Publications by authors named "Ying Hefner"

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PMkbase (version 1.0): an interactive web-based tool for tracking bacterial metabolic traits using phenotype microarrays made interoperable with sequence information and visualizing/processing PM data.
K Jayanth Krishnan, Ying Hefner, Richard Szubin, Jonathan Monk, David T Pride

Microbiol Spectr· November 2025

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Multi-strain Analysis of Reveals the Metabolic and Genetic Diversity of the Species.
Joshua Mueller, Kalpathy Jayanth Krishnan, Qixing Wei, Ying Hefner, Jonathan M Monk

bioRxiv· November 2025

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Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.
Kevin Rychel, Ke Chen, Edward A Catoiu, Elina Olson, Troy E Sandberg, Ying Hefner

Genome Biol Evol· September 2025

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Interpreting roles of mutations associated with the emergence of USA300 strains using transcriptional regulatory network reconstruction.
Saugat Poudel, Jason Hyun, Ying Hefner, Jon Monk, Victor Nizet

Elife· April 2025

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Diversity of Transcriptional Regulatory Adaptation in E. coli.
Christopher Dalldorf, Ying Hefner, Richard Szubin, Josefin Johnsen, Elsayed Mohamed

Mol Biol Evol· November 2024

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The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel

mSystems· July 2024

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Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.
Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry

Nat Commun· June 2024

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Reconstructing the transcriptional regulatory network of probiotic is enabled by transcriptomics and machine learning.
Jonathan Josephs-Spaulding, Akanksha Rajput, Ying Hefner, Richard Szubin, Archana Balasubramanian

mSystems· March 2024

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Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species.
Jason C Hyun, Jonathan M Monk, Richard Szubin, Ying Hefner, Bernhard O Palsson

Nat Commun· November 2023

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Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.
Kevin Rychel, Justin Tan, Arjun Patel, Cameron Lamoureux, Ying Hefner

Cell Rep· September 2023

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The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.
Christopher Dalldorf, Kevin Rychel, Richard Szubin, Ying Hefner, Arjun Patel

Res Sq· April 2023

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Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.
Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry

bioRxiv· February 2023

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Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains.
Saugat Poudel, Ying Hefner, Richard Szubin, Anand Sastry, Ye Gao

mSystems· December 2022

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Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity.
Amitesh Anand, Arjun Patel, Ke Chen, Connor A Olson, Patrick V Phaneuf, Ying Hefner

Nat Commun· June 2022

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A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli.
Irina A Rodionova, Ye Gao, Jonathan Monk, Ying Hefner, Nicholas Wong

Sci Rep· May 2022

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Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.
Irina A Rodionova, Ye Gao, Anand Sastry, Ying Hefner, Hyun Gyu Lim

Commun Biol· August 2021

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Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility.
Anand V Sastry, Nicholas Dillon, Amitesh Anand, Saugat Poudel, Ying Hefner

mSphere· August 2021

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Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus.
Henrique Machado, Yara Seif, George Sakoulas, Connor A Olson, Ying Hefner

Commun Biol· June 2021

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Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers.
David Heckmann, Anaamika Campeau, Colton J Lloyd, Patrick V Phaneuf, Ying Hefner

Proc Natl Acad Sci U S A· September 2020

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Metabolic and genetic basis for auxotrophies in Gram-negative species.
Yara Seif, Kumari Sonal Choudhary, Ying Hefner, Amitesh Anand, Laurence Yang

Proc Natl Acad Sci U S A· March 2020

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Adaptive laboratory evolution of under acid stress.
Bin Du, Connor A Olson, Anand V Sastry, Xin Fang, Patrick V Phaneuf, Ying Hefner

Microbiology (Reading)· February 2020

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Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration.
Amitesh Anand, Ke Chen, Laurence Yang, Anand V Sastry, Connor A Olson, Ying Hefner

Proc Natl Acad Sci U S A· December 2019

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The Escherichia coli transcriptome mostly consists of independently regulated modules.
Anand V Sastry, Ye Gao, Richard Szubin, Ying Hefner, Sibei Xu

Nat Commun· December 2019

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Cellular responses to reactive oxygen species are predicted from molecular mechanisms.
Laurence Yang, Nathan Mih, Amitesh Anand, Joon Ho Park, Justin Tan, Ying Hefner

Proc Natl Acad Sci U S A· July 2019

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Enzyme promiscuity shapes adaptation to novel growth substrates.
Gabriela I Guzmán, Troy E Sandberg, Ryan A LaCroix, Ákos Nyerges, Henrietta Papp, Ying Hefner

Mol Syst Biol· April 2019

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