Author

Ataberk Donmez

National Institutes of HealthORCID 0000-0002-4817-0637Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genetic & Genomic Medicine· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:variant calling· 3 Approach:experimental assay· 2 Organism:human· 2 Assay:long-read sequencing· 2 Research Focus:benchmarking· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Mikhail KolmogoroviD· 3 shared Anton GoretskyiD· 2 shared Asher BryantiD· 2 shared Ayşe Gökçe KeşküşiD· 2 shared Bao Quoc TraniD· 2 shared Benedict PateniD· 2 shared Brandy McNulty· 2 shared Byunggil YooiD· 2 shared

Activity by Year

2024-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersGenetic & Genomic Medicine

Mikhail KolmogorovORCID

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3 papers

Recent·Most cited

Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing

Tanveer Ahmad, Ayşe Gökçe Keşküş, Sergey S. Aganezov, Anton Goretsky, Isabel Rodriguez, Byunggil Yoo, Lisa A. Lansdon, Elena A. Repnikova, Lei Zhang, Yuelin Liu, Ataberk Donmez, Asher Bryant, Sonam Tulsyan, Jimin Park, Joshua Gardner, , Mikhail Kolmogorov

Wakhan reconstructs chromosome-scale copy number profiles of tumor genomes using long-read sequencing, showing better consistency with data than existing methods.

medRxiv · Dec 15, 2025 · PreprintGenetic & Genomic Medicine

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Ayşe Gökçe Keşküş, Asher Bryant, Tanveer Ahmad, Byunggil Yoo, Sergey S. Aganezov, Anton Goretsky, Ataberk Donmez, Lisa A. Lansdon, Isabel Rodriguez, Jimin Park, Yuelin Liu, Xiwen Cui, Joshua Gardner, Brandy McNulty, Samuel Sacco, , Mikhail Kolmogorov

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

Nature Biotechnology · Apr 4, 2025Peer-reviewedGenetic & Genomic Medicine

Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing

Ekaterina Kazantseva, Ataberk Donmez, Maria S. Frolova, Mihai Pop, Mikhail Kolmogorov

Strainy assembles and phases strain haplotypes from long-read metagenome data, outperforming existing methods in accuracy and completeness.

Nature Methods · Sep 26, 2024Peer-reviewedBioinformatics