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1.
Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations.
PLoS Genet
; 18(8): e1010324, 2022 08.
Article
in English
| MEDLINE | ID: mdl-35981004
2.
Maintenance of Metabolic Plasticity despite Relaxed Selection in a Long-Term Evolution Experiment with Escherichia coli.
Am Nat
; 198(1): 93-112, 2021 07.
Article
in English
| MEDLINE | ID: mdl-34143718
3.
Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection.
PLoS Genet
; 14(1): e1007199, 2018 01.
Article
in English
| MEDLINE | ID: mdl-29385126
4.
Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.
Mol Biol Evol
; 32(11): 2897-904, 2015 Nov.
Article
in English
| MEDLINE | ID: mdl-26199375
5.
Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli.
Proc Biol Sci
; 282(1821): 20152292, 2015 12 22.
Article
in English
| MEDLINE | ID: mdl-26674951
6.
Programming Dynamic Division of Labor Using Horizontal Gene Transfer.
ACS Synth Biol
; 13(4): 1142-1151, 2024 04 19.
Article
in English
| MEDLINE | ID: mdl-38568420
7.
Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria.
Nat Commun
; 15(1): 1449, 2024 Feb 16.
Article
in English
| MEDLINE | ID: mdl-38365845
8.
Programming dynamic division of labor using horizontal gene transfer.
bioRxiv
; 2023 Oct 03.
Article
in English
| MEDLINE | ID: mdl-37873187
9.
Phylogenomic analysis of the uracil-DNA glycosylase superfamily.
Mol Biol Evol
; 28(3): 1307-17, 2011 Mar.
Article
in English
| MEDLINE | ID: mdl-21135150
10.
Idiosyncratic Purifying Selection on Metabolic Enzymes in the Long-Term Evolution Experiment with Escherichia coli.
Genome Biol Evol
; 14(12)2022 12 07.
Article
in English
| MEDLINE | ID: mdl-35975326
11.
Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection.
Nat Ecol Evol
; 6(5): 555-564, 2022 05.
Article
in English
| MEDLINE | ID: mdl-35347261
12.
Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli.
Genome Biol Evol
; 13(6)2021 06 08.
Article
in English
| MEDLINE | ID: mdl-33856016
13.
Selection Maintains Protein Interactome Resilience in the Long-Term Evolution Experiment with Escherichia coli.
Genome Biol Evol
; 13(6)2021 06 08.
Article
in English
| MEDLINE | ID: mdl-33878164
14.
Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences.
Nat Commun
; 12(1): 1396, 2021 03 02.
Article
in English
| MEDLINE | ID: mdl-33654096
15.
A universal RNAi-based logic evaluator that operates in mammalian cells.
Nat Biotechnol
; 25(7): 795-801, 2007 Jul.
Article
in English
| MEDLINE | ID: mdl-17515909
16.
Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli.
Genome Biol Evol
; 12(9): 1591-1603, 2020 09 01.
Article
in English
| MEDLINE | ID: mdl-32853353
17.
Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment.
Elife
; 92020 05 29.
Article
in English
| MEDLINE | ID: mdl-32469311
18.
Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings.
Nat Microbiol
; 4(2): 328-338, 2019 02.
Article
in English
| MEDLINE | ID: mdl-30510172
19.
Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature.
Evolution
; 72(10): 2234-2243, 2018 10.
Article
in English
| MEDLINE | ID: mdl-30152871
20.
Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli.
Genome Biol Evol
; 9(4): 1072-1083, 2017 Apr 01.
Article
in English
| MEDLINE | ID: mdl-28379360