Publications by authors named "Michael Baym"

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Spatiotemporal microbial evolution on antibiotic landscapes.
Michael Baym, Tami D Lieberman, Eric D Kelsic, Remy Chait, Rotem Gross, Idan Yelin, Roy Kishony

Science· September 2016

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Intracellular competition shapes plasmid population dynamics.
Fernando Rossine, Carlos Sanchez, Daniel Eaton, Johan Paulsson, Michael Baym

Science· December 2025

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Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics.
Arya Kaul, Célia Souque, Mische Holland, Michael Baym

Microb Genom· September 2025

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Phage DisCo: targeted discovery of bacteriophages by co-culture.
Eleanor A Rand, Natalia Quinones-Olvera, Kesther D C Jean, Carmen Hernandez-Perez, Siân V Owen, Michael Baym

mSystems· June 2025

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Efficient and robust search of microbial genomes via phylogenetic compression.
Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Michael Baym

Nat Methods· April 2025

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Sustainable solutions to the continuous threat of antimicrobial resistance.
Brad Spellberg, David N Gilbert, Michael Baym, Gonzalo Bearman, Tom Boyles

Health Aff Sch· February 2025

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Intracellular competition shapes plasmid population dynamics.
Fernando Rossine, Carlos Sanchez, Daniel Eaton, Johan Paulsson, Michael Baym

bioRxiv· February 2025

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RNA-guided nucleases enable a gene drive of insertion sequences in plasmids.
Kepler S Mears, Fernando W Rossine, Natalia Quinones-Olvera, Célia Souque, Michael Baym

bioRxiv· February 2025

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Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics.
Arya Kaul, Célia Souque, Mische Holland, Michael Baym

bioRxiv· January 2025

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From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance.
Célia Souque, Indra González Ojeda, Michael Baym

Annu Rev Microbiol· November 2024

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Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.
Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Michael Baym

bioRxiv· May 2024

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Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.
Steven G Sutcliffe, Susanne A Kraemer, Isaac Ellmen, Jennifer J Knapp, Alyssa K Overton, Michael Baym

Microb Genom· May 2024

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Diverse and abundant phages exploit conjugative plasmids.
Natalia Quinones-Olvera, Siân V Owen, Lucy M McCully, Maximillian G Marin, Eleanor A Rand, Michael Baym

Nat Commun· April 2024

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Changing fitness effects of mutations through long-term bacterial evolution.
Alejandro Couce, Anurag Limdi, Melanie Magnan, Siân V Owen, Cristina M Herren, Michael Baym

Science· January 2024

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Diverse and abundant phages exploit conjugative plasmids.
Natalia Quinones-Olvera, Siân V Owen, Lucy M McCully, Maximillian G Marin, Eleanor A Rand, Michael Baym

bioRxiv· December 2023

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Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs.
Anurag Limdi, Michael Baym

J Mol Evol· June 2023

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Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection.
Charles L Dulberger, Carlos A Guerrero-Bustamante, Siân V Owen, Sean Wilson, Michael G Wuo, Michael Baym

Nat Microbiol· April 2023

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A swapped genetic code prevents viral infections and gene transfer.
Akos Nyerges, Svenja Vinke, Regan Flynn, Siân V Owen, Eleanor A Rand, Michael Baym

Nature· March 2023

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Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.
Jasmijn A Baaijens, Alessandro Zulli, Isabel M Ott, Ioanna Nika, Mart J van der Lugt, Michael Baym

Genome Biol· November 2022

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Decreased thermal niche breadth as a trade-off of antibiotic resistance.
Cristina M Herren, Michael Baym

ISME J· July 2022

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The bacterial toxin colibactin triggers prophage induction.
Justin E Silpe, Joel W H Wong, Siân V Owen, Michael Baym, Emily P Balskus

Nature· March 2022

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Prophages encode phage-defense systems with cognate self-immunity.
Siân V Owen, Nicolas Wenner, Charles L Dulberger, Ella V Rodwell, Arthur Bowers-Barnard, Michael Baym

Cell Host Microbe· November 2021

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Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.
Jasmijn A Baaijens, Alessandro Zulli, Isabel M Ott, Mary E Petrone, Tara Alpert, Michael Baym

medRxiv· September 2021

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Identification of a pathway for electron uptake in Shewanella oneidensis.
Annette R Rowe, Farshid Salimijazi, Leah Trutschel, Joshua Sackett, Oluwakemi Adesina, Michael H Baym

Commun Biol· August 2021

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Perfect as the enemy of good: tracing transmissions with low-sensitivity tests to mitigate SARS-CoV-2 outbreaks.
Lee Kennedy-Shaffer, Michael Baym, William P Hanage

Lancet Microbe· May 2021

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Simplitigs as an efficient and scalable representation of de Bruijn graphs.
Karel Břinda, Michael Baym, Gregory Kucherov

Genome Biol· April 2021

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