Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules von Shin, Jongoh, Zielinski, Daniel C, Palsson, Bernhard O

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Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models von Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O.

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A multi-scale expression and regulation knowledge base for Escherichia coli von Lamoureux, Cameron R, Decker, Katherine T, Sastry, Anand V, Rychel, Kevin, Gao, Ye, McConn, John Luke, Zielinski, Daniel C, Palsson, Bernhard O

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A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models von Opdam, Sjoerd, Richelle, Anne, Kellman, Benjamin, Li, Shanzhong, Zielinski, Daniel C., Lewis, Nathan E.

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MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics von Haiman, Zachary B, Zielinski, Daniel C, Koike, Yuko, Yurkovich, James T, Palsson, Bernhard O

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Empowering drug off-target discovery with metabolic and structural analysis von Chowdhury, Sourav, Zielinski, Daniel C., Dalldorf, Christopher, Rodrigues, Joao V., Palsson, Bernhard O., Shakhnovich, Eugene I.

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The quantitative metabolome is shaped by abiotic constraints von Akbari, Amir, Yurkovich, James T., Zielinski, Daniel C., Palsson, Bernhard O.

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PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining von Sun, Binhuan, Pashkova, Liubov, Pieters, Pascal Aldo, Harke, Archana Sanjay, Mohite, Omkar Satyavan, Santos, Alberto, Zielinski, Daniel C, Palsson, Bernhard O, Phaneuf, Patrick Victor

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Recon 2.2: from reconstruction to model of human metabolism von Swainston, Neil, Smallbone, Kieran, Hefzi, Hooman, Dobson, Paul D., Brewer, Judy, Hanscho, Michael, Zielinski, Daniel C., Ang, Kok Siong, Gardiner, Natalie J., Gutierrez, Jahir M., Kyriakopoulos, Sarantos, Lakshmanan, Meiyappan, Li, Shangzhong, Liu, Joanne K., Martínez, Veronica S., Orellana, Camila A., Quek, Lake-Ee, Thomas, Alex, Zanghellini, Juergen, Borth, Nicole, Lee, Dong-Yup, Nielsen, Lars K., Kell, Douglas B., Lewis, Nathan E., Mendes, Pedro

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Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics von Bordbar, Aarash, McCloskey, Douglas, Zielinski, Daniel C., Sonnenschein, Nikolaus, Jamshidi, Neema, Palsson, Bernhard O.

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Inferred regulons are consistent with regulator binding sequences in E. coli von Qiu, Sizhe, Wan, Xinlong, Liang, Yueshan, Lamoureux, Cameron, Akbari, Amir, Palsson, Bernhard O, Zielinski, Daniel C

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Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates von Heckmann, David, Zielinski, Daniel C., Palsson, Bernhard O.

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iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia von Sastry, Anand V, Yuan, Yuan, Poudel, Saugat, Rychel, Kevin, Yoo, Reo, Lamoureux, Cameron R, Li, Gaoyuan, Burrows, Joshua T, Chauhan, Siddharth, Haiman, Zachary B, Al Bulushi, Tahani, Seif, Yara, Palsson, Bernhard O, Zielinski, Daniel C

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Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks von Yurkovich, James T., Zielinski, Daniel C., Yang, Laurence, Paglia, Giuseppe, Rolfsson, Ottar, Sigurjónsson, Ólafur E., Broddrick, Jared T., Bordbar, Aarash, Wichuk, Kristine, Brynjólfsson, Sigurður, Palsson, Sirus, Gudmundsson, Sveinn, Palsson, Bernhard O.

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Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli von Feist, Adam M., Zielinski, Daniel C., Orth, Jeffrey D., Schellenberger, Jan, Herrgard, Markus J., Palsson, Bernhard Ø.

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A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks von Nam, Hojung, Campodonico, Miguel, Bordbar, Aarash, Hyduke, Daniel R, Kim, Sangwoo, Zielinski, Daniel C, Palsson, Bernhard O

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Topological and kinetic determinants of the modal matrices of dynamic models of metabolism von Du, Bin, Zielinski, Daniel C, Palsson, Bernhard O

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Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis von Zielinski, Daniel C., Filipp, Fabian V., Bordbar, Aarash, Jensen, Kasper, Smith, Jeffrey W., Herrgard, Markus J., Mo, Monica L., Palsson, Bernhard O.

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Escherichia coli non-coding regulatory regions are highly conserved von Lamoureux, Cameron R, Phaneuf, Patrick V, Palsson, Bernhard O, Zielinski, Daniel C

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Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways von Mattei, Gianluca, Gan, Zhuohui, Ramazzotti, Matteo, Palsson, Bernhard O., Zielinski, Daniel C.

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