34 Publications

Mark all

[34]
2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7
View | Files available | DOI
 
[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. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035
View | Files available | DOI
 
[32]
2018 | Journal Article | IST-REx-ID: 67 | OA
Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. Nature Publishing Group. https://doi.org/10.1038/s41559-018-0651-y
View | Files available | DOI
 
[31]
2018 | Research Data | IST-REx-ID: 5585 | OA
Igler, C., Lagator, M., Tkačik, 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., de 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. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
View | Files available | DOI
 
[29]
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. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921
View | Files available | DOI
 
[28]
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. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
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. Oxford University Press. 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. BioMed Central. https://doi.org/10.1186/1471-2164-15-663
View | Files available | DOI
 
[25]
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. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13
View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 2412 | OA
Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54
View | Files available | DOI
 
[23]
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. BioMed Central. https://doi.org/10.1186/1471-2148-13-222
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. Oxford University Press. 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. Genetics Society of America. 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. Genetics Society of America. https://doi.org/10.1534/genetics.107.085019
View | DOI | Download (ext.)
 
[19]
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
 
[18]
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. University of California Press. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
View | DOI
 
[17]
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. Public Library of Science. https://doi.org/10.1371/journal.pone.0000197
View | DOI
 
[16]
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. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.5890907
View | DOI | Download (ext.)
 
[15]
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. Oxford University Press. https://doi.org/10.1093/molbev/msm056
View | DOI
 
[14]
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. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.6254707
View | DOI
 
[13]
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. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006
View | DOI
 
[12]
2006 | Journal Article | IST-REx-ID: 4351
Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88
View | DOI
 
[11]
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. American Society of Tropical Medicine and Hygiene.
View | Download (ext.)
 
[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. Oxford University Press. 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. Oxford University Press. https://doi.org/10.1080/10635150390197028
View | DOI
 
[7]
2002 | Journal Article | IST-REx-ID: 4347
Huelsenbeck, J., Bollback, J. P., & Levine, A. (2002). Inferring the root of a phylogenetic tree. Systematic Biology. Oxford University Press. https://doi.org/10.1080/106351502753475862
View | DOI
 
[6]
2002 | Journal Article | IST-REx-ID: 4349
Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. Oxford University Press.
View | Download (ext.)
 
[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: 3438
Huelsenbeck, J., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1065889
View | DOI
 
[3]
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. Wiley-Blackwell. https://doi.org/ 10.1046/j.1471-8278.2001.00078.x
View | DOI
 
[2]
2001 | Journal Article | IST-REx-ID: 3440
Huelsenbeck, J., & Bollback, J. P. (2001). Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. Oxford University Press. https://doi.org/10.1080/10635150119871
View | DOI
 
[1]
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. Springer. https://doi.org/10.1007/s002390010140
View | DOI
 

Search

Filter Publications

34 Publications

Mark all

[34]
2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7
View | Files available | DOI
 
[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. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035
View | Files available | DOI
 
[32]
2018 | Journal Article | IST-REx-ID: 67 | OA
Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. Nature Publishing Group. https://doi.org/10.1038/s41559-018-0651-y
View | Files available | DOI
 
[31]
2018 | Research Data | IST-REx-ID: 5585 | OA
Igler, C., Lagator, M., Tkačik, 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., de 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. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
View | Files available | DOI
 
[29]
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. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921
View | Files available | DOI
 
[28]
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. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
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. Oxford University Press. 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. BioMed Central. https://doi.org/10.1186/1471-2164-15-663
View | Files available | DOI
 
[25]
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. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13
View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 2412 | OA
Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54
View | Files available | DOI
 
[23]
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. BioMed Central. https://doi.org/10.1186/1471-2148-13-222
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. Oxford University Press. 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. Genetics Society of America. 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. Genetics Society of America. https://doi.org/10.1534/genetics.107.085019
View | DOI | Download (ext.)
 
[19]
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
 
[18]
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. University of California Press. https://doi.org/10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
View | DOI
 
[17]
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. Public Library of Science. https://doi.org/10.1371/journal.pone.0000197
View | DOI
 
[16]
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. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.5890907
View | DOI | Download (ext.)
 
[15]
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. Oxford University Press. https://doi.org/10.1093/molbev/msm056
View | DOI
 
[14]
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. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.6254707
View | DOI
 
[13]
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. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006
View | DOI
 
[12]
2006 | Journal Article | IST-REx-ID: 4351
Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88
View | DOI
 
[11]
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. American Society of Tropical Medicine and Hygiene.
View | Download (ext.)
 
[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. Oxford University Press. 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. Oxford University Press. https://doi.org/10.1080/10635150390197028
View | DOI
 
[7]
2002 | Journal Article | IST-REx-ID: 4347
Huelsenbeck, J., Bollback, J. P., & Levine, A. (2002). Inferring the root of a phylogenetic tree. Systematic Biology. Oxford University Press. https://doi.org/10.1080/106351502753475862
View | DOI
 
[6]
2002 | Journal Article | IST-REx-ID: 4349
Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. Oxford University Press.
View | Download (ext.)
 
[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: 3438
Huelsenbeck, J., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1065889
View | DOI
 
[3]
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. Wiley-Blackwell. https://doi.org/ 10.1046/j.1471-8278.2001.00078.x
View | DOI
 
[2]
2001 | Journal Article | IST-REx-ID: 3440
Huelsenbeck, J., & Bollback, J. P. (2001). Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. Oxford University Press. https://doi.org/10.1080/10635150119871
View | DOI
 
[1]
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. Springer. https://doi.org/10.1007/s002390010140
View | DOI
 

Search

Filter Publications