Alan Murphy
@al-murphy.bsky.social
Postdoctoral Research Scientist, Koo lab at Cold Spring Harbor Laboratory | Deep Learning for genomics
Great work Žiga! Bit of a technical Q - "Predictions are adapted to the specific organism (human or mouse) by incorporating learned, organism-specific embeddings within these functions" - how were these embeddings learnt? During AlphaGenome training? Also how are they incorporated
July 17, 2025 at 2:26 PM
Great work Žiga! Bit of a technical Q - "Predictions are adapted to the specific organism (human or mouse) by incorporating learned, organism-specific embeddings within these functions" - how were these embeddings learnt? During AlphaGenome training? Also how are they incorporated
Completely agree these benchmarks are necessary! This is something we benchmarked against and in some settings sometimes only *just* bet even using enformer as a pretrained model when predicting epigenetic signals across cell types www.nature.com/articles/s41...
Predicting cell type-specific epigenomic profiles accounting for distal genetic effects - Nature Communications
Enformer Celltyping is a genomic deep learning model that predicts epigenetic signals in unseen cell types using distal DNA interactions and chromatin accessibility data. Here, authors show it general...
www.nature.com
February 12, 2025 at 11:16 AM
Completely agree these benchmarks are necessary! This is something we benchmarked against and in some settings sometimes only *just* bet even using enformer as a pretrained model when predicting epigenetic signals across cell types www.nature.com/articles/s41...
Great work! Did you look into how well hashFrag scales with large input windows (approaching Enformer/Borzoi receptive fields)? I'm guessing the MPRA data used in the paper must be ~200 bps?
January 29, 2025 at 11:41 AM
Great work! Did you look into how well hashFrag scales with large input windows (approaching Enformer/Borzoi receptive fields)? I'm guessing the MPRA data used in the paper must be ~200 bps?
Massive thanks to all co-authors for their work on this William Beardall, @marekrei.bsky.social, Mike Phuycharoen and Nathan Skene.
November 18, 2024 at 8:57 AM
Massive thanks to all co-authors for their work on this William Beardall, @marekrei.bsky.social, Mike Phuycharoen and Nathan Skene.
A key finding was the current limitations of such models at genetic variant effect prediction - the same as others have found, like Ioannidis & Mostafavi labs. Despite this, Enformer Celltyping can also be used to study cell type-specific genetic enrichment of complex traits.
November 18, 2024 at 8:57 AM
A key finding was the current limitations of such models at genetic variant effect prediction - the same as others have found, like Ioannidis & Mostafavi labs. Despite this, Enformer Celltyping can also be used to study cell type-specific genetic enrichment of complex traits.