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Cellular responses to reactive oxygen species are predicted from molecular mechanisms File

Yang, Laurence , Mih, Nathan , Anand, Amitesh , Park, Joon Ho , Tan, Justin , Yurkovich, James T. , Monk, Jonathan M. , Lloyd, Colton J. , Sandberg, Troy E. , Seo, Sang Woo , et al

Article Issue Date2019-07 View14

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow File

Brunk, Elizabeth , Chang, Roger L. , Xia, Jing , Hefzi, Hooman , Yurkovich, James T. , Kim, Donghyuk , Buckmiller, Evan , Wang, Harris H. , Cho, Byung-Kwan , Yang, Chen , et al

Article Issue Date2018-10 View18

Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling File

Kim, Donghyuk , Hong, Jay Sung-Joong , Qiu, Yu , Nagarajan, Harish , Seo, Joo-Hyun , Cho, Byung-Kwan , Tsai, Shih-Feng , Palsson, Bernhard O.

Article Issue Date2012-08 View24

Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli File

Seo, Sang Woo , Kim, Donghyuk , Latif, Haythem , O'Brien, Edward J. , Szubin, Richard , Palsson, Bernhard O.

Article Issue Date2014-09 View18

Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli File

Seo, Sang Woo , Kim, Donghyuk , O'Brien, Edward J. , Szubin, Richard , Palsson, Bernhard O.

Article Issue Date2015-08 View22

Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution File

Lee, Sang-Mok , Le, Hoa Thi , Taizhanova, Assiya , Nong, Linh Khanh , Park, Joon Young , Lee, Eun-Jin , Palsson, Bernhard O. , Kim, Donghyuk

Article Issue Date2024-01 View31

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states File

Cho, Byung-Kwan , Kim, Donghyuk , Knight, Eric M. , Zengler, Karsten , Palsson, Bernhard O.

Article Issue Date2014-01 View19

Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655 File

Seo, Sang Woo , Kim, Donghyuk , Szubin, Richard , Palsson, Bernhard O.

Article Issue Date2015-08 View19

Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities File

Fang, Xin , Sastry, Anand , Mih, Nathan , Kim, Donghyuk , Tan, Justin , Yurkovich, James T. , Lloyd, Colton J. , Gao, Ye , Yang, Laurence , Palsson, Bernhard O.

Article Issue Date2017-09 View17

Multi-omic data integration enables discovery of hidden biological regularities File

Ebrahim, Ali , Brunk, Elizabeth , Tan, Justin , O'Brien, Edward J. , Kim, Donghyuk , Szubin, Richard , Lerman, Joshua A. , Lechner, Anna , Sastry, Anand , Bordbar, Aarash , et al

Article Issue Date2016-10 View19

Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features File

Seo, Joo-Hyun , Hong, Jay Sung-Joong , Kim, Donghyuk , Cho, Byung-Kwan , Huang, Tzu-Wen , Tsai, Shih-Feng , Palsson, Bernhard O. , Charusanti, Pep

Article Issue Date2012-11 View22

Network Context and Selection in the Evolution to Enzyme Specificity File

Nam, Hojung , Lewis, Nathan E. , Lerman, Joshua A. , Lee, Dae-Hee , Chang, Roger L. , Kim, Donghyuk , Palsson, Bernhard O.

Article Issue Date2012-08 View22

proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms File File

Decker, Katherine T. , Gao, Ye , Rychel, Kevin , Al Bulushi, Tahani , Chauhan, Siddharth M. , Kim, Donghyuk , Cho, Byung-Kwan , Palsson, Bernhard O.

Article Issue Date2022-01 View16

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655 File

Seo, Sang Woo , Gao, Ye , Kim, Donghyuk , Szubin, Richard , Yang, Jina , Cho, Byung-Kwan , Palsson, Bernhard O.

Article Issue Date2017-05 View23

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli File

Chang, Roger L. , Andrews, Kathleen , Kim, Donghyuk , Li, Zhanwen , Godzik, Adam , Palsson, Bernhard O.

Article Issue Date2013-06 View14

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 File

Gao, Ye , Yurkovich, James T. , Seo, Sang Woo , Kabimoldayev, Ilyas , Draeger, Andreas , Chen, Ke , Sastry, Anand V. , Fang, Xin , Mih, Nathan , Yang, Laurence , et al

Article Issue Date2018-11 View17

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP File

Kim, Donghyuk , Seo, Sang Woo , Gao, Ye , Nam, Hojung , Guzman, Gabriela I. , Cho, Byung-Kwan , Palsson, Bernhard O.

Article Issue Date2018-04 View16

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data File

Yang, Laurence , Tan, Justin , O'Brien, Edward J. , Monk, Jonathan M. , Kim, Donghyuk , Li, Howard J. , Charusanti, Pep , Ebrahim, Ali , Lloyd, Colton J. , Yurkovich, James T. , et al

Article Issue Date2015-08 View20

The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets File File

Gao, Ye , Bang, Ina , Seif, Yara , Kim, Donghyuk , Palsson, Bernhard O.

Article Issue Date2023-05 View32

The Escherichia coli transcriptome mostly consists of independently regulated modules File File

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

Article Issue Date2019-12 View22

The PurR regulon in Escherichia coli K-12 MG1655 File

Cho, Byung-Kwan , Federowicz, Stephen A. , Embree, Mallory , Park, Young-Seoub , Kim, Donghyuk , Palsson, Bernhard O.

Article Issue Date2011-08 View12

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