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Multidrug evolutionary strategies to reverse antibiotic resistance

Science (American Association for the Advancement of Science), 2016-01, Vol.351 (6268), p.40-40

2016

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Inexpensive multiplexed library preparation for megabase-sized genomes

PloS one, 2015-05, Vol.10 (5), p.e0128036-e0128036

2015

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Spatiotemporal microbial evolution on antibiotic landscapes

Science (American Association for the Advancement of Science), 2016-09, Vol.353 (6304), p.1147-1151

2016

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Simplitigs as an efficient and scalable representation of de Bruijn graphs

Genome Biology, 2021-04, Vol.22 (1), p.96-96, Article 96

2021

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Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

Nature biotechnology, 2017-07, Vol.35 (7), p.653-658

2017

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IsoRankN: spectral methods for global alignment of multiple protein networks

Bioinformatics, 2009-06, Vol.25 (12), p.i253-i258

2009

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Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes

Nature communications, 2015-06, Vol.6 (1), p.7385-7385, Article 7385

2015

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Metastable hybridization-based DNA information storage to allow rapid and permanent erasure

Nature communications, 2020-10, Vol.11 (1), p.5008-5008, Article 5008

2020

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Identification of a pathway for electron uptake in Shewanella oneidensis

Communications biology, 2021-08, Vol.4 (1), p.957-957, Article 957

2021

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Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku

Nature communications, 2016-11, Vol.7 (1), p.13270-13270, Article 13270

2016

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Escape mutations circumvent a tradeoff between resistance to a beta-lactam and resistance to a beta-lactamase inhibitor

Nature communications, 2020-04, Vol.11 (1), p.2029-9, Article 2029

2020

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Diverse and abundant phages exploit conjugative plasmids

Nature communications, 2024-04, Vol.15 (1), p.3197-3197, Article 3197

2024

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Barcode extension for analysis and reconstruction of structures

Nature communications, 2017-03, Vol.8 (1), p.14698-9, Article 14698

2017

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The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid

PLoS pathogens, 2019-09, Vol.15 (9), p.e1007948

2019

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Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs

Journal of molecular evolution, 2023-06, Vol.91 (3), p.325-333

2023

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Large-scale identification of genetic design strategies using local search

Molecular systems biology, 2009, Vol.5 (1), p.296-n/a

2009

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Compressive genomics for protein databases

Bioinformatics, 2013-07, Vol.29 (13), p.i283-i290

2013

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Perfect as the enemy of good: tracing transmissions with low-sensitivity tests to mitigate SARS-CoV-2 outbreaks

The Lancet. Microbe, 2021-05, Vol.2 (5), p.e219-e224

2021

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The Separatrix Algorithm for synthesis and analysis of stochastic simulations with applications in disease modeling

PloS one, 2014-07, Vol.9 (7), p.e103467-e103467

2014

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Decreased thermal niche breadth as a trade-off of antibiotic resistance

The ISME Journal, 2022-07, Vol.16 (7), p.1843-1852

2022

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Compressive genomics

Nature biotechnology, 2012-07, Vol.30 (7), p.627-630

2012

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The bacterial toxin colibactin triggers prophage induction

Nature (London), 2022-03, Vol.603 (7900), p.315-320

2022

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Prophages encode phage-defense systems with cognate self-immunity

Cell host & microbe, 2021-11, Vol.29 (11), p.1620-1633.e8

2021

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A swapped genetic code prevents viral infections and gene transfer

Nature (London), 2023-03, Vol.615 (7953), p.720-727

2023

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Changing fitness effects of mutations through long-term bacterial evolution

Science (American Association for the Advancement of Science), 2024-01, Vol.383 (6681), p.eadd1417-eadd1417

2024

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Multidrug evolutionary strategies to reverse antibiotic resistance

Inexpensive multiplexed library preparation for megabase-sized genomes

Spatiotemporal microbial evolution on antibiotic landscapes

Simplitigs as an efficient and scalable representation of de Bruijn graphs

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

IsoRankN: spectral methods for global alignment of multiple protein networks

Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes

Metastable hybridization-based DNA information storage to allow rapid and permanent erasure

Identification of a pathway for electron uptake in Shewanella oneidensis

Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku

Escape mutations circumvent a tradeoff between resistance to a beta-lactam and resistance to a beta-lactamase inhibitor

Diverse and abundant phages exploit conjugative plasmids

Barcode extension for analysis and reconstruction of structures

The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid

Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs

Large-scale identification of genetic design strategies using local search

Compressive genomics for protein databases

Perfect as the enemy of good: tracing transmissions with low-sensitivity tests to mitigate SARS-CoV-2 outbreaks

The Separatrix Algorithm for synthesis and analysis of stochastic simulations with applications in disease modeling

Decreased thermal niche breadth as a trade-off of antibiotic resistance

Compressive genomics

The bacterial toxin colibactin triggers prophage induction

Prophages encode phage-defense systems with cognate self-immunity

A swapped genetic code prevents viral infections and gene transfer

Changing fitness effects of mutations through long-term bacterial evolution

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