>

Publications

2025

Baltrus DA, Merrikh H, Uecker H, Wong A, Nearly a century of discoveries in bacterial genetics and their continuing impact on the field G3 (Bethesda, Md.). 2025 Nov 12; 15 (11)

2024

Browning KR, Merrikh H, Replication-Transcription Conflicts: A Perpetual War on the Chromosome Annual review of biochemistry. 2024 Jul 2; 93 (1) 21-46
Carvajal-Garcia J, Bracey H, Johnson AE, Hernandez Viera AJ, Egli M, Simsek EN, Jaremba EA, Kim K, Merrikh H, A small molecule that inhibits the evolution of antibiotic resistance NAR molecular medicine. 2024 Jan 23; 1 (1) ugae001

2023

Carvajal-Garcia J, Samadpour AN, Hernandez Viera AJ, Merrikh H, Oxidative stress drives mutagenesis through transcription-coupled repair in bacteria Proceedings of the National Academy of Sciences of the United States of America. 2023 Jun 26; 120 (27) e2300761120
Huang D, Johnson AE, Sim BS, Lo TW, Merrikh H, Wiggins PA, The in vivo measurement of replication fork velocity and pausing by lag-time analysis Nature communications. 2023 Mar 30; 14 (1) 1762
Stoy H, Zwicky K, Kuster D, Lang KS, Krietsch J, Crossley MP, Schmid JA, Cimprich KA, Merrikh H, Lopes M, Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids Nature structural & molecular biology. 2023 Mar 2; 30 (3) 348-359

2022

Stoy H, S Lang K, Merrikh H, Lopes M, Locus-Specific Analysis of Replication Dynamics and Detection of DNA-RNA Hybrids by Immuno Electron Microscopy Methods in molecular biology (Clifton, N.J.). 2022 May 1; 2528 67-89
Merrikh H, Merrikh C, Reply to: Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes Nature communications. 2022 May 12; 13 (1) 2627
Huang D, Lo T, Merrikh H, Wiggins PA, Characterizing stochastic cell-cycle dynamics in exponential growth Physical review. E. 2022 Jan 3; 105 (1-1) 014420

2021

Ragheb MN, Merrikh C, Browning K, Merrikh H, Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs Proceedings of the National Academy of Sciences of the United States of America. 2021 Jan 5; 118 (1)

2020

Merrikh H, Kohli RM, Targeting evolution to inhibit antibiotic resistance The FEBS journal. 2020 Jun 8; 287 (20) 4341-4353

2019

Ragheb MN, Thomason MK, Hsu C, Nugent P, Gage J, Samadpour AN, Kariisa A, Merrikh CN, Miller SI, Sherman DR, Merrikh H, Inhibiting the Evolution of Antibiotic Resistance Molecular cell. 2019 Jan 3;

2018

Merrikh CN, Merrikh H, Gene inversion potentiates bacterial evolvability and virulence Nature communications. 2018 Nov 7; 9 (1) 4662
Ma D, Wang Z, Merrikh CN, Lang KS, Lu P, Li X, Merrikh H, Rao Z, Xu W, Crystal structure of a membrane-bound O-acyltransferase Nature. 2018 Oct 3; 562 (7726) 286-290
Samadpour AN, Merrikh H, DNA gyrase activity regulates DnaA-dependent replication initiation in Bacillus subtilis Molecular microbiology. 2018 Mar 6; 108 (2) 115-127
Mangiameli SM, Cass JA, Merrikh H, Wiggins PA, The bacterial replisome has factory-like localization Current genetics. 2018 Apr 9; 64 (5) 1029-1036
Lang KS, Merrikh H, The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria Annual review of microbiology. 2018 Jun 1; 72 71-88

2017

Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H, Transcription leads to pervasive replisome instability in bacteria eLife. 2017 Jan 16; 6
Mangiameli SM, Veit BT, Merrikh H, Wiggins PA, The Replisomes Remain Spatially Proximal throughout the Cell Cycle in Bacteria PLoS genetics. 2017 Jan 23; 13 (1) e1006582
Merrikh H, Spatial and Temporal Control of Evolution through Replication-Transcription Conflicts Trends in microbiology. 2017 Feb 16; 25 (7) 515-521
Lang KS, Hall AN, Merrikh CN, Ragheb M, Tabakh H, Pollock AJ, Woodward JJ, Dreifus JE, Merrikh H, Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis Cell. 2017 170 (4) 787-799.e18
Loftie-Eaton W, Bashford K, Quinn H, Dong K, Millstein J, Hunter S, Thomason MK, Merrikh H, Ponciano JM, Top EM, Compensatory mutations improve general permissiveness to antibiotic resistance plasmids Nature ecology & evolution. 2017 Aug 7; 1 (9) 1354-1363

2016

Merrikh CN, Weiss E, Merrikh H, The Accelerated Evolution of Lagging Strand Genes Is Independent of Sequence Context Genome biology and evolution. 2016 8 (12) 3696-3702

2015

Million-Weaver S, Samadpour AN, Moreno-Habel DA, Nugent P, Brittnacher MJ, Weiss E, Hayden HS, Miller SI, Liachko I, Merrikh H, An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis Proceedings of the National Academy of Sciences of the United States of America. 2015 Feb 23; 112 (10) E1096-105
Million-Weaver S, Samadpour AN, Merrikh H, Replication Restart after Replication-Transcription Conflicts Requires RecA in Bacillus subtilis Journal of bacteriology. 2015 May 4; 197 (14) 2374-82
Merrikh CN, Brewer BJ, Merrikh H, The B. subtilis Accessory Helicase PcrA Facilitates DNA Replication through Transcription Units PLoS genetics. 2015 Jun 12; 11 (6) e1005289

2013

Paul S, Million-Weaver S, Chattopadhyay S, Sokurenko E, Merrikh H, Accelerated gene evolution through replication-transcription conflicts Nature. 2013 495 (7442) 512-5

2012

Merrikh H, Zhang Y, Grossman AD, Wang JD, Replication-transcription conflicts in bacteria Nature reviews. Microbiology. 2012 Jun 6; 10 (7) 449-58