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Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

Nature communications, 2021-03, Vol.12 (1), p.1396-1396, Article 1396

2021

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Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations

PLoS genetics, 2022-08, Vol.18 (8), p.e1010324-e1010324

2022

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Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

PLoS genetics, 2018-01, Vol.14 (1), p.e1007199-e1007199

2018

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Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection

Nature ecology & evolution, 2022-05, Vol.6 (5), p.555

2022

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Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria

Nature communications, 2024-02, Vol.15 (1), p.1449-1449, Article 1449

2024

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Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

eLife, 2020-05, Vol.9

2020

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Idiosyncratic Purifying Selection on Metabolic Enzymes in the Long-Term Evolution Experiment with Escherichia coli

Genome biology and evolution, 2022-12, Vol.14 (12)

2022

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Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli

Genome biology and evolution, 2021-06, Vol.13 (6)

2021

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Selection Maintains Protein Interactome Resilience in the Long-Term Evolution Experiment with Escherichia coli

Genome biology and evolution, 2021-06, Vol.13 (6)

2021

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Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings

Nature microbiology, 2019-02, Vol.4 (2), p.328

2019

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Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

PloS one, 2016-01, Vol.11 (1), p.e0147229-e0147229

2016

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Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

Genetics (Austin), 2015-06, Vol.200 (2), p.619-631

2015

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A universal RNAi-based logic evaluator that operates in mammalian cells

Nature biotechnology, 2007-07, Vol.25 (7), p.795-801

2007

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Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli

Genome biology and evolution, 2020-09, Vol.12 (9), p.1591-1603

2020

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Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome

Mobile genetic elements, 2016-01, Vol.6 (1), p.e1137380-e1137380

Maddamsetti, Rohan

2016

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Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

Proceedings of the Royal Society. B, Biological sciences, 2015-12, Vol.282 (1821), p.20152292-20152292

2015

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Programming Dynamic Division of Labor Using Horizontal Gene Transfer

ACS synthetic biology, 2024-04, Vol.13 (4), p.1142-1151

2024

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Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature

Evolution, 2018-10, Vol.72 (10), p.2234-2243

2018

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Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli

Genome biology and evolution, 2017-04, Vol.9 (4), p.1072-1083

2017

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Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment

Molecular biology and evolution, 2015-11, Vol.32 (11), p.2897-2904

2015

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Phylogenomic analysis of the uracil-DNA glycosylase superfamily

Molecular biology and evolution, 2011-03, Vol.28 (3), p.1307-1317

2011

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Evolution of laboratory and natural populations of Escherichia coli

Maddamsetti, Rohan

2016

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Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

Proceedings of the Royal Society. B, Biological sciences, 2015-12, Vol.282 (1821), p.1-9

2015

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Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli

2017

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Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli

2017

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Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations

Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection

Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Idiosyncratic Purifying Selection on Metabolic Enzymes in the Long-Term Evolution Experiment with Escherichia coli

Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli

Selection Maintains Protein Interactome Resilience in the Long-Term Evolution Experiment with Escherichia coli

Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

A universal RNAi-based logic evaluator that operates in mammalian cells

Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli

Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome

Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

Programming Dynamic Division of Labor Using Horizontal Gene Transfer

Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature

Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli

Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment

Phylogenomic analysis of the uracil-DNA glycosylase superfamily

Evolution of laboratory and natural populations of Escherichia coli

Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli

Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli

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