Author

Onur Yukselen

University of Massachusetts Chan Medical School

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Developmental Biology· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Assay:bulk RNA-seq· 2 Organism:C. elegans· 2 Approach:statistical model· 2 Assay:ATAC-seq· 1 Research Focus:cell type annotation· 1 Assay:ChIP-seq· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Alper KüçükuraliD· 5 shared Manuel G. GarberiD· 4 shared Ahmet Rasit OzturkiD· 1 shared Albertha J.M. WalhoutiD· 1 shared Alexandra Elisabeth SchneideriD· 1 shared Blair K. Schneider· 1 shared Colin C. ConineiD· 1 shared Deniz Mahmut ÖzataiD· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

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5 shared papersDevelopmental Biology

Alper KüçükuralORCID

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5 papers

Recent·Most cited

tRNA-derived RNA processing in sperm transmits non-genetically inherited phenotypes to offspring in C. elegans

Nikoletta Galambos, Olivia J Crocker, Blair K. Schneider, Kennelly S. Allerton, Katrin E. Gross, Alexandra Elisabeth Schneider, Jared Lynch, Onur Yukselen, Alper Küçükural, Colin C. Conine

The paper shows that tRNA-derived RNAs (tDRs) in sperm of C. elegans can transmit epigenetic phenotypes to offspring through RNaseT2-mediated regulation of tDR length.

Nature Communications · Mar 15, 2026Peer-reviewedDevelopmental Biology

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

Hefei Zhang, Xuhang Li, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Küçükural, Jingyi Jessica Li, Manuel G. Garber, Albertha J.M. Walhout

The paper introduces Worm Perturb-Seq (WPS) to perform high-resolution RNA-seq on perturbed C. elegans, identifying gene regulatory networks and showing pairwise modularity in nuclear hormone receptor regulation.

Nature Communications · May 22, 2025Peer-reviewedGenomics

An atlas of cell types in the mammalian epididymis and vas deferens

Vera D. Rinaldi, Elisa R. Donnard, Kyle J. Gellatly, Morten Rasmussen, Alper Küçükural, Onur Yukselen, Manuel G. Garber, Upasna Sharma, Oliver J. Rando

The paper creates a single-cell atlas of the murine epididymis and vas deferens, identifying cell types and their regional specialization, and revealing potential signaling networks.

eLife · Jul 30, 2020Peer-reviewedDevelopmental Biology

DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

Onur Yukselen, Osman Türkyılmaz, Ahmet Rasit Ozturk, Manuel G. Garber, Alper Küçükural

DolphinNext provides a graphical interface for creating, deploying, and executing Nextflow pipelines to improve reproducibility and portability in genomic data analysis.

BMC Genomics · Apr 19, 2020Peer-reviewedBioinformatics

DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data

Alper Küçükural, Onur Yukselen, Deniz Mahmut Özata, Melissa J. Moore, Manuel G. Garber

DEBrowser provides an interactive tool for differential expression analysis of count data without programming skills, demonstrating its capabilities on published datasets.

BMC Genomics · Jan 5, 2019Peer-reviewedBioinformatics