Jonathan P Bollback

Bollback Group

37 Publications

Mark all

[37]
2022 | Journal Article | IST-REx-ID: 10736 | OA
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. Tkačik, ELife 11 (2022).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[36]
2020 | Journal Article | IST-REx-ID: 7652 | OA
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. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.
[Submitted Version] View | Files available | DOI | WoS
 
[35]
2018 | Journal Article | IST-REx-ID: 423 | OA
CRISPR-based herd immunity can limit phage epidemics in bacterial populations
P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).
[Published Version] View | Files available | DOI | WoS
 
[34]
2018 | Research Data Reference | IST-REx-ID: 9840 | OA
Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations
P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[33]
2018 | Journal Article | IST-REx-ID: 67 | OA
Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.
[Submitted Version] View | Files available | DOI | WoS
 
[32]
2018 | Research Data | IST-REx-ID: 5585 | OA
Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).
[Published Version] View | Files available | DOI
 
[31]
2017 | Journal Article | IST-REx-ID: 570 | OA
Regulatory network structure determines patterns of intermolecular epistasis
M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).
[Published Version] View | Files available | DOI
 
[30]
2017 | Journal Article | IST-REx-ID: 1077 | OA
Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family
R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).
[Published Version] View | Files available | DOI | WoS
 
[29]
2017 | Journal Article | IST-REx-ID: 954 | OA
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).
[Published Version] View | Files available | DOI | WoS
 
[28]
2016 | Journal Article | IST-REx-ID: 1427 | OA
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.
[Published Version] View | Files available | DOI
 
[27]
2016 | Research Data Reference | IST-REx-ID: 9864 | OA
Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family
R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[26]
2014 | Journal Article | IST-REx-ID: 2042 | OA
Motif depletion in bacteriophages infecting hosts with CRISPR systems
A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).
[Published Version] View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2412 | OA
Probabilistic models for CRISPR spacer content evolution
A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.
[Published Version] View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 2410 | OA
Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis
R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).
[Published Version] View | Files available | DOI
 
[23]
2013 | Journal Article | IST-REx-ID: 500 | OA
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).
[Published Version] View | Files available | DOI
 
[22]
2010 | Journal Article | IST-REx-ID: 4358
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.
View | DOI
 
[21]
2009 | Journal Article | IST-REx-ID: 4357
Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence
J.P. Bollback, J. Huelsenbeck, Genetics 181 (2009) 225–234.
View | DOI
 
[20]
2008 | Journal Article | IST-REx-ID: 3435 | OA
Estimation of 2Nes From Temporal Allele Frequency Data
J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.
View | DOI | Download (ext.)
 
[19]
2007 | Journal Article | IST-REx-ID: 4353
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).
View | DOI
 
[18]
2007 | Journal Article | IST-REx-ID: 4356
Genes under positive selection in Escherichia coli
L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research 17 (2007) 1336–1343.
View | DOI
 
[17]
2007 | Journal Article | IST-REx-ID: 4355
Clonal interference is alleviated by high mutation rates in large populations
J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007) 1397–1406.
View | DOI
 
[16]
2007 | Journal Article | IST-REx-ID: 4354
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.
View | DOI | Download (ext.)
 
[15]
2007 | Journal Article | IST-REx-ID: 3436
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.
View | DOI
 
[14]
2007 | Book Chapter | IST-REx-ID: 3432
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.
View | DOI
 
[13]
2006 | Journal Article | IST-REx-ID: 4352
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.
View | Download (ext.)
 
[12]
2006 | Journal Article | IST-REx-ID: 4351
SIMMAP: stochastic character mapping of discrete traits on phylogenies
J.P. Bollback, BMC Bioinformatics 7 (2006).
View | DOI
 
[11]
2006 | Journal Article | IST-REx-ID: 3437
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.
View | DOI
 
[10]
2005 | Book Chapter | IST-REx-ID: 3433
Posterior mapping and posterior predictive distributions
J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution, Springer, 2005, pp. 439–462.
View | DOI
 
[9]
2003 | Journal Article | IST-REx-ID: 4350
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.
View | DOI | PubMed | Europe PMC
 
[8]
2003 | Journal Article | IST-REx-ID: 4348
Stochastic mapping of morphological characters
J. Huelsenbeck, R. Nielsen, J.P. Bollback, Systematic Biology 52 (2003) 131–158.
View | DOI | PubMed | Europe PMC
 
[7]
2002 | Journal Article | IST-REx-ID: 4349
Bayesian model adequacy and choice in phylogenetics
J.P. Bollback, Molecular Biology and Evolution 19 (2002) 1171–80.
View | DOI | PubMed | Europe PMC
 
[6]
2002 | Journal Article | IST-REx-ID: 4347
Inferring the root of a phylogenetic tree
J. Huelsenbeck, J.P. Bollback, A. Levine, Systematic Biology 51 (2002) 32–43.
View | DOI | PubMed | Europe PMC
 
[5]
2001 | Journal Article | IST-REx-ID: 4229
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.
View | DOI | PubMed | Europe PMC
 
[4]
2001 | Journal Article | IST-REx-ID: 3439
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.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 3440
Empirical and hierarchical Bayesian estimation of ancestral states
J. Huelsenbeck, J.P. Bollback, Systematic Biology 50 (2001) 351–366.
View | DOI | PubMed | Europe PMC
 
[2]
2001 | Journal Article | IST-REx-ID: 3438
Bayesian inference of phylogeny and its impact on evolutionary biology
J. Huelsenbeck, F. Ronquist, R. Nielsen, J.P. Bollback, Science 294 (2001) 2310–2314.
View | DOI | PubMed | Europe PMC
 
[1]
2001 | Book Chapter | IST-REx-ID: 3434
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.
View | DOI
 
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37 Publications

Mark all

[37]
2022 | Journal Article | IST-REx-ID: 10736 | OA
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. Tkačik, ELife 11 (2022).
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[36]
2020 | Journal Article | IST-REx-ID: 7652 | OA
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. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.
[Submitted Version] View | Files available | DOI | WoS
 
[35]
2018 | Journal Article | IST-REx-ID: 423 | OA
CRISPR-based herd immunity can limit phage epidemics in bacterial populations
P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).
[Published Version] View | Files available | DOI | WoS
 
[34]
2018 | Research Data Reference | IST-REx-ID: 9840 | OA
Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations
P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[33]
2018 | Journal Article | IST-REx-ID: 67 | OA
Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.
[Submitted Version] View | Files available | DOI | WoS
 
[32]
2018 | Research Data | IST-REx-ID: 5585 | OA
Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring
C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).
[Published Version] View | Files available | DOI
 
[31]
2017 | Journal Article | IST-REx-ID: 570 | OA
Regulatory network structure determines patterns of intermolecular epistasis
M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).
[Published Version] View | Files available | DOI
 
[30]
2017 | Journal Article | IST-REx-ID: 1077 | OA
Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family
R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).
[Published Version] View | Files available | DOI | WoS
 
[29]
2017 | Journal Article | IST-REx-ID: 954 | OA
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).
[Published Version] View | Files available | DOI | WoS
 
[28]
2016 | Journal Article | IST-REx-ID: 1427 | OA
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.
[Published Version] View | Files available | DOI
 
[27]
2016 | Research Data Reference | IST-REx-ID: 9864 | OA
Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family
R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
[Published Version] View | Files available | DOI | Download Published Version (ext.)
 
[26]
2014 | Journal Article | IST-REx-ID: 2042 | OA
Motif depletion in bacteriophages infecting hosts with CRISPR systems
A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).
[Published Version] View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2412 | OA
Probabilistic models for CRISPR spacer content evolution
A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.
[Published Version] View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 2410 | OA
Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis
R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).
[Published Version] View | Files available | DOI
 
[23]
2013 | Journal Article | IST-REx-ID: 500 | OA
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).
[Published Version] View | Files available | DOI
 
[22]
2010 | Journal Article | IST-REx-ID: 4358
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.
View | DOI
 
[21]
2009 | Journal Article | IST-REx-ID: 4357
Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence
J.P. Bollback, J. Huelsenbeck, Genetics 181 (2009) 225–234.
View | DOI
 
[20]
2008 | Journal Article | IST-REx-ID: 3435 | OA
Estimation of 2Nes From Temporal Allele Frequency Data
J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.
View | DOI | Download (ext.)
 
[19]
2007 | Journal Article | IST-REx-ID: 4353
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).
View | DOI
 
[18]
2007 | Journal Article | IST-REx-ID: 4356
Genes under positive selection in Escherichia coli
L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research 17 (2007) 1336–1343.
View | DOI
 
[17]
2007 | Journal Article | IST-REx-ID: 4355
Clonal interference is alleviated by high mutation rates in large populations
J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007) 1397–1406.
View | DOI
 
[16]
2007 | Journal Article | IST-REx-ID: 4354
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.
View | DOI | Download (ext.)
 
[15]
2007 | Journal Article | IST-REx-ID: 3436
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.
View | DOI
 
[14]
2007 | Book Chapter | IST-REx-ID: 3432
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.
View | DOI
 
[13]
2006 | Journal Article | IST-REx-ID: 4352
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.
View | Download (ext.)
 
[12]
2006 | Journal Article | IST-REx-ID: 4351
SIMMAP: stochastic character mapping of discrete traits on phylogenies
J.P. Bollback, BMC Bioinformatics 7 (2006).
View | DOI
 
[11]
2006 | Journal Article | IST-REx-ID: 3437
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.
View | DOI
 
[10]
2005 | Book Chapter | IST-REx-ID: 3433
Posterior mapping and posterior predictive distributions
J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution, Springer, 2005, pp. 439–462.
View | DOI
 
[9]
2003 | Journal Article | IST-REx-ID: 4350
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.
View | DOI | PubMed | Europe PMC
 
[8]
2003 | Journal Article | IST-REx-ID: 4348
Stochastic mapping of morphological characters
J. Huelsenbeck, R. Nielsen, J.P. Bollback, Systematic Biology 52 (2003) 131–158.
View | DOI | PubMed | Europe PMC
 
[7]
2002 | Journal Article | IST-REx-ID: 4349
Bayesian model adequacy and choice in phylogenetics
J.P. Bollback, Molecular Biology and Evolution 19 (2002) 1171–80.
View | DOI | PubMed | Europe PMC
 
[6]
2002 | Journal Article | IST-REx-ID: 4347
Inferring the root of a phylogenetic tree
J. Huelsenbeck, J.P. Bollback, A. Levine, Systematic Biology 51 (2002) 32–43.
View | DOI | PubMed | Europe PMC
 
[5]
2001 | Journal Article | IST-REx-ID: 4229
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.
View | DOI | PubMed | Europe PMC
 
[4]
2001 | Journal Article | IST-REx-ID: 3439
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.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 3440
Empirical and hierarchical Bayesian estimation of ancestral states
J. Huelsenbeck, J.P. Bollback, Systematic Biology 50 (2001) 351–366.
View | DOI | PubMed | Europe PMC
 
[2]
2001 | Journal Article | IST-REx-ID: 3438
Bayesian inference of phylogeny and its impact on evolutionary biology
J. Huelsenbeck, F. Ronquist, R. Nielsen, J.P. Bollback, Science 294 (2001) 2310–2314.
View | DOI | PubMed | Europe PMC
 
[1]
2001 | Book Chapter | IST-REx-ID: 3434
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.
View | DOI
 
Marked Publication(s)

Search

Filter Publications

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    Citation Style: Default

    Export / Embed