Jonathan Bollback

Research Interests

The core focus of my research is on better understanding the genetics of adaptation in viruses. To accomplish this I integrate empirical and theoretical approaches focusing on the use of experimental evolutionary, population genetic, phylogenetic, and computational methods.

My current research projects focus primarily on molecular evolution of influenza. This work includes estimating rates of reassortment, coadaptation in the genome, and the effects of beneficial mutations on antigenicity. In addition, I am working on statistical approaches to model CpG evolution in primates, patterns of adaptive evolution in Escherichia coli genomes, and estimating selection from time-series allele frequency data.

I have recently moved to the Institute of Science and Technology, Vienna, Austria. Contact details can be found here: External website.

Publications

Total publications: 20
Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation.
Guinane CM, Zakour NLB, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay J, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penades J & Fitzgerald JR (2010) Genome Biology and Evolution 2, 454-466.
Estimation of 2Nes from temporal allele frequency data.
Bollback JP, York T & Nielsen R (2008) Genetics 179, 497?502.
Genes under positive selection in Escherichia coli.
Petersen L, Bollback JP, Dimmic M, Hubisz M & Nielsen R (2007) Genome Res 17, 1336-1343.
Clonal interference is alleviated by high mutation rates in large populations.
Bollback JP & Huelsenbeck JP (2007) Mol Biol Evol 24, 1397-1406.
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.
Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R & Willerslev E (2007) PLoS One 2, e197.
Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA.
Freyhult EK, Bollback JP & Gardner PP (2007) Genome Res 17, 117-125.
Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system.
Reynolds SM, Dryer K, Bollback JP, Uy JAC, Patricelli GL, Robson T, Borgia G & Braun MJ (2007) Auk 124, 857-867.
Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution.
Betancourt AJ & Bollback JP (2006) Curr Opin Genet Dev 16, 618-623.
SIMMAP: stochastic character mapping of discrete traits on phylogenies.
Bollback JP (2006) BMC Bioinformatics 7, 88.
Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil.
Conn JE, Vineis JH, Bollback JP, Onyabe DY, Wilkerson RC & Povoa MM (2006) Am J Trop Med Hyg 74, 798-806.
Posterior mapping and predictive distributions.
Bollback JP (2005) In "Statistical methods in Molecular Evolution", Springer-Verlag
True and false gharials: a nuclear gene phylogeny of crocodylia.
Harshman J, Huddleston CJ, Bollback JP, Parsons TJ & Braun MJ (2003) Syst Biol 52, 386-402.
Stochastic mapping of morphological characters.
Huelsenbeck JP, Nielsen R & Bollback JP (2003) Syst Biol 52, 131-158.
Inferring the root of a phylogenetic tree.
Huelsenbeck JP, Bollback JP & Levine AM (2002) Syst Biol 51, 32-43.
Bayesian model adequacy and choice in phylogenetics.
Bollback JP (2002) Mol Biol Evol 19, 1171-1180.
Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi.
Conn JE, Bollback JP, Onyabe DY, Robinson TN, Wilkerson RC & Povoa MM (2001) Mol Ecol Notes 1, 223-225.
Empirical and hierarchical Bayesian estimation of ancestral states.
Huelsenbeck JP & Bollback JP (2001) Syst Biol 50, 351-366.
Application of the likelihood function in phylogenetic analysis.
Huelsenbeck JP & Bollback JP (2001) In "Handbook of Statistical Genetics", John Wiley and Sons CH. 15, 415-439.
Bayesian inference of phylogeny and its impact on evolutionary biology.
Huelsenbeck JP, Ronquist F, Nielsen R & Bollback JP (2001) Science 294, 2310-2314.
Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae).
Bollback JP & Huelsenbeck JP (2001) J Mol Evol 52, 117-128.
 
Andrew Rambaut, 2007