Ted Cohen

A comparison of scalable approaches for the pairwise analysis of large pathogen genomic and spatial datasets: an application to studying Mycobacterium tuberculosis transmission

The paper compares case-control and divide-and-conquer methods for efficient pairwise analysis of large pathogen genomic and spatial datasets, finding the case-control approach more robust for estimating transmission associations.

The global phylogeography of rapidly expanding multidrug resistant Ural lineage 4.2 Mycobacterium tuberculosis

The paper identifies a rapidly expanding multidrug-resistant M. tuberculosis clade originating from Russia and circulating in Moldova, posing a threat to MDR-TB control.

e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology

The paper introduces e3SIM, a simulator that models epidemiological, ecological, and evolutionary processes in pathogens, demonstrating its use with SARS-CoV-2 and Mycobacterium tuberculosis.

Large-scale genomic analysis of SARS-CoV-2 Omicron BA.5 emergence in the United States

This study analyzes the genomic data of SARS-CoV-2 Omicron BA.5 variants in the U.S. to understand their emergence patterns and transmission dynamics.

Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens

This paper develops tiled amplicon sequencing panels for whole-genome sequencing of pathogenic bacteria without culturing, enabling drug resistance classification from clinical samples.

A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission

MixInfect2 accurately detects mixed Mycobacterium tuberculosis infections and estimates strain proportions, improving upon previous methods.

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

This study quantifies antibiotic resistance in tuberculosis using genomic data and MIC measurements to identify genetic determinants of resistance and hypersensitivity across multiple drugs.

vCOMBAT: a Novel Tool to Create and Visualize a COmputational Model of Bacterial Antibiotic Target-binding

The paper introduces vCOMBAT, a web-based tool for creating and visualizing computational models of bacterial antibiotic target-binding using clinical drug concentration data.

Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference

This study shows that different genomic variant calling methods lead to inconsistent transmission inferences and phylogenies in Mycobacterium tuberculosis outbreaks.

Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions

The paper introduces a transmission-based clustering method for identifying outbreak clusters using whole genome sequencing data, showing it outperforms SNP threshold methods in some scenarios.

How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance

This study shows that competition between resistant and sensitive pathogens determines whether aggressive or moderate antibiotic treatment better minimizes resistance.