Author

Duncan J. Smith

New York UniversityORCID 0000-0002-0898-8629Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 8 Organism:yeast· 7 Assay:DNA methylation· 4 Assay:whole-genome sequencing· 3 Research Focus:variant calling· 2 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Research Focus:genome assembly· 1

Frequent Co-Authors

Rani Yeung· 3 shared Bertrand TheulotiD· 2 shared Daphne N. KrameriD· 2 shared Joseph OsmundsoniD· 2 shared Malik KahliiD· 2 shared Natasha C. KoussaiD· 2 shared A. C. Kim· 1 shared Amir AharoniiD· 1 shared

Activity by Year

2016-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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3 shared papersMolecular Biology

Rani Yeung

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Author profile →

8 papers

Recent·Most cited

Genome-wide mapping of helicase-generated ssDNA reveals Hrq1 activity at RNA polymerase III-transcribed genes

Shaili Regmi, Noof Alsulaiti, Daniel Darling, Anastasiya Bolgova, Bertrand Theulot, Spencer J Gray, Matthew L. Bochman, Duncan J. Smith

The paper maps helicase activity genome-wide using AID-mediated mutational footprints, revealing Hrq1's association with RNA polymerase III-transcribed genes.

bioRxiv · Aug 18, 2026 · PreprintMolecular Biology

Cruciform-forming AT/TA repeats are acted upon by structure selective endonucleases and Rad51 prior to repositioning to the nuclear periphery for repair

Jan Leendert Boer, Sara Crippen, A. C. Kim, Daphne N. Kramer, Bertrand Theulot, Daniel Dovrat, Amir Aharoni, Duncan J. Smith, Catherine H. Freudenreich

The paper shows that AT/TA repeats form DNA structures that are processed by nucleases and repositioned to the nuclear periphery for repair.

Nucleic Acids Research · Feb 24, 2026Peer-reviewedGenetics

Limiting DNA polymerase delta alters replication dynamics and leads to a dependence on checkpoint activation and recombination-mediated DNA repair

Natasha C. Koussa, Duncan J. Smith

This study shows that reducing DNA polymerase delta in yeast causes replication stress, genome instability, and reliance on repair pathways.

PLoS Genetics · Jan 25, 2021Peer-reviewedMolecular Biology

Separable, Ctf4-mediated recruitment of DNA Polymerase α for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation

Sarina Y. Porcella, Natasha C. Koussa, Colin P. Tang, Daphne N. Kramer, Priyanka Srivastava, Duncan J. Smith

The paper investigates the role of DNA Polymerase α and Ctf4 in DNA replication initiation and lagging-strand priming in S. cerevisiae, showing distinct sensitivities to Ctf4 and Pol levels.

PLoS Genetics · May 7, 2020Peer-reviewedMolecular Biology

The impediment to replication at tRNA genes in S. cerevisiae does not require tRNA transcription, and is facilitated by topoisomerases and Rad18-dependent repair pathways

Rani Yeung, Duncan J. Smith

The study shows that tRNA gene replication fork pausing in yeast is not due to transcription but involves topoisomerases and Rad18 repair, even when transcription is blocked.

bioRxiv · Jan 29, 2020 · PreprintMolecular Biology

Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replication in vivo

Malik Kahli, Joseph Osmundson, Rani Yeung, Duncan J. Smith

The paper investigates the roles of Rad27, Dna2, and Exo1 in processing Okazaki fragments in vivo, showing Rad27's primary role and the uncoupling of nuclease activity from DNA replication.

Nucleic Acids Research · Nov 30, 2018Peer-reviewedMolecular Biology

Transcription drives DNA replication initiation and termination in human cells

Yu-Hung Chen, Sarah Keegan, Malik Kahli, Peter Tonzi, David Fenyö, Tony T. Huang, Duncan J. Smith

This study shows that DNA replication initiation and termination in human cells are coupled with transcription, with initiation near transcription start sites and termination at polyadenylation sites.

bioRxiv · May 16, 2018 · PreprintMolecular Biology

Pif1-family helicases cooperate to suppress widespread replication fork arrest at tRNA genes

Joseph Osmundson, Jayashree Kumar, Rani Yeung, Duncan J. Smith

The paper investigates the roles of Pif1 and Rrm3 helicases in suppressing replication fork arrest at tRNA genes in yeast.

Nature Structural & Molecular Biology · Dec 19, 2016Peer-reviewedMolecular Biology