Predicting bacterial promoter function and evolution from random sequences
M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkadik, ELife 11 (2022).

Gene amplification as a form of population-level gene expression regulation
I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkadik, C.C. Guet, Nature Ecology &; Evolution 4 (2020) 612–625.

CRISPR-based herd immunity can limit phage epidemics in bacterial populations
P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).

Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations
P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).

Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkadik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.

Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkadik, J.P. Bollback, C.C. Guet, (2018).

Regulatory network structure determines patterns of intermolecular epistasis
M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).

Evolutionary interplay between structure, energy and epistasis in the coat protein of the =54 phage family
R.A. Fernandes Redondo, H. de Vladar, T. Wodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).

On the mechanistic nature of epistasis in a canonical cis-regulatory element
M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).

Epistatic interactions in the arabinose cis-regulatory element
M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769.

Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the =54 phage family
R.A. Fernandes Redondo, H. de Vladar, T. Wodarski, J.P. Bollback, (2016).

Motif depletion in bacteriophages infecting hosts with CRISPR systems
A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).

Probabilistic models for CRISPR spacer content evolution 
A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.

Complete genome sequence of the novel phage MG- infecting bacillus weihenstephanensis
R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).

Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza
M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013).

Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation
C. Guinane, N. Ben Zakour, M. Tormo Mas, L. Weinert, B. Lowder, R. Cartwright, D. Smyth, C. Smyth, J. Lindsay, K. Gould, A. Witney, J. Hinds, J.P. Bollback, A. Rambaut, J. Penades, J.R. Fitzgerald, Genome Biology and Evolution 2 (2010) 454–466.

Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence
J.P. Bollback, J. Huelsenbeck, Genetics 181 (2009) 225–234.

Estimation of 2Nes From Temporal Allele Frequency Data
J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
J. Binladen, M.T. Gilbert, J.P. Bollback, F. Panitz, C. Bendixen, R. Nielsen, E. Willerslev, PLoS One 2 (2007).

Genes under positive selection in Escherichia coli
L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research 17 (2007) 1336–1343.

Clonal interference is alleviated by high mutation rates in large populations
J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007) 1397–1406.

Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA
E. Freyhult, J.P. Bollback, P. Gardner, Genome Research 17 (2007) 117–25.

Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system
S. Reynolds, K. Dryer, J.P. Bollback, J.A. Uy, G. Patricelli, T. Robson, G. Borgia, M. Braun, The Auk 124 (2007) 857–867.

Estimating the history of mutations on a phylogeny
J.P. Bollback, P. Gardner, R. Nielsen, in:, D. Liberles (Ed.), Ancestral Sequence Reconstruction, Oxford University Press, 2007, pp. 69–79.

Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil
J. Conn, J. Vineis, J.P. Bollback, D. Onyabe, R. Wilkerson, M. Povoa, The American Journal of Tropical Medicine and Hygiene 74 (2006) 798–806.

SIMMAP: stochastic character mapping of discrete traits on phylogenies
J.P. Bollback, BMC Bioinformatics 7 (2006).

Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution
A. Betancourt, J.P. Bollback, Current Opinion in Genetics &; Development 16 (2006) 618–623.

Posterior mapping and posterior predictive distributions
J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution, Springer, 2005, pp. 439–462.

True and false gharials: A nuclear gene phylogeny of crocodylia
J. Harshman, C. Huddleston, J.P. Bollback, T. Parsons, M. Braun, Systematic Biology 52 (2003) 386–402.

Stochastic mapping of morphological characters
J. Huelsenbeck, R. Nielsen, J.P. Bollback, Systematic Biology 52 (2003) 131–158.

Bayesian model adequacy and choice in phylogenetics
J.P. Bollback, Molecular Biology and Evolution 19 (2002) 1171–80.

Inferring the root of a phylogenetic tree
J. Huelsenbeck, J.P. Bollback, A. Levine, Systematic Biology 51 (2002) 32–43.

Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae)
J.P. Bollback, J. Huelsenbeck, Journal of Molecular Evolution 52 (2001) 117–128.

Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi
J. Conn, J.P. Bollback, D. Onyabe, T. Robinson, R. Wilkerson, M. Povoa, Molecular Ecology Notes 1 (2001) 223–225.

Empirical and hierarchical Bayesian estimation of ancestral states
J. Huelsenbeck, J.P. Bollback, Systematic Biology 50 (2001) 351–366.

Bayesian inference of phylogeny and its impact on evolutionary biology
J. Huelsenbeck, F. Ronquist, R. Nielsen, J.P. Bollback, Science 294 (2001) 2310–2314.

Application of the likelihood function in phylogenetic analysis
J. Huelsenbeck, J.P. Bollback, in:, D. Balding, M. Bishop, C. Cannings (Eds.), Handbook of Statistical Genetics, Wiley-Blackwell, 2001, pp. 415–439.