From f1a412295d6614dd2c0a3ab7396fb636c6616993 Mon Sep 17 00:00:00 2001 From: Gonzalo Benegas Date: Wed, 9 Sep 2026 12:04:29 -0400 Subject: [PATCH] Update GPN-Star citation to Nature --- README.md | 18 +++++++++--------- docs/index.md | 2 +- docs/models/gpn-star.md | 2 +- docs/models/index.md | 2 +- docs/reference/citations.md | 14 +++++++------- 5 files changed, 19 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 637ad03..4778b53 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ ![GPN-Star architecture, evolutionary scales, and genomic prediction tasks](docs/_static/gpn_star_overview.png) -Code and resources for genomic language models [GPN](https://doi.org/10.1073/pnas.2311219120), [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w), [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) and [GPN-Star](https://doi.org/10.1101/2025.09.21.677619). +Code and resources for genomic language models [GPN](https://doi.org/10.1073/pnas.2311219120), [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w), [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) and [GPN-Star](https://www.nature.com/articles/s41586-026-11005-5). ## Quick start @@ -38,7 +38,7 @@ Explore the [GPN-Star models, alignments, scores, and benchmark datasets](https: | [GPN](https://gpn.readthedocs.io/en/latest/models/gpn/) | [Benegas et al. 2023](https://doi.org/10.1073/pnas.2311219120) | Requires unaligned genomes | | [GPN-MSA](https://gpn.readthedocs.io/en/latest/models/gpn-msa/) | [Benegas et al. 2025](https://www.nature.com/articles/s41587-024-02511-w) | Requires aligned genomes for training and inference; deprecated in favor of GPN-Star | | [PhyloGPN](https://gpn.readthedocs.io/en/latest/models/phylogpn/) | [Albors et al. 2025](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) | Uses an alignment during training, but does not require it for inference or fine-tuning | -| [GPN-Star](https://gpn.readthedocs.io/en/latest/models/gpn-star/) | [Ye et al. 2025](https://doi.org/10.1101/2025.09.21.677619) | Requires aligned genomes for training and inference | +| [GPN-Star](https://gpn.readthedocs.io/en/latest/models/gpn-star/) | [Ye et al. 2026](https://www.nature.com/articles/s41586-026-11005-5) | Requires aligned genomes for training and inference | ## Command line @@ -116,16 +116,16 @@ GPN is developed in the [Song Lab at UC Berkeley](https://people.eecs.berkeley.e } ``` -[GPN-Star](https://doi.org/10.1101/2025.09.21.677619): +[GPN-Star](https://www.nature.com/articles/s41586-026-11005-5): ```bibtex -@article{ye2025predicting, - title={Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models}, +@article{ye2026predicting, + title={Predicting genome-wide functional constraints with GPN-Star}, author={Ye, Chengzhong and Benegas, Gonzalo and Albors, Carlos and Li, Jianan Canal and Prillo, Sebastian and Fields, Peter D and Clarke, Brian and Song, Yun S}, - journal={bioRxiv}, - pages={2025--09}, - year={2025}, - publisher={Cold Spring Harbor Laboratory} + journal={Nature}, + pages={1--10}, + year={2026}, + publisher={Nature Publishing Group} } ``` diff --git a/docs/index.md b/docs/index.md index 52332d0..39497c5 100644 --- a/docs/index.md +++ b/docs/index.md @@ -8,7 +8,7 @@ myst: # GPN -Code and resources for genomic language models [GPN](https://doi.org/10.1073/pnas.2311219120), [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w), [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) and [GPN-Star](https://doi.org/10.1101/2025.09.21.677619). +Code and resources for genomic language models [GPN](https://doi.org/10.1073/pnas.2311219120), [GPN-MSA](https://www.nature.com/articles/s41587-024-02511-w), [PhyloGPN](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) and [GPN-Star](https://www.nature.com/articles/s41586-026-11005-5). diff --git a/docs/models/gpn-star.md b/docs/models/gpn-star.md index 0e105a5..fe8c945 100644 --- a/docs/models/gpn-star.md +++ b/docs/models/gpn-star.md @@ -24,7 +24,7 @@ recipe lives in ## Published assets The [GPN-Star collection](https://huggingface.co/collections/songlab/gpn-star-68c0c055acc2ee51d5c4f129) -accompanies the [bioRxiv paper](https://doi.org/10.1101/2025.09.21.677619). +accompanies the [Nature paper](https://www.nature.com/articles/s41586-026-11005-5). ### Alignments and scores diff --git a/docs/models/index.md b/docs/models/index.md index 6d541e6..42c1740 100644 --- a/docs/models/index.md +++ b/docs/models/index.md @@ -8,7 +8,7 @@ inputs and modeling objectives. | {doc}`GPN ` | [Benegas et al. 2023](https://doi.org/10.1073/pnas.2311219120) | Requires unaligned genomes | | {doc}`GPN-MSA ` | [Benegas et al. 2025](https://www.nature.com/articles/s41587-024-02511-w) | Requires aligned genomes for training and inference; deprecated in favor of GPN-Star | | {doc}`PhyloGPN ` | [Albors et al. 2025](https://link.springer.com/chapter/10.1007/978-3-031-90252-9_7) | Uses an alignment during training, but does not require it for inference or fine-tuning | -| {doc}`GPN-Star ` | [Ye et al. 2025](https://doi.org/10.1101/2025.09.21.677619) | Requires aligned genomes for training and inference | +| {doc}`GPN-Star ` | [Ye et al. 2026](https://www.nature.com/articles/s41586-026-11005-5) | Requires aligned genomes for training and inference | ## Maintained support diff --git a/docs/reference/citations.md b/docs/reference/citations.md index 5b4e9a7..bed8dfa 100644 --- a/docs/reference/citations.md +++ b/docs/reference/citations.md @@ -43,16 +43,16 @@ Please cite the paper for each model or fine-tuned application you use. } ``` -## [GPN-Star](https://doi.org/10.1101/2025.09.21.677619) +## [GPN-Star](https://www.nature.com/articles/s41586-026-11005-5) ```bibtex -@article{ye2025predicting, - title={Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models}, +@article{ye2026predicting, + title={Predicting genome-wide functional constraints with GPN-Star}, author={Ye, Chengzhong and Benegas, Gonzalo and Albors, Carlos and Li, Jianan Canal and Prillo, Sebastian and Fields, Peter D and Clarke, Brian and Song, Yun S}, - journal={bioRxiv}, - pages={2025--09}, - year={2025}, - publisher={Cold Spring Harbor Laboratory} + journal={Nature}, + pages={1--10}, + year={2026}, + publisher={Nature Publishing Group} } ```