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Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq

Methods in molecular biology (Clifton, N.J.), 2014-01, Vol.1151, p.165

2014

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The dynamics of molecular evolution over 60,000 generations

Nature (London), 2017-11, Vol.551 (7678), p.45-50

2017

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Genomic analysis of a key innovation in an experimental Escherichia coli population

Nature (London), 2012-09, Vol.489 (7417), p.513-518

2012

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Engineered symbionts activate honey bee immunity and limit pathogens

Science (American Association for the Advancement of Science), 2020-01, Vol.367 (6477), p.573-576

2020

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Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Nature communications, 2021-02, Vol.12 (1), p.980-12, Article 980

2021

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Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences

PloS one, 2024-05, Vol.19 (5), p.e0304164-e0304164

2024

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Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

Science (American Association for the Advancement of Science), 2012-01, Vol.335 (6067), p.428-432

2012

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The distributions, mechanisms, and structures of metabolite-binding riboswitches

Genome biology, 2007-01, Vol.8 (11), p.R239-R239

2007

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Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

BMC genomics, 2014-11, Vol.15 (1), p.1039-1039

2014

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Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli

PLoS biology, 2024-05, Vol.22 (5), p.e3002418-e3002418

2024

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Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides

PLoS genetics, 2018-04, Vol.14 (4), p.e1007348-e1007348

2018

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No assembly required: Time for stronger, simpler publishing standards for DNA sequences

PLoS biology, 2023-11, Vol.21 (11), p.e3002376-e3002376

2023

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Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

Proceedings of the National Academy of Sciences - PNAS, 2013-01, Vol.110 (1), p.222-227

2013

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The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm

PloS one, 2015-06, Vol.10 (6), p.e0130639

2015

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Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria

Nature communications, 2019-12, Vol.10 (1), p.5809-12, Article 5809

2019

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Disentangling the Evolutionary History of Feo, the Major Ferrous Iron Transport System in Bacteria

mBio, 2022-02, Vol.13 (1), p.e0351221-e0351221

2022

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Balancing robustness and evolvability

PLoS biology, 2006-12, Vol.4 (12), p.e428-e428

2006

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Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host

PloS one, 2011-01, Vol.6 (1), p.e16399-e16399

2011

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Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

Proceedings of the National Academy of Sciences - PNAS, 2014-02, Vol.111 (6), p.2217-2222

2014

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Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

mBio, 2014-09, Vol.5 (5), p.e01377

2014

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Genome dynamics during experimental evolution

Nature reviews. Genetics, 2013-12, Vol.14 (12), p.827

2013

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Vertical Transmission at the Pathogen-Symbiont Interface: Serratia symbiotica and Aphids

mBio, 2021-04, Vol.12 (2)

2021

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Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

eLife, 2015-10, Vol.4

2015

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Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria

Cell, 2003-05, Vol.113 (5), p.577-586

2003

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Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals

BMC biology, 2022-12, Vol.20 (1), p.290-290, Article 290

2022

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Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq

The dynamics of molecular evolution over 60,000 generations

Genomic analysis of a key innovation in an experimental Escherichia coli population

Engineered symbionts activate honey bee immunity and limit pathogens

Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences

Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

The distributions, mechanisms, and structures of metabolite-binding riboswitches

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli

Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides

No assembly required: Time for stronger, simpler publishing standards for DNA sequences

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm

Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria

Disentangling the Evolutionary History of Feo, the Major Ferrous Iron Transport System in Bacteria

Balancing robustness and evolvability

Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

Genome dynamics during experimental evolution

Vertical Transmission at the Pathogen-Symbiont Interface: Serratia symbiotica and Aphids

Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria

Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals

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