Ouzhang's picture
Upload folder using huggingface_hub
a80f3c0 verified
Raw
History Blame Contribute Delete
4.84 kB
@article{dealmeida2022deepstarr,
title = {DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers},
author = {de Almeida, Bernardo P. and Reiter, Franziska and Pagani, Michaela and Stark, Alexander},
journal = {Nature Genetics},
volume = {54},
pages = {613--624},
year = {2022},
doi = {10.1038/s41588-022-01048-5},
url = {https://www.nature.com/articles/s41588-022-01048-5}
}
@article{zrimec2022expressiongan,
title = {Controlling gene expression with deep generative design of regulatory DNA},
author = {Zrimec, Jan and Fu, Xiaozhi and Sheikh Muhammad, Azam and Skrekas, Christos and Jauniskis, Vykintas and Speicher, Nora K. and B{\"o}rlin, Christoph S. and Verendel, Vilhelm and Haghir Chehreghani, Morteza and Dubhashi, Devdatt and Siewers, Verena and David, Florian and Nielsen, Jens and Zelezniak, Aleksej},
journal = {Nature Communications},
volume = {13},
number = {1},
pages = {5099},
year = {2022},
doi = {10.1038/s41467-022-32818-8},
url = {https://www.nature.com/articles/s41467-022-32818-8}
}
@article{taskiran2024celltypedirected,
title = {Cell-type-directed design of synthetic enhancers},
author = {Taskiran, Ibrahim I. and Spanier, Katina I. and Dickm{\"a}nken, Hannah and Kempynck, Niklas and Pan{\v{c}}{\'i}kov{\'a}, Alexandra and Ek{\c{s}}i, Eren Can and Hulselmans, Gert and Ismail, Joy N. and Theunis, Koen and Vandepoel, Roel and Christiaens, Valerie and Mauduit, David and Aerts, Stein},
journal = {Nature},
volume = {626},
pages = {212--220},
year = {2024},
doi = {10.1038/s41586-023-06936-2},
url = {https://www.nature.com/articles/s41586-023-06936-2}
}
@article{gosai2024coda,
title = {Machine-guided design of cell-type-targeting cis-regulatory elements},
author = {Gosai, Shariq J. and Castro, Rodrigo I. and Fuentes, Natalia and Butts, John C. and Mouri, Kousuke and Alasoadura, Michael and Kales, Susan and Nguyen, Thanh Thanh L. and Noche, Ramil R. and Rao, Arya S. and Joy, Mary T. and Sabeti, Pardis C. and Reilly, Steven K. and Tewhey, Ryan},
journal = {Nature},
volume = {634},
pages = {1211--1220},
year = {2024},
doi = {10.1038/s41586-024-08070-z},
url = {https://www.nature.com/articles/s41586-024-08070-z}
}
@article{dasilva2026dnadiffusion,
title = {Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion},
author = {DaSilva, Lucas F. and Senan, Simon and Kribelbauer-Swietek, Judith F. and Patel, Zain Munir and Louis, Lithin Karmel and Reddy, Aniketh Janardhan and Gabbita, Sameer and Rosen, Jonathan D. and Nussbaum, Zach and C{\'o}rdova, C{\'e}sar Miguel Valdez and Wenteler, Aaron and Weber, Noah and Tunjic, Tin M. and Mansoldo, Martino and Khan, Talha Ahmad and Hwang, Gue-Ho and Gardeux, Vincent and Humphreys, David T. and Smith, Cameron and Bejan, Matei and Bromley, Peter and Connell, Will and Deplancke, Bart and Love, Michael I. and Wong, Emily S. and Meuleman, Wouter and Pinello, Luca},
journal = {Nature Genetics},
volume = {58},
number = {1},
pages = {180--194},
year = {2026},
doi = {10.1038/s41588-025-02441-6},
url = {https://www.nature.com/articles/s41588-025-02441-6}
}
@article{sarkar2024d3,
title = {Designing DNA With Tunable Regulatory Activity Using Score-Entropy Discrete Diffusion},
author = {Sarkar, Anirban and Kang, Yijie and Somia, Nirali and Mantilla Puccetti, Pablo and Zhou, Jessica and Nagai, Masayuki and Tang, Ziqi and Zhao, Chris and Koo, Peter K.},
journal = {bioRxiv},
year = {2024},
doi = {10.1101/2024.05.23.595630},
url = {https://www.biorxiv.org/content/10.1101/2024.05.23.595630v1},
note = {Preprint}
}
@article{wang2024drakes,
title = {Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design},
author = {Wang, Chenyu and Uehara, Masatoshi and He, Yichun and Wang, Amy and Biancalani, Tommaso and Lal, Avantika and Jaakkola, Tommi and Levine, Sergey and Wang, Hanchen and Regev, Aviv},
journal = {arXiv preprint arXiv:2410.13643},
year = {2024},
doi = {10.48550/arXiv.2410.13643},
url = {https://arxiv.org/abs/2410.13643}
}
@article{su2025atgcgen,
title = {Language Models for Controllable DNA Sequence Design},
author = {Su, Xingyu and Li, Xiner and Lin, Yuchao and Xie, Ziqian and Zhi, Degui and Ji, Shuiwang},
journal = {Transactions on Machine Learning Research},
year = {2025},
doi = {10.48550/arXiv.2507.19523},
url = {https://openreview.net/forum?id=itwnoEu60S}
}
@article{yang2025rldna,
title = {Regulatory DNA Sequence Design with Reinforcement Learning},
author = {Yang, Zhao and Su, Bing and Cao, Chuan and Wen, Ji-Rong},
journal = {arXiv preprint arXiv:2503.07981},
year = {2025},
doi = {10.48550/arXiv.2503.07981},
url = {https://arxiv.org/abs/2503.07981}
}