Jonathan P Bollback

Bollback Group

37 Publications

Mark all

[37]
2022 | Journal Article | IST-REx-ID: 10736 | OA
Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[36]
2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7
[Submitted Version] View | Files available | DOI | WoS
 
[35]
2018 | Journal Article | IST-REx-ID: 423 | OA
Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035
[Published Version] View | Files available | DOI | WoS
 
[34]
2018 | Research Data Reference | IST-REx-ID: 9840 | OA
Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[33]
2018 | Journal Article | IST-REx-ID: 67 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y
[Submitted Version] View | Files available | DOI | WoS
 
[32]
2018 | Research Data | IST-REx-ID: 5585 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108
[Published Version] View | Files available | DOI
 
[31]
2017 | Journal Article | IST-REx-ID: 570 | OA
Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921
[Published Version] View | Files available | DOI
 
[30]
2017 | Journal Article | IST-REx-ID: 1077 | OA
Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
[Published Version] View | Files available | DOI | WoS
 
[29]
2017 | Journal Article | IST-REx-ID: 954 | OA
Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
[Published Version] View | Files available | DOI | WoS
 
[28]
2016 | Journal Article | IST-REx-ID: 1427 | OA
Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269
[Published Version] View | Files available | DOI
 
[27]
2016 | Research Data Reference | IST-REx-ID: 9864 | OA
Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[26]
2014 | Journal Article | IST-REx-ID: 2042 | OA
Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663
[Published Version] View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2412 | OA
Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54
[Published Version] View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 2410 | OA
Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 2013;1(3). doi:10.1128/genomeA.00216-13
[Published Version] View | Files available | DOI
 
[23]
2013 | Journal Article | IST-REx-ID: 500 | OA
Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-222
[Published Version] View | Files available | DOI
 
[22]
2010 | Journal Article | IST-REx-ID: 4358
Guinane C, Ben Zakour N, Tormo Mas M, et al. Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution. 2010;2:454-466. doi:10.1093/gbe/evq031
View | DOI
 
[21]
2009 | Journal Article | IST-REx-ID: 4357
Bollback JP, Huelsenbeck J. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics. 2009;181(1):225-234. doi:10.1534/genetics.107.085225
View | DOI
 
[20]
2008 | Journal Article | IST-REx-ID: 3435 | OA
Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. 2008;179(1):497-502. doi:10.1534/genetics.107.085019
View | DOI | Download (ext.)
 
[19]
2007 | Journal Article | IST-REx-ID: 4353
Binladen J, Gilbert MT, Bollback JP, et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One. 2007;2(2). doi:10.1371/journal.pone.0000197
View | DOI
 
[18]
2007 | Journal Article | IST-REx-ID: 4356
Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive selection in Escherichia coli. Genome Research. 2007;17(9):1336-1343. doi:10.1101/gr.6254707
View | DOI
 
[17]
2007 | Journal Article | IST-REx-ID: 4355
Bollback JP, Huelsenbeck J. Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution. 2007;24(6):1397-1406. doi:10.1093/molbev/msm056
View | DOI
 
[16]
2007 | Journal Article | IST-REx-ID: 4354
Freyhult E, Bollback JP, Gardner P. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 2007;17(1):117-125. doi:10.1101/gr.5890907
View | DOI | Download (ext.)
 
[15]
2007 | Journal Article | IST-REx-ID: 3436
Reynolds S, Dryer K, Bollback JP, et al. Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. The Auk. 2007;124(3):857-867. doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
View | DOI
 
[14]
2007 | Book Chapter | IST-REx-ID: 3432
Bollback JP, Gardner P, Nielsen R. Estimating the history of mutations on a phylogeny. In: Liberles D, ed. Ancestral Sequence Reconstruction. Oxford University Press; 2007:69-79. doi:10.1093/acprof:oso/9780199299188.003.0006
View | DOI
 
[13]
2006 | Journal Article | IST-REx-ID: 4352
Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 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. 2006;74(5):798-806.
View | Download (ext.)
 
[12]
2006 | Journal Article | IST-REx-ID: 4351
Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88
View | DOI
 
[11]
2006 | Journal Article | IST-REx-ID: 3437
Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006
View | DOI
 
[10]
2005 | Book Chapter | IST-REx-ID: 3433
Bollback JP. Posterior mapping and posterior predictive distributions. In: Nielsen R, ed. Statistical Methods in Molecular Evolution. Springer; 2005:439-462. doi:10.1007/0-387-27733-1
View | DOI
 
[9]
2003 | Journal Article | IST-REx-ID: 4350
Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 2003;52(3):386-402. doi:10.1080/10635150390197028
View | DOI | PubMed | Europe PMC
 
[8]
2003 | Journal Article | IST-REx-ID: 4348
Huelsenbeck J, Nielsen R, Bollback JP. Stochastic mapping of morphological characters. Systematic Biology. 2003;52(2):131-158. doi:10.1080/10635150390192780
View | DOI | PubMed | Europe PMC
 
[7]
2002 | Journal Article | IST-REx-ID: 4349
Bollback JP. Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. 2002;19(7):1171-1180. doi:10.1093/oxfordjournals.molbev.a004175
View | DOI | PubMed | Europe PMC
 
[6]
2002 | Journal Article | IST-REx-ID: 4347
Huelsenbeck J, Bollback JP, Levine A. Inferring the root of a phylogenetic tree. Systematic Biology. 2002;51(1):32-43. doi:10.1080/106351502753475862
View | DOI | PubMed | Europe PMC
 
[5]
2001 | Journal Article | IST-REx-ID: 4229
Bollback JP, Huelsenbeck J. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). Journal of Molecular Evolution. 2001;52(2):117-128. doi:10.1007/s002390010140
View | DOI | PubMed | Europe PMC
 
[4]
2001 | Journal Article | IST-REx-ID: 3439
Conn J, Bollback JP, Onyabe D, Robinson T, Wilkerson R, Povoa M. Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi. Molecular Ecology Notes. 2001;1(4):223-225. doi: 10.1046/j.1471-8278.2001.00078.x
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 3440
Huelsenbeck J, Bollback JP. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. 2001;50(3):351-366. doi:10.1080/10635150119871
View | DOI | PubMed | Europe PMC
 
[2]
2001 | Journal Article | IST-REx-ID: 3438
Huelsenbeck J, Ronquist F, Nielsen R, Bollback JP. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 2001;294(5550):2310-2314. doi:10.1126/science.1065889
View | DOI | PubMed | Europe PMC
 
[1]
2001 | Book Chapter | IST-REx-ID: 3434
Huelsenbeck J, Bollback JP. Application of the likelihood function in phylogenetic analysis. In: Balding D, Bishop M, Cannings C, eds. Handbook of Statistical Genetics. Wiley-Blackwell; 2001:415-439. doi:10.1002/9780470061619.ch15
View | DOI
 
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37 Publications

Mark all

[37]
2022 | Journal Article | IST-REx-ID: 10736 | OA
Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[36]
2020 | Journal Article | IST-REx-ID: 7652 | OA
Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7
[Submitted Version] View | Files available | DOI | WoS
 
[35]
2018 | Journal Article | IST-REx-ID: 423 | OA
Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035
[Published Version] View | Files available | DOI | WoS
 
[34]
2018 | Research Data Reference | IST-REx-ID: 9840 | OA
Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[33]
2018 | Journal Article | IST-REx-ID: 67 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y
[Submitted Version] View | Files available | DOI | WoS
 
[32]
2018 | Research Data | IST-REx-ID: 5585 | OA
Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108
[Published Version] View | Files available | DOI
 
[31]
2017 | Journal Article | IST-REx-ID: 570 | OA
Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921
[Published Version] View | Files available | DOI
 
[30]
2017 | Journal Article | IST-REx-ID: 1077 | OA
Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
[Published Version] View | Files available | DOI | WoS
 
[29]
2017 | Journal Article | IST-REx-ID: 954 | OA
Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
[Published Version] View | Files available | DOI | WoS
 
[28]
2016 | Journal Article | IST-REx-ID: 1427 | OA
Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269
[Published Version] View | Files available | DOI
 
[27]
2016 | Research Data Reference | IST-REx-ID: 9864 | OA
Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[26]
2014 | Journal Article | IST-REx-ID: 2042 | OA
Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663
[Published Version] View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2412 | OA
Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54
[Published Version] View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 2410 | OA
Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 2013;1(3). doi:10.1128/genomeA.00216-13
[Published Version] View | Files available | DOI
 
[23]
2013 | Journal Article | IST-REx-ID: 500 | OA
Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-222
[Published Version] View | Files available | DOI
 
[22]
2010 | Journal Article | IST-REx-ID: 4358
Guinane C, Ben Zakour N, Tormo Mas M, et al. Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution. 2010;2:454-466. doi:10.1093/gbe/evq031
View | DOI
 
[21]
2009 | Journal Article | IST-REx-ID: 4357
Bollback JP, Huelsenbeck J. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics. 2009;181(1):225-234. doi:10.1534/genetics.107.085225
View | DOI
 
[20]
2008 | Journal Article | IST-REx-ID: 3435 | OA
Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. 2008;179(1):497-502. doi:10.1534/genetics.107.085019
View | DOI | Download (ext.)
 
[19]
2007 | Journal Article | IST-REx-ID: 4353
Binladen J, Gilbert MT, Bollback JP, et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One. 2007;2(2). doi:10.1371/journal.pone.0000197
View | DOI
 
[18]
2007 | Journal Article | IST-REx-ID: 4356
Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive selection in Escherichia coli. Genome Research. 2007;17(9):1336-1343. doi:10.1101/gr.6254707
View | DOI
 
[17]
2007 | Journal Article | IST-REx-ID: 4355
Bollback JP, Huelsenbeck J. Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution. 2007;24(6):1397-1406. doi:10.1093/molbev/msm056
View | DOI
 
[16]
2007 | Journal Article | IST-REx-ID: 4354
Freyhult E, Bollback JP, Gardner P. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research. 2007;17(1):117-125. doi:10.1101/gr.5890907
View | DOI | Download (ext.)
 
[15]
2007 | Journal Article | IST-REx-ID: 3436
Reynolds S, Dryer K, Bollback JP, et al. Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. The Auk. 2007;124(3):857-867. doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2
View | DOI
 
[14]
2007 | Book Chapter | IST-REx-ID: 3432
Bollback JP, Gardner P, Nielsen R. Estimating the history of mutations on a phylogeny. In: Liberles D, ed. Ancestral Sequence Reconstruction. Oxford University Press; 2007:69-79. doi:10.1093/acprof:oso/9780199299188.003.0006
View | DOI
 
[13]
2006 | Journal Article | IST-REx-ID: 4352
Conn J, Vineis J, Bollback JP, Onyabe D, Wilkerson R, Povoa M. 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. 2006;74(5):798-806.
View | Download (ext.)
 
[12]
2006 | Journal Article | IST-REx-ID: 4351
Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88
View | DOI
 
[11]
2006 | Journal Article | IST-REx-ID: 3437
Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006
View | DOI
 
[10]
2005 | Book Chapter | IST-REx-ID: 3433
Bollback JP. Posterior mapping and posterior predictive distributions. In: Nielsen R, ed. Statistical Methods in Molecular Evolution. Springer; 2005:439-462. doi:10.1007/0-387-27733-1
View | DOI
 
[9]
2003 | Journal Article | IST-REx-ID: 4350
Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 2003;52(3):386-402. doi:10.1080/10635150390197028
View | DOI | PubMed | Europe PMC
 
[8]
2003 | Journal Article | IST-REx-ID: 4348
Huelsenbeck J, Nielsen R, Bollback JP. Stochastic mapping of morphological characters. Systematic Biology. 2003;52(2):131-158. doi:10.1080/10635150390192780
View | DOI | PubMed | Europe PMC
 
[7]
2002 | Journal Article | IST-REx-ID: 4349
Bollback JP. Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. 2002;19(7):1171-1180. doi:10.1093/oxfordjournals.molbev.a004175
View | DOI | PubMed | Europe PMC
 
[6]
2002 | Journal Article | IST-REx-ID: 4347
Huelsenbeck J, Bollback JP, Levine A. Inferring the root of a phylogenetic tree. Systematic Biology. 2002;51(1):32-43. doi:10.1080/106351502753475862
View | DOI | PubMed | Europe PMC
 
[5]
2001 | Journal Article | IST-REx-ID: 4229
Bollback JP, Huelsenbeck J. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). Journal of Molecular Evolution. 2001;52(2):117-128. doi:10.1007/s002390010140
View | DOI | PubMed | Europe PMC
 
[4]
2001 | Journal Article | IST-REx-ID: 3439
Conn J, Bollback JP, Onyabe D, Robinson T, Wilkerson R, Povoa M. Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi. Molecular Ecology Notes. 2001;1(4):223-225. doi: 10.1046/j.1471-8278.2001.00078.x
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 3440
Huelsenbeck J, Bollback JP. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. 2001;50(3):351-366. doi:10.1080/10635150119871
View | DOI | PubMed | Europe PMC
 
[2]
2001 | Journal Article | IST-REx-ID: 3438
Huelsenbeck J, Ronquist F, Nielsen R, Bollback JP. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 2001;294(5550):2310-2314. doi:10.1126/science.1065889
View | DOI | PubMed | Europe PMC
 
[1]
2001 | Book Chapter | IST-REx-ID: 3434
Huelsenbeck J, Bollback JP. Application of the likelihood function in phylogenetic analysis. In: Balding D, Bishop M, Cannings C, eds. Handbook of Statistical Genetics. Wiley-Blackwell; 2001:415-439. doi:10.1002/9780470061619.ch15
View | DOI
 
Marked Publication(s)

Search

Filter Publications

    • Display / Sort

    Citation Style: AMA

    Export / Embed