Author

Ahmed Daoud

Colorado State UniversityORCID 0009-0004-6172-0543Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 2 Approach:deep learning· 2 Assay:DNA methylation· 2 Research Focus:gene regulatory network inference· 2 Organism:Arabidopsis· 1 Research Focus:benchmarking· 1 Research Focus:differential expression· 1 Assay:Hi-C· 1

Frequent Co-Authors

Asa Ben‐HuriD· 2 shared A. Sathyanarayana ReddyiD· 1 shared Haoxuan ZengiD· 1 shared Jiakang Wang· 1 shared Jie LiuiD· 1 shared Paul Duclos Parodi· 1 shared Soumyadip RoyiD· 1 shared Xinyu BaoiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

9 top collaborators · 36 mutual co-author links

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2 shared papersGenomics

Asa Ben‐HurORCID

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2 papers

Recent·Most cited

GenomicsbioRxivPreprintApr 9, 2026

Deep-Plant: a supervised foundation model for plant regulatory genomics

Ahmed Daoud, Soumyadip Roy, Haoxuan Zeng…·Asa Ben‐Hur

This paper introduces a supervised foundation model for plant regulatory genomics that predicts chromatin state from genomic sequence, showing improved speed, accuracy, and interpretability over DNA language models.

DOI 10.64898/2026.04.06.716755

Arabidopsisrat

𝕏 PostBluesky

BioinformaticsPLoS Computational BiologyPeer-reviewedJan 10, 2025

The role of chromatin state in intron retention: a case study in leveraging large scale deep learning models

Ahmed Daoud, Asa Ben‐Hur

The paper uses large-scale deep learning models to study intron retention, showing that chromatin state plays a key role in its regulation.

6 citations

DNA methylationChIP-seq

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