Author

H. Merrikh

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 3 Biophysics· 2 Biochemistry· 1 Cell Biology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 6 Approach:statistical model· 4 Research Focus:chromatin & epigenetic regulation· 3 Approach:experimental assay· 3 Research Focus:gene regulatory network inference· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Assay:DNA methylation· 2

Frequent Co-Authors

P. A. Wiggins· 3 shared A. E. Johnson· 2 shared C. Merrikh· 2 shared D. Huang· 2 shared T. Lo· 2 shared A. J. H. Viera· 1 shared B. S. Sim· 1 shared B. T. Veit· 1 shared

Activity by Year

2016-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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3 shared papersBiophysics

P. A. Wiggins

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

Pathogenic bacteria experience pervasive RNA polymerase backtracking during infection

K. R. Browning, H. Merrikh

The paper develops PIC-seq to study RNA polymerase dynamics in Salmonella during infection, finding increased RNAP backtracking and its role in virulence.

bioRxiv · May 12, 2023Biochemistry

A small molecule that inhibits the evolution of antibiotic resistance

A. E. Johnson, H. Bracey, A. J. H. Viera, J. Carvajal-Garcia, E. N. Simsek, K. Kim, H. Merrikh

This paper identifies a small molecule, ARM-1, that inhibits bacterial evolution by targeting Mfd, delaying AMR development across multiple pathogens.

bioRxiv · Sep 26, 2022 · PreprintMicrobiology

The high-resolution in vivo measurement of replication fork velocity and pausing by lag-time analysis

D. Huang, A. E. Johnson, B. S. Sim, T. Lo, H. Merrikh, P. A. Wiggins

This paper introduces lag-time analysis to measure replication fork velocity and pausing in vivo, finding locus- and time-dependent dynamics and novel pauses at rDNA.

bioRxiv · Aug 13, 2022 · PreprintBiophysics

Characterizing stochastic cell cycle dynamics in exponential growth

D. Huang, T. Lo, H. Merrikh, P. A. Wiggins

The paper establishes an exact correspondence between deterministic and stochastic cell cycle models, showing deterministic models can well-fit exponential culture demographics even with stochastic state timing.

bioRxiv · Aug 24, 2021Biophysics

Lagging strand encoding promotes adaptive evolution

C. Merrikh, L. Harris, S. Mangiameli, H. Merrikh

The paper investigates whether lagging strand genes evolve faster due to replication-transcription conflicts and finds convergent mutations are enriched in these genes, suggesting adaptive evolution.

bioRxiv · Jun 23, 2020 · PreprintEvolutionary Biology

Response to No support for the adaptive hypothesis of lagging-9 strand encoding in bacterial genomes

H. Merrikh, C. Merrikh

The paper responds to criticism of their adaptive hypothesis of lagging-strand gene orientation by providing empirical evidence supporting their original findings and introducing an improved GC skew method.

bioRxiv · May 26, 2020 · PreprintEvolutionary Biology

Gene inversion increases evolvability in bacteria

C. N. Merrikh, H. Merrikh

This study shows that gene inversion in bacteria increases evolvability by promoting head-on replication-transcription collisions, leading to higher mutation rates and positive selection in head-on genes.

bioRxiv · Apr 3, 2018Evolutionary Biology

The replisomes remain spatially proximal throughout the cell cycle in bacteria

S. M. Mangiameli, B. T. Veit, H. Merrikh, P. A. Wiggins

This paper uses time-lapse imaging to show that replication forks remain spatially close in two bacterial species, supporting the Factory Model over the Track Model.

bioRxiv · Dec 30, 2016Cell Biology