Search Results - "Bollback, Jonathan P."

SIMMAP: stochastic character mapping of discrete traits on phylogenies by Bollback, Jonathan P

“…Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution…”
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Experimental determination of evolutionary barriers to horizontal gene transfer by Acar Kirit, Hande, Lagator, Mato, Bollback, Jonathan P

“…Horizontal gene transfer, the acquisition of genes across species boundaries, is a major source of novel phenotypes that enables microbes to rapidly adapt to…”
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The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing by Binladen, Jonas, Gilbert, M Thomas P, Bollback, Jonathan P, Panitz, Frank, Bendixen, Christian, Nielsen, Rasmus, Willerslev, Eske

“…The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence…”
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Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors by Bhatia, Rama P., Kirit, Hande A., Predeus, Alexander V., Bollback, Jonathan P.

“…Environmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene…”
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Author Correction: Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors by Bhatia, Rama P., Kirit, Hande A., Predeus, Alexander V., Bollback, Jonathan P.

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Estimation of 2Nes From Temporal Allele Frequency Data by Bollback, Jonathan P, York, Thomas L, Nielsen, Rasmus

“…We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from…”
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CRISPR-based herd immunity can limit phage epidemics in bacterial populations by Payne, Pavel, Geyrhofer, Lukas, Barton, Nicholas H, Bollback, Jonathan P

“…Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even…”
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Genes under positive selection in Escherichia coli by Petersen, Lise, Bollback, Jonathan P, Dimmic, Matt, Hubisz, Melissa, Nielsen, Rasmus

“…We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including…”
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Predicting bacterial promoter function and evolution from random sequences by Lagator, Mato, Sarikas, Srdjan, Steinrueck, Magdalena, Toledo-Aparicio, David, Bollback, Jonathan P, Guet, Calin C, Tkačik, Gašper

“…Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a…”
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Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology by Huelsenbeck, John P., Ronquist, Fredrik, Nielsen, Rasmus, Bollback, Jonathan P.

“…As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life,…”
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Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence by Bollback, Jonathan P, Huelsenbeck, John P

“…Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying…”
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Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA by Freyhult, Eva K, Bollback, Jonathan P, Gardner, Paul P

“…Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding…”
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Regulatory network structure determines patterns of intermolecular epistasis by Lagator, Mato, Sarikas, Srdjan, Acar, Hande, Bollback, Jonathan P, Guet, Călin C

“…Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known…”
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On the mechanistic nature of epistasis in a canonical cis -regulatory element by Lagator, Mato, Paixão, Tiago, Barton, Nicholas H, Bollback, Jonathan P, Guet, Călin C

“…Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly…”
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The Role of the Environment in Horizontal Gene Transfer by Acar Kirit, Hande, Bollback, Jonathan P, Lagator, Mato

“…Gene-by-environment interactions play a crucial role in horizontal gene transfer by affecting how the transferred genes alter host fitness. However, how the…”
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True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia by Harshman, John, Huddleston, Christopher J., Bollback, Jonathan P., Parsons, Thomas J., Braun, Michael J., Baker, Allan

“…The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false…”
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Stochastic Mapping of Morphological Characters by Huelsenbeck, John P., Nielsen, Rasmus, Bollback, Jonathan P., Schultz, Ted

“…Many questions in evolutionary biology are best addressed by comparing traits in different species. Often such studies involve mapping characters on…”
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Motif depletion in bacteriophages infecting hosts with CRISPR systems by Kupczok, Anne, Bollback, Jonathan P

“…CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome,…”
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Bayesian model adequacy and choice in phylogenetics by Bollback, Jonathan P

“…Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large…”
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Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae) by Bollback, J P, Huelsenbeck, J P

“…Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species, such as Q beta and MS2, have been…”
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