Publications
Selected publications
- CRISPR-based herd immunity can limit phage epidemics in bacterial populations (Journal article - 2018)
- Regulatory network structure determines patterns of intermolecular epistasis (Journal article - 2017)
- Evolutionary potential of transcription factors for gene regulatory rewiring (Journal article - 2018)
- On the mechanistic nature of epistasis in a canonical cis-regulatory element (Journal article - 2017)
- Evolution - Bayesian inference of phylogeny and its impact on evolutionary biology (Journal article - 2001)
2023
Evolutionary Barriers to Horizontal Gene Transfer in macrophage associated Salmonella.
Bollback, J. (2023). Evolutionary Barriers to Horizontal Gene Transfer in macrophage associated Salmonella.. Evolution Letters. doi:10.1093/evlett/qrad020
2022
The Role of the Environment in Horizontal Gene Transfer
Kirit, H. A., Bollback, J. P., & Lagator, M. (2022). The Role of the Environment in Horizontal Gene Transfer. MOLECULAR BIOLOGY AND EVOLUTION, 39(11). doi:10.1093/molbev/msac220
Transcriptomic profiling of <i>Escherichia coli</i> K-12 in response to a compendium of stressors (vol 8, 8788, 2022)
Bhatia, R. P., Kirit, H. A., Predeus, A. V., & Bollback, J. P. (2022). Transcriptomic profiling of <i>Escherichia coli</i> K-12 in response to a compendium of stressors (vol 8, 8788, 2022). SCIENTIFIC REPORTS, 12(1). doi:10.1038/s41598-022-21625-2
Transcriptomic profiling of <i>Escherichia coli</i> K-12 in response to a compendium of stressors
Bhatia, R. P., Kirit, H. A., Predeus, A. V., & Bollback, J. P. (2022). Transcriptomic profiling of <i>Escherichia coli</i> K-12 in response to a compendium of stressors. SCIENTIFIC REPORTS, 12(1). doi:10.1038/s41598-022-12463-3
Evolutionary barriers to horizontal gene transfer in macrophage associated <i>Salmonella</i>
Predicting bacterial promoter function and evolution from random sequences
Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkacik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELIFE, 11. doi:10.7554/eLife.64543
2020
Experimental determination of evolutionary barriers to horizontal gene transfer
Acar Kirit, H., Lagator, M., & Bollback, J. P. (2020). Experimental determination of evolutionary barriers to horizontal gene transfer. BMC MICROBIOLOGY, 20(1). doi:10.1186/s12866-020-01983-5
Structure and Evolution of Constitutive Bacterial Promoters
Gene amplification as a form of population-level gene expression regulation
Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkacik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology and Evolution, 4, 612-625. doi:10.1038/s41559-020-1132-7
2018
Evolutionary potential of transcription factors for gene regulatory rewiring
Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. NATURE ECOLOGY & EVOLUTION, 2(10), 1633-1643. doi:10.1038/s41559-018-0651-y
CRISPR-based herd immunity can limit phage epidemics in bacterial populations
Payne, P., Geyrhofer, L., Barton, N., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife, 2018(7). doi:10.7554/eLife.32035
2017
Regulatory network structure determines patterns of intermolecular epistasis
Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. eLife, 6. doi:10.7554/eLife.28921
On the mechanistic nature of epistasis in a canonical cis-regulatory element
Lagator, M., Paixão, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife, 6. doi:10.7554/elife.25192
Evolutionary interplay between structure, energy and epistasis in the coat protein of the phi X174 phage family
Redondo, R. A. F., de Vladar, H. P., Wlodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the phi X174 phage family. Journal of the Royal Society Interface, 14(126). doi:10.1098/rsif.2016.0139
2016
Epistatic Interactions in the Arabinose Cis-Regulatory Element.
Lagator, M., Igler, C., Moreno, A. B., Guet, C. C., & Bollback, J. P. (2016). Epistatic Interactions in the Arabinose Cis-Regulatory Element. MOLECULAR BIOLOGY AND EVOLUTION, 33(3), 761-769. doi:10.1093/molbev/msv269
2014
Motif depletion in bacteriophages infecting hosts with CRISPR systems
Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC GENOMICS, 15. doi:10.1186/1471-2164-15-663
2013
Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza
Ward, M. J., Lycett, S. J., Avila, D., Bollback, J. P., & Brown, A. J. L. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC EVOLUTIONARY BIOLOGY, 13. doi:10.1186/1471-2148-13-222
Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus weihenstephanensis.
Redondo, R. A. F., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus weihenstephanensis.. Genome announcements, 1(3), e00216-e00213. doi:10.1128/genomea.00216-13
Probabilistic models for CRISPR spacer content evolution
Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution. BMC EVOLUTIONARY BIOLOGY, 13. doi:10.1186/1471-2148-13-54
2012
Ancient DNA extracted from Danish aurochs (<i>Bos primigenius</i>): Genetic diversity and preservation
Gravlund, P., Aaris-Sorensen, K., Hofreiter, M., Meyer, M., Bollback, J. P., & Noe-Nygaard, N. (2012). Ancient DNA extracted from Danish aurochs (<i>Bos primigenius</i>): Genetic diversity and preservation. ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER, 194(1), 103-111. doi:10.1016/j.aanat.2011.10.011
2010
Evolutionary Genomics of <i>Staphylococcus aureus</i> Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation
Guinane, C. M., Ben Zakour, N. L., Tormo-Mas, M. A., Weinert, L. A., Lowder, B. V., Cartwright, R. A., . . . Fitzgerald, J. R. (2010). Evolutionary Genomics of <i>Staphylococcus aureus</i> Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation. GENOME BIOLOGY AND EVOLUTION, 2, 454-466. doi:10.1093/gbe/evq031
2009
Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence
Bollback, J. P., & Huelsenbeck, J. P. (2009). Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence. GENETICS, 181(1), 225-234. doi:10.1534/genetics.107.085225
2008
Estimation of 2<i>N<sub>e</sub>s</i> from temporal allele frequency data
Bollback, J. P., York, T. L., & Nielsen, R. (2008). Estimation of 2<i>N<sub>e</sub>s</i> from temporal allele frequency data. GENETICS, 179(1), 497-502. doi:10.1534/genetics.107.085019
2007
Genes under positive selection in <i>Escherichia coli</i>
Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., & Nielsen, R. (2007). Genes under positive selection in <i>Escherichia coli</i>. GENOME RESEARCH, 17(9), 1336-1343. doi:10.1101/gr.6254707
Application of the Likelihood Function in Phylogenetic Analysis
Huelsenbeck, J. P., & Bollback, J. P. (2007). Application of the Likelihood Function in Phylogenetic Analysis. In Unknown Book (pp. 460-488). Wiley. doi:10.1002/9780470061619.ch15
Clonal interference is alleviated by high mutation rates in large populations
Bollback, J. P., & Huelsenbeck, J. P. (2007). Clonal interference is alleviated by high mutation rates in large populations. MOLECULAR BIOLOGY AND EVOLUTION, 24(6), 1397-1406. doi:10.1093/molbev/msm056
Estimating the history of mutations on a phylogeny
Bollback, J. P., Gardner, P. P., & Nielsen, R. (2007). Estimating the history of mutations on a phylogeny. In Ancestral Sequence Reconstruction (pp. 69-79). Oxford University PressOxford. doi:10.1093/acprof:oso/9780199299188.003.0006
The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing
Binladen, J., Gilbert, M. T. P., Bollback, J. P., Panitz, F., Bendixen, C., Nielsen, R., & Willerslev, E. (2007). The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing. PLOS ONE, 2(2). doi:10.1371/journal.pone.0000197
Behavioral paternity predicts genetic paternity in Satin Bowerbirds (<i>Ptilonorhynchus violaceus</i>), a species with a non-resource-based mating system
Reynolds, S. M., Dryer, K., Bollback, J., Uy, J. A. C., Patricelli, G. L., Robson, T., . . . Braun, M. J. (2007). Behavioral paternity predicts genetic paternity in Satin Bowerbirds (<i>Ptilonorhynchus violaceus</i>), a species with a non-resource-based mating system. AUK, 124(3), 857-867. doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA
Freyhult, E. K., Bollback, J. P., & Gardner, P. P. (2007). Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA. GENOME RESEARCH, 17(1), 117-125. doi:10.1101/gr.5890907
2006
SIMMAP: Stochastic character mapping of discrete traits on phylogenies
Bollback, J. P. (2006). SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC BIOINFORMATICS, 7. doi:10.1186/1471-2105-7-88
Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution
Betancourt, A. J., & Bollback, J. P. (2006). Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. CURRENT OPINION IN GENETICS & DEVELOPMENT, 16(6), 618-623. doi:10.1016/j.gde.2006.10.006
Population structure of the malaria vector <i>Anopheles darlingi</i> in a malaria-endemic region of eastern Amazonian Brazil
Conn, J. E., Vineis, J. H., Bollback, J. P., & Onyabe, D. Y. (2006). Population structure of the malaria vector <i>Anopheles darlingi</i> in a malaria-endemic region of eastern Amazonian Brazil. AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 74(5), 798-806. doi:10.4269/ajtmh.2006.74.798
2003
True and false gharials: A nuclear gene phylogeny of Crocodylia
Harshman, J., Huddleston, C. J., Bollback, J. P., Parsons, T. J., & Braun, M. J. (2003). True and false gharials: A nuclear gene phylogeny of Crocodylia. SYSTEMATIC BIOLOGY, 52(3), 386-402. doi:10.1080/10635150390197028
Stochastic mapping of morphological characters
Huelsenbeck, J. P., Nielsen, R., & Bollback, J. P. (2003). Stochastic mapping of morphological characters. Systematic Biology, 52(2), 131-158. doi:10.1080/10635150390192780
2002
Bayesian model adequacy and choice in phylogenetics
Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics. MOLECULAR BIOLOGY AND EVOLUTION, 19(7), 1171-1180. doi:10.1093/oxfordjournals.molbev.a004175
Inferring the root of a phylogenetic tree
Huelsenbeck, J. P., Bollback, J. P., & Levine, A. M. (2002). Inferring the root of a phylogenetic tree. SYSTEMATIC BIOLOGY, 51(1), 32-43. doi:10.1080/106351502753475862
2001
Evolution - Bayesian inference of phylogeny and its impact on evolutionary biology
Huelsenbeck, J. P., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001). Evolution - Bayesian inference of phylogeny and its impact on evolutionary biology. SCIENCE, 294(5550), 2310-2314. doi:10.1126/science.1065889
Isolation of polymorphic microsatellite markers from the malaria vector <i>Anopheles darlingi</i>
Conn, J. E., Bollback, J. P., Onyabe, D. Y., Robinson, T. N., Wilkerson, R. C., & Póvoa, M. M. (2001). Isolation of polymorphic microsatellite markers from the malaria vector <i>Anopheles darlingi</i>. MOLECULAR ECOLOGY NOTES, 1(4), 223-225. doi:10.1046/j.1471-8278.2001.00078.x
Empirical and hierarchical Bayesian estimation of ancestral states
Huelsenbeck, J. P., & Bollback, J. P. (2001). Empirical and hierarchical Bayesian estimation of ancestral states. SYSTEMATIC BIOLOGY, 50(3), 351-366. doi:10.1080/106351501300317978
Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae)
Bollback, J. P., & Huelsenbeck, J. P. (2001). Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae). JOURNAL OF MOLECULAR EVOLUTION, 52(2), 117-128. doi:10.1007/s002390010140