Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species

por Hyun, Jason C., Monk, Jonathan M., Szubin, Richard, Hefner, Ying, Palsson, Bernhard O.
Publicado 2023

Metabolic and genetic basis for auxotrophies in Gram-negative species

por Seif, Yara, Choudhary, Kumari Sonal, Hefner, Ying, Anand, Amitesh, Yang, Laurence, Palsson, Bernhard O.
Publicado 2020

Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains

por Poudel, Saugat, Hefner, Ying, Szubin, Richard, Sastry, Anand, Gao, Ye, Nizet, Victor, Palsson, Bernhard O.
Publicado 2022

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

por Dalldorf, Christopher, Rychel, Kevin, Szubin, Richard, Hefner, Ying, Patel, Arjun, Zielinski, Daniel C., Palsson, Bernhard O.
Publicado 2023

Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

por McCloskey, Douglas, Xu, Sibei, Sandberg, Troy E., Brunk, Elizabeth, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.
Publicado 2018

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

por McCloskey, Douglas, Xu, Sibei, Sandberg, Troy E., Brunk, Elizabeth, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.
Publicado 2018

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli

por Rodionova, Irina A., Gao, Ye, Sastry, Anand, Hefner, Ying, Lim, Hyun Gyu, Rodionov, Dmitry A., Saier, Milton H., Palsson, Bernhard O.
Publicado 2021

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

por Sastry, Anand V., Dillon, Nicholas, Anand, Amitesh, Poudel, Saugat, Hefner, Ying, Xu, Sibei, Szubin, Richard, Feist, Adam M., Nizet, Victor, Palsson, Bernhard
Publicado 2021

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

por Patel, Arjun, McGrosso, Dominic, Hefner, Ying, Campeau, Anaamika, Sastry, Anand V., Maurya, Svetlana, Rychel, Kevin, Gonzalez, David J, Palsson, Bernhard O.
Publicado 2023

The Escherichia coli transcriptome mostly consists of independently regulated modules

por Sastry, Anand V., Gao, Ye, Szubin, Richard, Hefner, Ying, Xu, Sibei, Kim, Donghyuk, Choudhary, Kumari Sonal, Yang, Laurence, King, Zachary A., Palsson, Bernhard O.
Publicado 2019

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

por Heckmann, David, Campeau, Anaamika, Lloyd, Colton J., Phaneuf, Patrick V., Hefner, Ying, Carrillo-Terrazas, Marvic, Feist, Adam M., Gonzalez, David J., Palsson, Bernhard O.
Publicado 2020

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

por Anand, Amitesh, Patel, Arjun, Chen, Ke, Olson, Connor A., Phaneuf, Patrick V., Lamoureux, Cameron, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.
Publicado 2022

Reframing gene essentiality in terms of adaptive flexibility

por Guzmán, Gabriela I., Olson, Connor A., Hefner, Ying, Phaneuf, Patrick V., Catoiu, Edward, Crepaldi, Lais B., Micas, Lucas Goldschmidt, Palsson, Bernhard O., Feist, Adam M.
Publicado 2018

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus

por Machado, Henrique, Seif, Yara, Sakoulas, George, Olson, Connor A., Hefner, Ying, Anand, Amitesh, Jones, Ying Z., Szubin, Richard, Palsson, Bernhard O., Nizet, Victor, Feist, Adam M.
Publicado 2021

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

por Rodionova, Irina A., Gao, Ye, Monk, Jonathan, Hefner, Ying, Wong, Nicholas, Szubin, Richard, Lim, Hyun Gyu, Rodionov, Dmitry A., Zhang, Zhongge, Saier, Milton H., Palsson, Bernhard O.
Publicado 2022

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

por Anand, Amitesh, Chen, Ke, Yang, Laurence, Sastry, Anand V., Olson, Connor A., Poudel, Saugat, Seif, Yara, Hefner, Ying, Phaneuf, Patrick V., Xu, Sibei, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.
Publicado 2019

The genetic basis for adaptation of model-designed syntrophic co-cultures

por Lloyd, Colton J., King, Zachary A., Sandberg, Troy E., Hefner, Ying, Olson, Connor A., Phaneuf, Patrick V., O’Brien, Edward J., Sanders, Jon G., Salido, Rodolfo A., Sanders, Karenina, Brennan, Caitriona, Humphrey, Gregory, Knight, Rob, Feist, Adam M.
Publicado 2019

Enzyme promiscuity shapes adaptation to novel growth substrates

por Guzmán, Gabriela I, Sandberg, Troy E, LaCroix, Ryan A, Nyerges, Ákos, Papp, Henrietta, de Raad, Markus, King, Zachary A, Hefner, Ying, Northen, Trent R, Notebaart, Richard A, Pál, Csaba, Palsson, Bernhard O, Papp, Balázs, Feist, Adam M
Publicado 2019