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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

First Published December 9, 2025

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

First Published December 11, 2023

Analyzing rare mutations in metagenomes assembled using long and accurate reads

Marcus W. Fedarko
Mikhail Kolmogorov
Pavel A. Pevzner

First Published November 23, 2022

Fast and accurate mapping of long reads to complete genome assemblies with VerityMap

Andrey V. Bzikadze
Alla Mikheenko
Pavel A. Pevzner

First Published November 15, 2022

Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data

Kaixuan Luo
Jianling Zhong
Alexias Safi
Linda K. Hong
Alok K. Tewari
Lingyun Song
... [+1 authors] ...,
Timothy E. Reddy
Li Ma
Gregory E. Crawford
Alexander J. Hartemink

First Published May 24, 2022

Automated annotation of human centromeres with HORmon

Olga Kunyavskaya
Tatiana Dvorkina
Andrey V. Bzikadze
Ivan A. Alexandrov
Pavel A. Pevzner

First Published May 11, 2022

Gene prediction in the immunoglobulin loci

Vikram Sirupurapu
Yana Safonova
Pavel A. Pevzner

First Published May 11, 2022

Variations in antibody repertoires correlate with vaccine responses

Yana Safonova
Sung Bong Shin
Luke Kramer
James Reecy
Corey T. Watson
Timothy P.L. Smith
Pavel A. Pevzner

First Published March 31, 2022

Linking the dynamics of chromatin occupancy and transcription with predictive models

Trung Q. Tran
Heather K. MacAlpine
Vinay Tripuraneni
Sneha Mitra
David M. MacAlpine
Alexander J. Hartemink

First Published April 23, 2021

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
Alexander J. Hartemink
James E. Haber
David M. MacAlpine

First Published April 2, 2021

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