The Escherichia coli transcriptome mostly consists of independently regulated modules von Sastry, Anand V., Gao, Ye, Szubin, Richard, Hefner, Ying, Xu, Sibei, Kim, Donghyuk, Choudhary, Kumari Sonal, Yang, Laurence, King, Zachary A., Palsson, Bernhard O.

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Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers von Heckmann, David, Campeau, Anaamika, Lloyd, Colton J., Phaneuf, Patrick V., Hefner, Ying, Carrillo-Terrazas, Marvic, Feist, Adam M., Gonzalez, David J., Palsson, Bernhard O.

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

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

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Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism von McCloskey, Douglas, Xu, Sibei, Sandberg, Troy E., Brunk, Elizabeth, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.

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Proteome allocation is linked to transcriptional regulation through a modularized transcriptome von Patel, Arjun, McGrosso, Dominic, Hefner, Ying, Campeau, Anaamika, Sastry, Anand V., Maurya, Svetlana, Rychel, Kevin, Gonzalez, David J., Palsson, Bernhard O.

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Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity von Anand, Amitesh, Patel, Arjun, Chen, Ke, Olson, Connor A., Phaneuf, Patrick V., Lamoureux, Cameron, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.

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Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains von Poudel, Saugat, Hefner, Ying, Szubin, Richard, Sastry, Anand, Gao, Ye, Nizet, Victor, Palsson, Bernhard O

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Enzyme promiscuity shapes adaptation to novel growth substrates von 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

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Adaptive laboratory evolution of Escherichia coli under acid stress von Du, Bin, Olson, Connor A, Sastry, Anand V, Fang, Xin, Phaneuf, Patrick V, Chen, Ke, Wu, Muyao, Szubin, Richard, Xu, Sibei, Gao, Ye, Hefner, Ying, Feist, Adam M, Palsson, Bernhard O

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Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus von 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.

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Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning von Josephs-Spaulding, Jonathan, Rajput, Akanksha, Hefner, Ying, Szubin, Richard, Balasubramanian, Archana, Li, Gaoyuan, Zielinski, Daniel C, Jahn, Leonie, Sommer, Morten, Phaneuf, Patrick, Palsson, Bernhard O

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The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions von Dalldorf, Christopher, Rychel, Kevin, Szubin, Richard, Hefner, Ying, Patel, Arjun, Zielinski, Daniel C, Palsson, Bernhard O

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Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance von Rychel, Kevin, Tan, Justin, Patel, Arjun, Lamoureux, Cameron, Hefner, Ying, Szubin, Richard, Johnsen, Josefin, Mohamed, Elsayed Tharwat Tolba, Phaneuf, Patrick V., Anand, Amitesh, Olson, Connor A., Park, Joon Ho, Sastry, Anand V., Yang, Laurence, Feist, Adam M., Palsson, Bernhard O.

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Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli von Rodionova, Irina A., Gao, Ye, Sastry, Anand, Hefner, Ying, Lim, Hyun Gyu, Rodionov, Dmitry A., Saier, Milton H., Palsson, Bernhard O.

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Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome von McCloskey, Douglas, Xu, Sibei, Sandberg, Troy E, Brunk, Elizabeth, Hefner, Ying, Szubin, Richard, Feist, Adam M, Palsson, Bernhard O

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

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Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility von Sastry, Anand V, Dillon, Nicholas, Anand, Amitesh, Poudel, Saugat, Hefner, Ying, Xu, Sibei, Szubin, Richard, Feist, Adam M, Nizet, Victor, Palsson, Bernhard

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Serine 727 Phosphorylation and Activation of Cytosolic Phospholipase A2 by MNK1-related Protein Kinases von Hefner, Ying, Börsch-Haubold, Angelika G., Murakami, Makomoto, Wilde, Jonathan I., Pasquet, Sophie, Schieltz, David, Ghomashchi, Farideh, Yates, John R., Armstrong, Christopher G., Paterson, Andrew, Cohen, Philip, Fukunaga, Rikiro, Hunter, Tony, Kudo, Ichiro, Watson, Steve P., Gelb, Michael H.

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Pseudogene repair driven by selection pressure applied in experimental evolution von Anand, Amitesh, Olson, Connor A., Yang, Laurence, Sastry, Anand V., Catoiu, Edward, Choudhary, Kumari Sonal, Phaneuf, Patrick V., Sandberg, Troy E., Xu, Sibei, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.

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