Publications

The RNA_RNA interactome between a phage and its satellite virus reveals a small RNA that differentially regulates gene expression across both genomes

Second author • Molecular Microbiology • 2023

Led initial development of software to process ligated RNA-RNA sequence data into intra/inter-genome interactome maps with a GUI visualization interface.

Emergence and Evolutionary Response of Vibrio cholerae to Novel Bacteriophage, Democratic Republic of the Congo

Supporting author • Emerging Infectious Diseases • 2022

Provided guidance on bacteriophage genomic comparison, alignment and phylogenetic analysis.

A phage weaponizes a satellite recombinase to subvert viral restriction

Supporting author • Nucleic acids research • 2022

Built bioinformatics pipelines that compare DNA sequencing coverage between experimental conditions to identify regions with patterns of differential enzymatic restriction.

Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts

Supporting author • Science • 2021

Collected and assembled a database of Vibrio cholerae genomes and developed methods to identify and categorize a large suite of mobile genetic elements via comparative genomic analysis.

Bacteriophage ICP1: A persistent predator of Vibrio cholerae

Second author • Annual Review of Virology • 2021

Assembled and annotated a collection of 67 highly related V. cholerae-specific bacteriophage genomes. Performed extensive phylogenetic and genomic analyses to determine evolutionary trajectories. 

Evolutionary sweeps of subviral parasites and their phage host bring unique parasite variants and disappearance of a phage CRISPR-Cas system

Lead author • mBio • 2021

Developed numerous bioinformatic approaches to identify rapid co-evolutionary shifts in the antagonistic arms race between bacteriophage and phage-defense satellites in V. cholerae. This comprehensive project included mining large public genomic databases, analysis of genomes from three years of novel patient samples, identification of phage-borne CRIPSR systems, discovery of several new phage defense satellites, and detailed laboratory investigation of the most recently discovered defense satellite.

Genome replication dynamics of a bacteriophage and its satellite reveal strategies for parasitism and viral restriction

Supporting author • Nucleic acids research • 2020

Performed DNA-seq mapping and generated visualizations to track bacteriophage genome replication during the course of infection.

A Family of Viral Satellites Manipulates Invading Virus Gene Expression and Can Affect Cholera Toxin Mobilization

Supporting author • Msystems • 2020

Calculated gene expression profiles and overall transcript levels for multiple genomes during a bacteriophage infection. Developed GUI software to visualize RNA-seq mapping data across multiple timepoints.

Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: insights from a natural arms race

Supporting author • Philosophical Transactions of the Royal Society B • 2019

Performed genome assembly, sequence mapping and visualization to identify CRISPR protospacer acquisition events and non-canonical spacer-recognition motifs during bacteriophage infection.

Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period

Lead author • Viruses • 2018

Performed the first analysis of bacteriophage strains from within a single species. Assembled and annotated genomes, calculated phylogenetic relationships, and determined genome mosaicism through analysis of core vs. accessory meta-genomes.

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient

Lead author • PeerJ • 2018

Performed 16S microbial community sampling from a fully-factorial salt marsh sediment transplant experiment. Built bioinformatic tools and statistical models to track community dynamics across temporal and geographic shifts in environmental conditions.

Spartina alterniflora Biomass Allocation and Temperature: Implications for Salt Marsh Persistence with Sea-Level Rise

Second author • Estuaries and Coasts • 2017

Assisted with sediment transplant project design and execution. Performed environmental sampling and logging.

Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria

Lead author • Environmental microbiology • 2016

Determined biogeographical dispersal limitations of sulfate reducing bacterial communities in salt marsh sediments. Used bioinformatic and statistical approaches to discover decoupled distributions between species and sulfate-reducing genes. 

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs

Minor author • Cell host & microbe • 2015

Assisted with determining biofilm phenotypic variation among Pseudomonas aeruginosa strains from cystic fibrosis patients.

Conditions associated with the cystic fibrosis defect promote chronic Pseudomonas aeruginosa infection

Minor author • American journal of respiratory and critical care medicine • 2014

Helped to determine biofilm formation phenotypes in Pseudomonas aeruginosa strains with motility defects.

Targeting a bacterial stress response to enhance antibiotic action

Minor author • Proceedings of the National Academy of Sciences • 2009

Performed antibiotic screens of Pseudomonas aeruginosa patient isolates.