34 Publications

Mark all

[34]
2020 | Journal Article | IST-REx-ID: 7652
Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
View | Files available | DOI
 
[33]
2018 | Journal Article | IST-REx-ID: 423   OA
Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.
View | Files available | DOI
 
[32]
2018 | Journal Article | IST-REx-ID: 67   OA
Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.
View | Files available | DOI
 
[31]
2018 | Research Data | IST-REx-ID: 5585
Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. IST Austria, 2018, doi:10.15479/AT:ISTA:108.
View | Files available | DOI
 
[30]
2017 | Journal Article | IST-REx-ID: 1077   OA
Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the FX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139.
View | Files available | DOI
 
[29]
2017 | Journal Article | IST-REx-ID: 954   OA
Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.
View | Files available | DOI
 
[28]
2017 | Journal Article | IST-REx-ID: 570   OA
Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.
View | Files available | DOI
 
[27]
2016 | Journal Article | IST-REx-ID: 1427   OA
Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269.
View | Files available | DOI
 
[26]
2014 | Journal Article | IST-REx-ID: 2042   OA
Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663.
View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2412   OA
Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:10.1186/1471-2148-13-54.
View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 500   OA
Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no. 1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222.
View | Files available | DOI
 
[23]
2013 | Journal Article | IST-REx-ID: 2410   OA
Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements, vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13.
View | Files available | DOI
 
[22]
2010 | Journal Article | IST-REx-ID: 4358
Guinane, Caitriona, et al. “Evolutionary Genomics of Staphylococcus Aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation.” Genome Biology and Evolution, vol. 2, Oxford University Press, 2010, pp. 454–66, doi:10.1093/gbe/evq031.
View | DOI
 
[21]
2009 | Journal Article | IST-REx-ID: 4357
Bollback, Jonathan P., and John Huelsenbeck. “Parallel Genetic Evolution within and between Bacteriophage Species of Varying Degrees of Divergence.” Genetics, vol. 181, no. 1, Genetics Society of America, 2009, pp. 225–34, doi:10.1534/genetics.107.085225.
View | DOI
 
[20]
2008 | Journal Article | IST-REx-ID: 3435   OA
Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency Data.” Genetics, vol. 179, no. 1, Genetics Society of America, 2008, pp. 497–502, doi:10.1534/genetics.107.085019.
View | DOI | Download (ext.)
 
[19]
2007 | Journal Article | IST-REx-ID: 4355
Bollback, Jonathan P., and John Huelsenbeck. “Clonal Interference Is Alleviated by High Mutation Rates in Large Populations.” Molecular Biology and Evolution, vol. 24, no. 6, Oxford University Press, 2007, pp. 1397–406, doi:10.1093/molbev/msm056.
View | DOI
 
[18]
2007 | Journal Article | IST-REx-ID: 4356
Petersen, Lise, et al. “Genes under Positive Selection in Escherichia Coli.” Genome Research, vol. 17, no. 9, Cold Spring Harbor Laboratory Press, 2007, pp. 1336–43, doi:10.1101/gr.6254707.
View | DOI
 
[17]
2007 | Journal Article | IST-REx-ID: 3436
Reynolds, Sheila, et al. “Behavioral Paternity Predicts Genetic Paternity in Satin Bowerbirds, a Species with a Non-Resource-Based Mating System.” The Auk, vol. 124, no. 3, University of California Press, 2007, pp. 857–67, doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2.
View | DOI
 
[16]
2007 | Book Chapter | IST-REx-ID: 3432
Bollback, Jonathan P., et al. “Estimating the History of Mutations on a Phylogeny.” Ancestral Sequence Reconstruction, edited by David Liberles, Oxford University Press, 2007, pp. 69–79, doi:10.1093/acprof:oso/9780199299188.003.0006.
View | DOI
 
[15]
2007 | Journal Article | IST-REx-ID: 4353
Binladen, Jonas, et al. “The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.” PLoS One, vol. 2, no. 2, Public Library of Science, 2007, doi:10.1371/journal.pone.0000197.
View | DOI
 
[14]
2007 | Journal Article | IST-REx-ID: 4354
Freyhult, Eva, et al. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” Genome Research, vol. 17, no. 1, Cold Spring Harbor Laboratory Press, 2007, pp. 117–25, doi:10.1101/gr.5890907.
View | DOI | Download (ext.)
 
[13]
2006 | Journal Article | IST-REx-ID: 4351
Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.
View | DOI
 
[12]
2006 | Journal Article | IST-REx-ID: 4352
Conn, Jan, et al. “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, vol. 74, no. 5, American Society of Tropical Medicine and Hygiene, 2006, pp. 798–806.
View | Download (ext.)
 
[11]
2006 | Journal Article | IST-REx-ID: 3437
Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp. 618–23, doi:10.1016/j.gde.2006.10.006.
View | DOI
 
[10]
2005 | Book Chapter | IST-REx-ID: 3433
Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, Springer, 2005, pp. 439–62, doi:10.1007/0-387-27733-1.
View | DOI
 
[9]
2003 | Journal Article | IST-REx-ID: 4348
Huelsenbeck, John, et al. “Stochastic Mapping of Morphological Characters.” Systematic Biology, vol. 52, no. 2, Oxford University Press, 2003, pp. 131–58, doi:10.1080/10635150390192780.
View | DOI
 
[8]
2003 | Journal Article | IST-REx-ID: 4350
Harshman, John, et al. “True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia.” Systematic Biology, vol. 52, no. 3, Oxford University Press, 2003, pp. 386–402, doi:10.1080/10635150390197028.
View | DOI
 
[7]
2002 | Journal Article | IST-REx-ID: 4349
Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.” Molecular Biology and Evolution, vol. 19, no. 7, Oxford University Press, 2002, pp. 1171–80.
View | Download (ext.)
 
[6]
2002 | Journal Article | IST-REx-ID: 4347
Huelsenbeck, John, et al. “Inferring the Root of a Phylogenetic Tree.” Systematic Biology, vol. 51, no. 1, Oxford University Press, 2002, pp. 32–43, doi:10.1080/106351502753475862.
View | DOI
 
[5]
2001 | Book Chapter | IST-REx-ID: 3434
Huelsenbeck, John, and Jonathan P. Bollback. “Application of the Likelihood Function in Phylogenetic Analysis.” Handbook of Statistical Genetics, edited by David Balding et al., Wiley-Blackwell, 2001, pp. 415–39, doi:10.1002/9780470061619.ch15.
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 3439
Conn, Jan, et al. “Isolation of Polymorphic Microsatellite Markers from the Malaria Vector Anopheles Darlingi.” Molecular Ecology Notes, vol. 1, no. 4, Wiley-Blackwell, 2001, pp. 223–25, doi: 10.1046/j.1471-8278.2001.00078.x.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 4229
Bollback, Jonathan P., and John Huelsenbeck. “Phylogeny, Genome Evolution, and Host Specificity of Single-Stranded RNA Bacteriophage (Family Leviviridae).” Journal of Molecular Evolution, vol. 52, no. 2, Springer, 2001, pp. 117–28, doi:10.1007/s002390010140.
View | DOI
 
[2]
2001 | Journal Article | IST-REx-ID: 3438
Huelsenbeck, John, et al. “Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology.” Science, vol. 294, no. 5550, American Association for the Advancement of Science, 2001, pp. 2310–14, doi:10.1126/science.1065889.
View | DOI
 
[1]
2001 | Journal Article | IST-REx-ID: 3440
Huelsenbeck, John, and Jonathan P. Bollback. “Empirical and Hierarchical Bayesian Estimation of Ancestral States.” Systematic Biology, vol. 50, no. 3, Oxford University Press, 2001, pp. 351–66, doi:10.1080/10635150119871.
View | DOI
 

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34 Publications

Mark all

[34]
2020 | Journal Article | IST-REx-ID: 7652
Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
View | Files available | DOI
 
[33]
2018 | Journal Article | IST-REx-ID: 423   OA
Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.
View | Files available | DOI
 
[32]
2018 | Journal Article | IST-REx-ID: 67   OA
Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.
View | Files available | DOI
 
[31]
2018 | Research Data | IST-REx-ID: 5585
Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. IST Austria, 2018, doi:10.15479/AT:ISTA:108.
View | Files available | DOI
 
[30]
2017 | Journal Article | IST-REx-ID: 1077   OA
Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the FX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139.
View | Files available | DOI
 
[29]
2017 | Journal Article | IST-REx-ID: 954   OA
Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.
View | Files available | DOI
 
[28]
2017 | Journal Article | IST-REx-ID: 570   OA
Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.
View | Files available | DOI
 
[27]
2016 | Journal Article | IST-REx-ID: 1427   OA
Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269.
View | Files available | DOI
 
[26]
2014 | Journal Article | IST-REx-ID: 2042   OA
Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663.
View | Files available | DOI
 
[25]
2013 | Journal Article | IST-REx-ID: 2412   OA
Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:10.1186/1471-2148-13-54.
View | Files available | DOI
 
[24]
2013 | Journal Article | IST-REx-ID: 500   OA
Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no. 1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222.
View | Files available | DOI
 
[23]
2013 | Journal Article | IST-REx-ID: 2410   OA
Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements, vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13.
View | Files available | DOI
 
[22]
2010 | Journal Article | IST-REx-ID: 4358
Guinane, Caitriona, et al. “Evolutionary Genomics of Staphylococcus Aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation.” Genome Biology and Evolution, vol. 2, Oxford University Press, 2010, pp. 454–66, doi:10.1093/gbe/evq031.
View | DOI
 
[21]
2009 | Journal Article | IST-REx-ID: 4357
Bollback, Jonathan P., and John Huelsenbeck. “Parallel Genetic Evolution within and between Bacteriophage Species of Varying Degrees of Divergence.” Genetics, vol. 181, no. 1, Genetics Society of America, 2009, pp. 225–34, doi:10.1534/genetics.107.085225.
View | DOI
 
[20]
2008 | Journal Article | IST-REx-ID: 3435   OA
Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency Data.” Genetics, vol. 179, no. 1, Genetics Society of America, 2008, pp. 497–502, doi:10.1534/genetics.107.085019.
View | DOI | Download (ext.)
 
[19]
2007 | Journal Article | IST-REx-ID: 4355
Bollback, Jonathan P., and John Huelsenbeck. “Clonal Interference Is Alleviated by High Mutation Rates in Large Populations.” Molecular Biology and Evolution, vol. 24, no. 6, Oxford University Press, 2007, pp. 1397–406, doi:10.1093/molbev/msm056.
View | DOI
 
[18]
2007 | Journal Article | IST-REx-ID: 4356
Petersen, Lise, et al. “Genes under Positive Selection in Escherichia Coli.” Genome Research, vol. 17, no. 9, Cold Spring Harbor Laboratory Press, 2007, pp. 1336–43, doi:10.1101/gr.6254707.
View | DOI
 
[17]
2007 | Journal Article | IST-REx-ID: 3436
Reynolds, Sheila, et al. “Behavioral Paternity Predicts Genetic Paternity in Satin Bowerbirds, a Species with a Non-Resource-Based Mating System.” The Auk, vol. 124, no. 3, University of California Press, 2007, pp. 857–67, doi:10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2.
View | DOI
 
[16]
2007 | Book Chapter | IST-REx-ID: 3432
Bollback, Jonathan P., et al. “Estimating the History of Mutations on a Phylogeny.” Ancestral Sequence Reconstruction, edited by David Liberles, Oxford University Press, 2007, pp. 69–79, doi:10.1093/acprof:oso/9780199299188.003.0006.
View | DOI
 
[15]
2007 | Journal Article | IST-REx-ID: 4353
Binladen, Jonas, et al. “The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.” PLoS One, vol. 2, no. 2, Public Library of Science, 2007, doi:10.1371/journal.pone.0000197.
View | DOI
 
[14]
2007 | Journal Article | IST-REx-ID: 4354
Freyhult, Eva, et al. “Exploring Genomic Dark Matter: A Critical Assessment of the Performance of Homology Search Methods on Noncoding RNA.” Genome Research, vol. 17, no. 1, Cold Spring Harbor Laboratory Press, 2007, pp. 117–25, doi:10.1101/gr.5890907.
View | DOI | Download (ext.)
 
[13]
2006 | Journal Article | IST-REx-ID: 4351
Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.
View | DOI
 
[12]
2006 | Journal Article | IST-REx-ID: 4352
Conn, Jan, et al. “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, vol. 74, no. 5, American Society of Tropical Medicine and Hygiene, 2006, pp. 798–806.
View | Download (ext.)
 
[11]
2006 | Journal Article | IST-REx-ID: 3437
Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp. 618–23, doi:10.1016/j.gde.2006.10.006.
View | DOI
 
[10]
2005 | Book Chapter | IST-REx-ID: 3433
Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, Springer, 2005, pp. 439–62, doi:10.1007/0-387-27733-1.
View | DOI
 
[9]
2003 | Journal Article | IST-REx-ID: 4348
Huelsenbeck, John, et al. “Stochastic Mapping of Morphological Characters.” Systematic Biology, vol. 52, no. 2, Oxford University Press, 2003, pp. 131–58, doi:10.1080/10635150390192780.
View | DOI
 
[8]
2003 | Journal Article | IST-REx-ID: 4350
Harshman, John, et al. “True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia.” Systematic Biology, vol. 52, no. 3, Oxford University Press, 2003, pp. 386–402, doi:10.1080/10635150390197028.
View | DOI
 
[7]
2002 | Journal Article | IST-REx-ID: 4349
Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.” Molecular Biology and Evolution, vol. 19, no. 7, Oxford University Press, 2002, pp. 1171–80.
View | Download (ext.)
 
[6]
2002 | Journal Article | IST-REx-ID: 4347
Huelsenbeck, John, et al. “Inferring the Root of a Phylogenetic Tree.” Systematic Biology, vol. 51, no. 1, Oxford University Press, 2002, pp. 32–43, doi:10.1080/106351502753475862.
View | DOI
 
[5]
2001 | Book Chapter | IST-REx-ID: 3434
Huelsenbeck, John, and Jonathan P. Bollback. “Application of the Likelihood Function in Phylogenetic Analysis.” Handbook of Statistical Genetics, edited by David Balding et al., Wiley-Blackwell, 2001, pp. 415–39, doi:10.1002/9780470061619.ch15.
View | DOI
 
[4]
2001 | Journal Article | IST-REx-ID: 3439
Conn, Jan, et al. “Isolation of Polymorphic Microsatellite Markers from the Malaria Vector Anopheles Darlingi.” Molecular Ecology Notes, vol. 1, no. 4, Wiley-Blackwell, 2001, pp. 223–25, doi: 10.1046/j.1471-8278.2001.00078.x.
View | DOI
 
[3]
2001 | Journal Article | IST-REx-ID: 4229
Bollback, Jonathan P., and John Huelsenbeck. “Phylogeny, Genome Evolution, and Host Specificity of Single-Stranded RNA Bacteriophage (Family Leviviridae).” Journal of Molecular Evolution, vol. 52, no. 2, Springer, 2001, pp. 117–28, doi:10.1007/s002390010140.
View | DOI
 
[2]
2001 | Journal Article | IST-REx-ID: 3438
Huelsenbeck, John, et al. “Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology.” Science, vol. 294, no. 5550, American Association for the Advancement of Science, 2001, pp. 2310–14, doi:10.1126/science.1065889.
View | DOI
 
[1]
2001 | Journal Article | IST-REx-ID: 3440
Huelsenbeck, John, and Jonathan P. Bollback. “Empirical and Hierarchical Bayesian Estimation of Ancestral States.” Systematic Biology, vol. 50, no. 3, Oxford University Press, 2001, pp. 351–66, doi:10.1080/10635150119871.
View | DOI
 

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