Publications – Center for Communicable Disease Dynamics

Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales.

Author(s): Li NK, Corander J, Grad YH, Chang HHJournal: Virus EvolPMID: 36601300 November 2022

Incomplete selection makes it challenging to infer selection on genes at short time scales, especially for microorganisms, due to stronger…

Causal discovery for the microbiome.

Author(s): Corander J, Hanage WP, Pensar JJournal: Lancet MicrobePMID: 36152674 September 2022

Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases…

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures.

Author(s): Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJJournal: ISME JPMID: 33408365 January 2021

Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes,…

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.

Author(s): Azarian T, Martinez PP, Arnold BJ, Qiu X, Grant LR, Corander J, Fraser C, Croucher NJ, Hammitt LL, Reid R, Santosham M, Weatherholtz RC, Bentley SD, O'Brien KL, Lipsitch M, Hanage WPJournal: PLoS BiolPMID: 33091022 October 2020

Predicting how pathogen populations will change over time is challenging. Such has been the case with Streptococcus pneumoniae, an important…

Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen.

Author(s): Arnold B, Sohail M, Wadsworth C, Corander J, Hanage WP, Sunyaev S, Grad YHJournal: Mol Biol EvolPMID: 31589312 October 2019

Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the…

Weak Epistasis May Drive Adaptation in Recombining Bacteria.

Author(s): Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WPJournal: GeneticsPMID: 29330348 March 2018

The impact of epistasis on the evolution of multi-locus traits depends on recombination. While sexually reproducing eukaryotes recombine so frequently…

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Author(s): Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJJournal: Nat Ecol EvolPMID: 29038424 December 2017

Many bacterial species are composed of multiple lineages distinguished by extensive variation in gene content. These often cocirculate in the…

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.

Author(s): Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen PJournal: Mol Biol EvolPMID: 28199698 May 2017

Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus…

Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States.

Author(s): Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WPJournal: J Clin MicrobiolPMID: 28100596 April 2017

Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic-resistant strains throughout the 2000s. However, diseases caused…

The impact of host metapopulation structure on the population genetics of colonizing bacteria.

Author(s): Numminen E, Gutmann M, Shubin M, Marttinen P, Méric G, van Schaik W, Coque TM, Baquero F, Willems RJ, Sheppard SK, Feil EJ, Hanage WP, Corander JJournal: J Theor BiolPMID: 26916623 May 2016

Many key bacterial pathogens are frequently carried asymptomatically, and the emergence and spread of these opportunistic pathogens can be driven,…