Publications by authors named "David MacAlpine"

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Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.
Kevin Moyung, Yulong Li, Heather K MacAlpine, Alexander J Hartemink, David M MacAlpine

Genome Res· December 2025

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DNA mutagenesis driven by transcription factor competition with mismatch repair.
Wei Zhu, Yuning Zhang, Harshit Sahay, Hana Wasserman, Ariel Afek, David M MacAlpine

Cell· October 2025

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Spt6-Spn1 interaction is required for RNA polymerase II association and precise nucleosome positioning along transcribed genes.
Boning Chen, Raghuvar Dronamraju, Whitney R Smith-Kinnaman, Sarah A Peck Justice, Austin J Hepperla, Heather K MacAlpine, David M MacAlpine

J Biol Chem· May 2025

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Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.
Kevin Moyung, Yulong Li, Alexander J Hartemink, David M MacAlpine

bioRxiv· May 2024

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Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase.
Boning Chen, Heather K MacAlpine, Alexander J Hartemink, David M MacAlpine

Genome Res· December 2023

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Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase.
Boning Chen, Heather K MacAlpine, Alexander J Hartemink, David M MacAlpine

bioRxiv· May 2023

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Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins.
Yulong Li, Alexander J Hartemink, David M MacAlpine

Genes (Basel)· December 2021

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Disruption of origin chromatin structure by helicase activation in the absence of DNA replication.
Rachel A Hoffman, Heather K MacAlpine, David M MacAlpine

Genes Dev· October 2021

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RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data.
Sneha Mitra, Jianling Zhong, Trung Q Tran, David M MacAlpine, Alexander J Hartemink

Nucleic Acids Res· August 2021

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Stochastic initiation of DNA replication across the human genome.
David M MacAlpine

Mol Cell· July 2021

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Linking the dynamics of chromatin occupancy and transcription with predictive models.
Trung Q Tran, Heather K MacAlpine, Vinay Tripuraneni, Sneha Mitra, David M MacAlpine

Genome Res· June 2021

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Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication.
Vinay Tripuraneni, Gonen Memisoglu, Heather K MacAlpine, Trung Q Tran, Wei Zhu, David M MacAlpine

Genome Res· May 2021

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RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy.
Sneha Mitra, Jianling Zhong, David M MacAlpine, Alexander J Hartemink

Res Comput Mol Biol· May 2020

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Capturing the primordial Kras mutation initiating urethane carcinogenesis.
Siqi Li, David M MacAlpine, Christopher M Counter

Nat Commun· April 2020

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Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork.
Mónica P Gutiérrez, Heather K MacAlpine, David M MacAlpine

Genome Res· July 2019

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Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats.
Eric J Foss, Tonibelle Gatbonton-Schwager, Adam H Thiesen, Erin Taylor, Rafael Soriano, David M MacAlpine

PLoS Genet· May 2019

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Correction to: DNA copy number evolution in Drosophila cell lines.
Hangnoh Lee, C Joel McManus, Dong-Yeon Cho, Matthew Eaton, Fioranna Renda, David MacAlpine

Genome Biol· March 2019

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Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in .
Robin L Armstrong, Taylor J R Penke, Brian D Strahl, A Gregory Matera, Daniel J McKay, David M MacAlpine

Genome Res· November 2018

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Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization.
Yating Wang, Abid Khan, Anna B Marks, Owen K Smith, Sumanprava Giri, David M MacAlpine

Nucleic Acids Res· March 2017

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Nucleosomes influence multiple steps during replication initiation.
Ishara F Azmi, Shinya Watanabe, Michael F Maloney, Sukhyun Kang, Jason A Belsky, David M MacAlpine

Elife· March 2017

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Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila.
Yulong Li, Robin L Armstrong, Robert J Duronio, David M MacAlpine

Nucleic Acids Res· September 2016

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ORChestrating the human DNA replication program.
David M MacAlpine

Proc Natl Acad Sci U S A· August 2016

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DNA replication origins-where do we begin?
Marie-Noëlle Prioleau, David M MacAlpine

Genes Dev· August 2016

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Noncoding Transcription Is a Driving Force for Nucleosome Instability in spt16 Mutant Cells.
Jianxun Feng, Haiyun Gan, Matthew L Eaton, Hui Zhou, Shuqi Li, David M MacAlpine

Mol Cell Biol· July 2016

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Mcm2-7 Is an Active Player in the DNA Replication Checkpoint Signaling Cascade via Proposed Modulation of Its DNA Gate.
Feng-Ling Tsai, Sriram Vijayraghavan, Joseph Prinz, Heather K MacAlpine, David M MacAlpine

Mol Cell Biol· June 2015

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