33 Publications

Mark all

[33]
2018 | Journal Article | IST-REx-ID: 423   OA
Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife, 7. https://doi.org/10.7554/eLife.32035
View | Files available | DOI
 
[32]
2018 | Journal Article | IST-REx-ID: 67
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution, 2(10), 1633–1643. https://doi.org/10.1038/s41559-018-0651-y
View | Files available | DOI
 
[31]
2018 | Research Data | IST-REx-ID: 5585
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria. https://doi.org/10.15479/AT:ISTA:108
View | Files available | DOI
 
[30]
2017 | Journal Article | IST-REx-ID: 1077   OA
Fernandes Redondo, R. A., Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the fX174 phage family. Journal of the Royal Society Interface, 14(126). https://doi.org/10.1098/rsif.2016.0139
View | Files available | DOI
 
[29]
2017 | Journal Article | IST-REx-ID: 954   OA
Lagator, M., Paixao, 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. https://doi.org/10.7554/eLife.25192
View | Files available | DOI
 
[28]
2017 | Journal Article | IST-REx-ID: 570   OA
Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife, 6. https://doi.org/10.7554/eLife.28921
View | Files available | DOI
 
[27]
2016 | Journal Article | IST-REx-ID: 1427   OA
Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution, 33(3), 761–769. https://doi.org/10.1093/molbev/msv269
View | Files available | DOI
 
[26]
2014 | Journal Article | IST-REx-ID: 2042   OA
Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-663
View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2412   OA
Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology, 13(1), 54–54. https://doi.org/10.1186/1471-2148-13-54
View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 500   OA
Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology, 13(1), 222. https://doi.org/10.1186/1471-2148-13-222
View | Files available | DOI
 
[23]
2013 | Journal Article | IST-REx-ID: 2410   OA
Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements, 1(3). https://doi.org/10.1128/genomeA.00216-13
View | Files available | DOI
 
[22]
2010 | Journal Article | IST-REx-ID: 4358
Guinane, C., Ben Zakour, N., Tormo Mas, M., Weinert, L., Lowder, B., Cartwright, R., … Fitzgerald, J. R. (2010). Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution, 2, 454–466. https://doi.org/10.1093/gbe/evq031
View | DOI
 
[21]
2009 | Journal Article | IST-REx-ID: 4357
Bollback, J. P., & Huelsenbeck, J. (2009). Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics, 181(1), 225–234. https://doi.org/10.1534/genetics.107.085225
View | DOI
 
[20]
2008 | Journal Article | IST-REx-ID: 3435   OA
Bollback, J. P., York, T., & Nielsen, R. (2008). Estimation of 2Nes From Temporal Allele Frequency Data. Genetics, 179(1), 497–502. https://doi.org/10.1534/genetics.107.085019
View | DOI | Download (ext.)
 
[19]
2007 | Journal Article | IST-REx-ID: 4355
Bollback, J. P., & Huelsenbeck, J. (2007). Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution, 24(6), 1397–1406. https://doi.org/10.1093/molbev/msm056
View | DOI
 
[18]
2007 | Journal Article | IST-REx-ID: 4356
Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., & Nielsen, R. (2007). Genes under positive selection in Escherichia coli. Genome Research, 17(9), 1336–1343. https://doi.org/10.1101/gr.6254707
View | DOI
 
[17]
2007 | Journal Article | IST-REx-ID: 3436
Reynolds, S., Dryer, K., Bollback, J. P., Uy, J. A., Patricelli, G., Robson, T., … Braun, M. (2007). Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. The Auk, 124(3), 857–867. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
View | DOI
 
[16]
2007 | Book Chapter | IST-REx-ID: 3432
Bollback, J. P., Gardner, P., & Nielsen, R. (2007). Estimating the history of mutations on a phylogeny. In D. Liberles (Ed.), Ancestral Sequence Reconstruction (pp. 69–79). Oxford University Press. https://doi.org/10.1093/acprof:oso/9780199299188.003.0006
View | DOI
 
[15]
2007 | Journal Article | IST-REx-ID: 4353
Binladen, J., Gilbert, M. T., 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). https://doi.org/10.1371/journal.pone.0000197
View | DOI
 
[14]
2007 | Journal Article | IST-REx-ID: 4354
Freyhult, E., Bollback, J. P., & Gardner, 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. https://doi.org/10.1101/gr.5890907
View | DOI | Download (ext.)
 
[13]
2006 | Journal Article | IST-REx-ID: 4351
Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7. https://doi.org/10.1186/1471-2105-7-88
View | DOI
 
[12]
2006 | Journal Article | IST-REx-ID: 4352
Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., & Povoa, M. (2006). Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene, 74(5), 798–806.
View | Download (ext.)
 
[11]
2006 | Journal Article | IST-REx-ID: 3437
Betancourt, A., & 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. https://doi.org/10.1016/j.gde.2006.10.006
View | DOI
 
[10]
2005 | Book Chapter | IST-REx-ID: 3433
Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions. In R. Nielsen (Ed.), Statistical methods in Molecular Evolution (pp. 439–462). Springer. https://doi.org/10.1007/0-387-27733-1
View | DOI
 
[9]
2003 | Journal Article | IST-REx-ID: 4348
Huelsenbeck, J., Nielsen, R., & Bollback, J. P. (2003). Stochastic mapping of morphological characters. Systematic Biology, 52(2), 131–158. https://doi.org/10.1080/10635150390192780
View | DOI
 
[8]
2003 | Journal Article | IST-REx-ID: 4350
Harshman, J., Huddleston, C., Bollback, J. P., Parsons, T., & Braun, M. (2003). True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology, 52(3), 386–402. https://doi.org/10.1080/10635150390197028
View | DOI
 
[7]
2002 | Journal Article | IST-REx-ID: 4349
Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution, 19(7), 1171–1180.
View | Download (ext.)
 
[6]
2002 | Journal Article | IST-REx-ID: 4347
Huelsenbeck, J., Bollback, J. P., & Levine, A. (2002). Inferring the root of a phylogenetic tree. Systematic Biology, 51(1), 32–43. https://doi.org/10.1080/106351502753475862
View | DOI
 
[5]
2001 | Book Chapter | IST-REx-ID: 3434
Huelsenbeck, J., & Bollback, J. P. (2001). Application of the likelihood function in phylogenetic analysis. In D. Balding, M. Bishop, & C. Cannings (Eds.), Handbook of Statistical Genetics (pp. 415–439). Wiley-Blackwell. https://doi.org/10.1002/9780470061619.ch15
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 3439
Conn, J., Bollback, J. P., Onyabe, D., Robinson, T., Wilkerson, R., & Povoa, M. (2001). Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi. Molecular Ecology Notes, 1(4), 223–225. https://doi.org/ 10.1046/j.1471-8278.2001.00078.x
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 4229
Bollback, J. P., & Huelsenbeck, J. (2001). Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). Journal of Molecular Evolution, 52(2), 117–128. https://doi.org/10.1007/s002390010140
View | DOI
 
[2]
2001 | Journal Article | IST-REx-ID: 3438
Huelsenbeck, J., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294(5550), 2310–2314. https://doi.org/10.1126/science.1065889
View | DOI
 
[1]
2001 | Journal Article | IST-REx-ID: 3440
Huelsenbeck, J., & Bollback, J. P. (2001). Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology, 50(3), 351–366. https://doi.org/10.1080/10635150119871
View | DOI
 

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33 Publications

Mark all

[33]
2018 | Journal Article | IST-REx-ID: 423   OA
Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife, 7. https://doi.org/10.7554/eLife.32035
View | Files available | DOI
 
[32]
2018 | Journal Article | IST-REx-ID: 67
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution, 2(10), 1633–1643. https://doi.org/10.1038/s41559-018-0651-y
View | Files available | DOI
 
[31]
2018 | Research Data | IST-REx-ID: 5585
Igler, C., Lagator, M., Tkacik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. IST Austria. https://doi.org/10.15479/AT:ISTA:108
View | Files available | DOI
 
[30]
2017 | Journal Article | IST-REx-ID: 1077   OA
Fernandes Redondo, R. A., Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the fX174 phage family. Journal of the Royal Society Interface, 14(126). https://doi.org/10.1098/rsif.2016.0139
View | Files available | DOI
 
[29]
2017 | Journal Article | IST-REx-ID: 954   OA
Lagator, M., Paixao, 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. https://doi.org/10.7554/eLife.25192
View | Files available | DOI
 
[28]
2017 | Journal Article | IST-REx-ID: 570   OA
Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife, 6. https://doi.org/10.7554/eLife.28921
View | Files available | DOI
 
[27]
2016 | Journal Article | IST-REx-ID: 1427   OA
Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution, 33(3), 761–769. https://doi.org/10.1093/molbev/msv269
View | Files available | DOI
 
[26]
2014 | Journal Article | IST-REx-ID: 2042   OA
Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-663
View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2412   OA
Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology, 13(1), 54–54. https://doi.org/10.1186/1471-2148-13-54
View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 500   OA
Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology, 13(1), 222. https://doi.org/10.1186/1471-2148-13-222
View | Files available | DOI
 
[23]
2013 | Journal Article | IST-REx-ID: 2410   OA
Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements, 1(3). https://doi.org/10.1128/genomeA.00216-13
View | Files available | DOI
 
[22]
2010 | Journal Article | IST-REx-ID: 4358
Guinane, C., Ben Zakour, N., Tormo Mas, M., Weinert, L., Lowder, B., Cartwright, R., … Fitzgerald, J. R. (2010). Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution, 2, 454–466. https://doi.org/10.1093/gbe/evq031
View | DOI
 
[21]
2009 | Journal Article | IST-REx-ID: 4357
Bollback, J. P., & Huelsenbeck, J. (2009). Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics, 181(1), 225–234. https://doi.org/10.1534/genetics.107.085225
View | DOI
 
[20]
2008 | Journal Article | IST-REx-ID: 3435   OA
Bollback, J. P., York, T., & Nielsen, R. (2008). Estimation of 2Nes From Temporal Allele Frequency Data. Genetics, 179(1), 497–502. https://doi.org/10.1534/genetics.107.085019
View | DOI | Download (ext.)
 
[19]
2007 | Journal Article | IST-REx-ID: 4355
Bollback, J. P., & Huelsenbeck, J. (2007). Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution, 24(6), 1397–1406. https://doi.org/10.1093/molbev/msm056
View | DOI
 
[18]
2007 | Journal Article | IST-REx-ID: 4356
Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., & Nielsen, R. (2007). Genes under positive selection in Escherichia coli. Genome Research, 17(9), 1336–1343. https://doi.org/10.1101/gr.6254707
View | DOI
 
[17]
2007 | Journal Article | IST-REx-ID: 3436
Reynolds, S., Dryer, K., Bollback, J. P., Uy, J. A., Patricelli, G., Robson, T., … Braun, M. (2007). Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. The Auk, 124(3), 857–867. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
View | DOI
 
[16]
2007 | Book Chapter | IST-REx-ID: 3432
Bollback, J. P., Gardner, P., & Nielsen, R. (2007). Estimating the history of mutations on a phylogeny. In D. Liberles (Ed.), Ancestral Sequence Reconstruction (pp. 69–79). Oxford University Press. https://doi.org/10.1093/acprof:oso/9780199299188.003.0006
View | DOI
 
[15]
2007 | Journal Article | IST-REx-ID: 4353
Binladen, J., Gilbert, M. T., 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). https://doi.org/10.1371/journal.pone.0000197
View | DOI
 
[14]
2007 | Journal Article | IST-REx-ID: 4354
Freyhult, E., Bollback, J. P., & Gardner, 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. https://doi.org/10.1101/gr.5890907
View | DOI | Download (ext.)
 
[13]
2006 | Journal Article | IST-REx-ID: 4351
Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7. https://doi.org/10.1186/1471-2105-7-88
View | DOI
 
[12]
2006 | Journal Article | IST-REx-ID: 4352
Conn, J., Vineis, J., Bollback, J. P., Onyabe, D., Wilkerson, R., & Povoa, M. (2006). Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. The American Journal of Tropical Medicine and Hygiene, 74(5), 798–806.
View | Download (ext.)
 
[11]
2006 | Journal Article | IST-REx-ID: 3437
Betancourt, A., & 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. https://doi.org/10.1016/j.gde.2006.10.006
View | DOI
 
[10]
2005 | Book Chapter | IST-REx-ID: 3433
Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions. In R. Nielsen (Ed.), Statistical methods in Molecular Evolution (pp. 439–462). Springer. https://doi.org/10.1007/0-387-27733-1
View | DOI
 
[9]
2003 | Journal Article | IST-REx-ID: 4348
Huelsenbeck, J., Nielsen, R., & Bollback, J. P. (2003). Stochastic mapping of morphological characters. Systematic Biology, 52(2), 131–158. https://doi.org/10.1080/10635150390192780
View | DOI
 
[8]
2003 | Journal Article | IST-REx-ID: 4350
Harshman, J., Huddleston, C., Bollback, J. P., Parsons, T., & Braun, M. (2003). True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology, 52(3), 386–402. https://doi.org/10.1080/10635150390197028
View | DOI
 
[7]
2002 | Journal Article | IST-REx-ID: 4349
Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution, 19(7), 1171–1180.
View | Download (ext.)
 
[6]
2002 | Journal Article | IST-REx-ID: 4347
Huelsenbeck, J., Bollback, J. P., & Levine, A. (2002). Inferring the root of a phylogenetic tree. Systematic Biology, 51(1), 32–43. https://doi.org/10.1080/106351502753475862
View | DOI
 
[5]
2001 | Book Chapter | IST-REx-ID: 3434
Huelsenbeck, J., & Bollback, J. P. (2001). Application of the likelihood function in phylogenetic analysis. In D. Balding, M. Bishop, & C. Cannings (Eds.), Handbook of Statistical Genetics (pp. 415–439). Wiley-Blackwell. https://doi.org/10.1002/9780470061619.ch15
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 3439
Conn, J., Bollback, J. P., Onyabe, D., Robinson, T., Wilkerson, R., & Povoa, M. (2001). Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi. Molecular Ecology Notes, 1(4), 223–225. https://doi.org/ 10.1046/j.1471-8278.2001.00078.x
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 4229
Bollback, J. P., & Huelsenbeck, J. (2001). Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). Journal of Molecular Evolution, 52(2), 117–128. https://doi.org/10.1007/s002390010140
View | DOI
 
[2]
2001 | Journal Article | IST-REx-ID: 3438
Huelsenbeck, J., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294(5550), 2310–2314. https://doi.org/10.1126/science.1065889
View | DOI
 
[1]
2001 | Journal Article | IST-REx-ID: 3440
Huelsenbeck, J., & Bollback, J. P. (2001). Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology, 50(3), 351–366. https://doi.org/10.1080/10635150119871
View | DOI
 

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