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Merrikh Lab Publications


Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts

Lang KS, Merrikh H.Cell Rep. 2021 Mar 2;34(9):108797. doi: 10.1016/j.celrep.2021.108797.PMID: 33657379


Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs

Ragheb MN, Merrikh C, Browning K, Merrikh H.Proc Natl Acad Sci U S A. 2021 Jan 5;118(1):e2008498118. doi: 10.1073/pnas.2008498118.PMID: 33443179



Replication-transcription conflicts promote adaptive evolution

Christopher N. MerrikhLeonard A. HarrisSarah Mangiameli, and Houra Merrikh

bioRxiv doi:


Targeting evolution to inhibit antibiotic resistance.

Merrikh H, Kohli RM.FEBS J. 2020 May 20.

doi: 10.1111/febs.15370. Online ahead of print.


Replication-transcription conflicts promote adaptive evolution

Christopher N. MerrikhLeonard A. HarrisSarah Mangiameli, and Houra Merrikh

bioRxiv doi:


The recent report by Liu and Zhang Claiming “No support for the adaptive hypothesis of lagging-strand encoding in bacterial genomes” is factually incorrect

Christopher Merrikh, Houra Merrikh

bioRxiv 2020.05.26.117366; doi:




RaghebMN, ThomasonMK, HsuC, NugentP, GageJ, SamadpourAN, KariisaA, MerrikhCN, MillerSI, ShermanDR, MerrikhH, Inhibiting the Evolution of Antibiotic ResistanceMolecular cell. 2019 Jan 3


MerrikhCN, MerrikhH, Gene inversion potentiates bacterial evolvability and virulenceNature communications. 2018 Nov 7 9 (1). 4662
MaD, WangZ, MerrikhCN, LangKS, LuP, LiX, MerrikhH, RaoZ, XuW, Crystal structure of a membrane-bound O-acyltransferaseNature. 2018 Oct 3 562 (7726). 286-290
SamadpourAN, MerrikhH, DNA gyrase activity regulates DnaA-dependent replication initiation in Bacillus subtilisMolecular microbiology. 2018 Mar 6 108 (2). 115-127
MangiameliSM, CassJA, MerrikhH, WigginsPA, The bacterial replisome has factory-like localizationCurrent genetics. 2018 Apr 9 64 (5). 1029-1036
LangKS, MerrikhH, The Clash of Macromolecular Titans: Replication-Transcription Conflicts in BacteriaAnnual review of microbiology. 2018 Jun 1 72 71-88


MangiameliSM, MerrikhCN, WigginsPA, MerrikhH, Transcription leads to pervasive replisome instability in bacteriaeLife. 2017 Jan 16 6
MangiameliSM, VeitBT, MerrikhH, WigginsPA, The Replisomes Remain Spatially Proximal throughout the Cell Cycle in BacteriaPLoS genetics. 2017 Jan 23 13 (1). e1006582
MerrikhH, Spatial and Temporal Control of Evolution through Replication-Transcription ConflictsTrends in microbiology. 2017 Feb 16 25 (7). 515-521
LangKS, HallAN, MerrikhCN, RaghebM, TabakhH, PollockAJ, WoodwardJJ, DreifusJE, MerrikhH, Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and PathogenesisCell. 2017 170 (4). 787-799.e18
Loftie-EatonW, BashfordK, QuinnH, DongK, MillsteinJ, HunterS, ThomasonMK, MerrikhH, PoncianoJM, TopEM, Compensatory mutations improve general permissiveness to antibiotic resistance plasmidsNature ecology & evolution. 2017 Aug 7 1 (9). 1354-1363


MerrikhCN, WeissE, MerrikhH, The Accelerated Evolution of Lagging Strand Genes Is Independent of Sequence ContextGenome biology and evolution. 2016 8 (12). 3696-3702


Million-WeaverS, SamadpourAN, Moreno-HabelDA, NugentP, BrittnacherMJ, WeissE, HaydenHS, MillerSI, LiachkoI, MerrikhH, An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilisProceedings of the National Academy of Sciences of the United States of America. 2015 Feb 23 112 (10). E1096-105
Million-WeaverS, SamadpourAN, MerrikhH, Replication Restart after Replication-Transcription Conflicts Requires RecA in Bacillus subtilisJournal of bacteriology. 2015 May 4 197 (14). 2374-82
MerrikhCN, BrewerBJ, MerrikhH, The B. subtilis Accessory Helicase PcrA Facilitates DNA Replication through Transcription UnitsPLoS genetics. 2015 Jun 12 11 (6). e1005289


PaulS, Million-WeaverS, ChattopadhyayS, SokurenkoE, MerrikhH, Accelerated gene evolution through replication-transcription conflictsNature. 2013 495 (7442). 512-5


MerrikhH, ZhangY, GrossmanAD, WangJD, Replication-transcription conflicts in bacteriaNature reviews. Microbiology. 2012 Jun 6 10 (7). 449-58

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