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Nucleotide Dependency Analysis of Genomic Language Models Detects Functional Elements

Nature Genetics 57. Oct. 2025

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Scooby: Modeling Multi-Modal Genomic Profiles From DNA Sequence at Single-Cell Resolution

Nature Methods. Oct. 2025

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Flashzoi: An Enhanced Borzoi for Accelerated Genomic Analysis

Bioinformatics 41.9. Sep. 2025

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Orthrus: A Pumilio-Family Gene Involved in Fruiting Body and Dark Stipe Development in Coprinopsis Cinerea

Frontiers in Fungal Biology 6. Jul. 2025

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Altered Translation Elongation Contributes to Key Hallmarks of Aging in the Killifish Brain

Science 389.6759. Jul. 2025

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Nucleotide Dependency Analysis of DNA Language Models Reveals Genomic Functional Elements

CSHL 2025

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Flashzoi: An Enhanced Borzoi Model for Accelerated Genomic Analysis

Preprint (Dec. 2024)

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Integration of Variant Annotations Using Deep Set Networks Boosts Rare Variant Association Testing

Nature Genetics 56. Sep. 2024

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Species-Aware DNA Language Models Capture Regulatory Elements and Their Evolution

Genome Biology 35.83. Apr. 2024

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Cellular Energy Regulates MRNA Translation and Degradation in a Codon-Specific Manner

Molecular Systems Biology 20.5. Mar. 2024

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Impaired Biogenesis of Basic Proteins Impacts Multiple Hallmarks of the Aging Brain

Preprint (Jan. 2024)

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Evaluation of Input Data Modality Choices on Functional Gene Embeddings

NAR Genomics and Bioinformatics 5.4. Dec. 2023

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