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...
Reposted by David Kelley
1/ DNA sequence models like Borzoi predict gene expression and variant effects across tissues — but how can someone adapt the model to a custom experiment? @drkbio.bsky.social, Johannes Linder and I propose a solution via parameter-efficient fine-tuning (PEFT).
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Parameter-Efficient Fine-Tuning of a Supervised Regulatory Sequence Model
DNA sequence deep learning models accurately predict epigenetic and transcriptional profiles, enabling analysis of gene regulation and genetic variant effects. While large-scale training models like E...
www.biorxiv.org
June 2, 2025 at 8:09 PM
1/ DNA sequence models like Borzoi predict gene expression and variant effects across tissues — but how can someone adapt the model to a custom experiment? @drkbio.bsky.social, Johannes Linder and I propose a solution via parameter-efficient fine-tuning (PEFT).
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The short talk and scholarship deadlines for the
@keystonesymposia.bsky.social
AI in Molecular Biology meeting in September were extended to June 3, so get your last minute submissions in! www.keystonesymposia.org/conferences/...
@keystonesymposia.bsky.social
AI in Molecular Biology meeting in September were extended to June 3, so get your last minute submissions in! www.keystonesymposia.org/conferences/...
AI in Molecular Biology | Keystone Symposia
Join us at the Keystone Symposia on AI in Molecular Biology, September 2025, in Santa Fe, with field leaders!
www.keystonesymposia.org
June 1, 2025 at 6:17 PM
The short talk and scholarship deadlines for the
@keystonesymposia.bsky.social
AI in Molecular Biology meeting in September were extended to June 3, so get your last minute submissions in! www.keystonesymposia.org/conferences/...
@keystonesymposia.bsky.social
AI in Molecular Biology meeting in September were extended to June 3, so get your last minute submissions in! www.keystonesymposia.org/conferences/...
The short talk and scholarship deadlines for the @keystonesymposia.bsky.social AI in Molecular Biology meeting in September are coming up fast, May 20th. Looking forward to seeing the submissions! www.keystonesymposia.org/conferences/...
May 11, 2025 at 9:29 PM
The short talk and scholarship deadlines for the @keystonesymposia.bsky.social AI in Molecular Biology meeting in September are coming up fast, May 20th. Looking forward to seeing the submissions! www.keystonesymposia.org/conferences/...
Working with a great team to organize
@keystonesymposia.bsky.social AI in MolecularBiology, this September! We aimed for a wide range of biological topics, and emphasized speakers who blend sophisticated machine learning with compelling biological questions and analysis.
@keystonesymposia.bsky.social AI in MolecularBiology, this September! We aimed for a wide range of biological topics, and emphasized speakers who blend sophisticated machine learning with compelling biological questions and analysis.
April 20, 2025 at 6:16 PM
Working with a great team to organize
@keystonesymposia.bsky.social AI in MolecularBiology, this September! We aimed for a wide range of biological topics, and emphasized speakers who blend sophisticated machine learning with compelling biological questions and analysis.
@keystonesymposia.bsky.social AI in MolecularBiology, this September! We aimed for a wide range of biological topics, and emphasized speakers who blend sophisticated machine learning with compelling biological questions and analysis.
Regulatory sequence ML has been widely applied to predict substitution SNP effects (to promising results!), but most teams have shied away from indels. www.biorxiv.org/content/10.1...
Shift augmentation improves DNA convolutional neural network indel effect predictions
Determining genetic variant effects on molecular phenotypes like gene expression is a task of paramount importance to medical genetics. DNA convolutional neural networks (CNNs) attain state-of-the-art...
www.biorxiv.org
April 17, 2025 at 12:39 AM
Regulatory sequence ML has been widely applied to predict substitution SNP effects (to promising results!), but most teams have shied away from indels. www.biorxiv.org/content/10.1...