Publications – Center for Communicable Disease Dynamics

Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana.

Author(s): Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DEJournal: bioRxivPMID: 38352461 February 2024

parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. However, in low transmission…

The inter-continental population dynamics of Neisseria gonorrhoeae

Author(s): Osnes MN, Brynildsrud OB, Alfsnes K, McKeand SA, Ross J, Town K, de Korne-Elenbaas J, van Dam A, Bruisten S, de Blasio BF, Caugant DA, Grad YH, Williamson DA, Balloux F, Didelot X, Eldholm V, Van Dorp LJournal: bioRxiv August 2023

Neisseria gonorrhoeae is a globally distributed sexually transmitted bacterial pathogen. Recent studies have revealed that its evolution has been shaped…

Enterobacteriaceae isolated from patients share antibiotic resistance conferring plasmids recently acquired from those isolated from sinks in the same treatment room

Author(s): Taylor BP, Che Y, Passarelli H, Smollan G, Cohen C, Rapaport R, Tal I, Zade NP, Jaber H, Keller N, Hanage WP, Regev-Yochay GJournal: bioRxiv November 2022

Identifying how and where pathogens acquire antibiotic resistance is crucial to developing effective strategies to limit its spread. Many bacterial…

Beyond consensus sequence: a quantitative scheme for inferring transmission using deep sequencing in a bacterial transmission model

Author(s): Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles SJournal: bioRxiv October 2022

Genomic surveillance provides a data source complementary to contact tracing to resolve putative transmission chains. However, the role of within-host…

Variation in supplemental carbon dioxide requirements defines lineage-specific antibiotic resistance acquisition in Neisseria gonorrhoeae

Author(s): Rubin DH, Ma KC, Westervelt KA, Hullahalli K, Waldor MK, Grad YHJournal: bioRxiv February 2022

The evolution of the obligate human pathogen Neisseria gonorrhoeae has been shaped by selective pressures from diverse host niche environments…

Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis

Author(s): Carrasquilla M, Early AM, Taylor AR, Knudson A, Echeverry DF, Anderson TJ, Mancilla E, Aponte S, Cárdenas P, Buckee CO, Rayner JC, Sáenz FE, Neafsey DE, Corredor VJournal: bioRxiv February 2022

The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most…

Genome wide association studies define minimal set of loci for prediction of penicillin and tetracycline susceptibility in Neisseria gonorrhoeae

Author(s): Mortimer TD, Zhang JJ, Ma KC, Grad YHJournal: bioRxiv August 2021

While Neisseria gonorrhoeae poses an urgent public health threat because of increasing antimicrobial resistance, much of the circulating population remains…

Modeling memory T cell states at single-cell resolution identifies in vivo state-dependence of eQTLs influencing disease

Author(s): Nathan A, Asgari S, Ishigaki K, Amariuta T, Luo Y, Beynor JI, Baglaenko Y, Suliman S, Price A, Lecca L, Murray MB, Moody DB, Raychaudhuri SJournal: bioRxiv July 2021

Many non-coding genetic variants cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated…

A sex-specific evolutionary interaction between ADCY9 and CETP

Author(s): Gamache I, Legault MA, Grenier JC, Sanchez R, Rhéaume E, Asgari S, Barhdadi A, Zada YF, Trochet H, Luo Y, Lecca L, Murray M, Raychaudhuri S, Tardif JC, Dubé MP, Hussin JGJournal: bioRxiv May 2021

Pharmacogenomic studies have revealed associations between rs1967309 in the adenylyl cyclase type 9 (ADCY9) gene and clinical responses to the…

Axes of inter-sample variability among transcriptional neighborhoods reveal disease associated cell states in single-cell data

Author(s): Reshef YA, Rumker L, Kang JB, Nathan A, Murray MB, Moody DB, Raychaudhuri SJournal: bioRxiv April 2021

As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples…