Leveraging metabolic modeling to identify functional metabolic alterations associated with COVID-19 disease severity
Dillard, L. R., Wase, N., Ramakrishnan, G., Park, J. J., Sherman, N. E., Carpenter, R., Young, M., Donlan, A. N., Petri, W., Papin, J. A.
Published in Metabolomics (11.07.2022)
Published in Metabolomics (11.07.2022)
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Journal Article
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J., König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E., Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L., Monk, Jonathan M., Nielsen, Jens, Nielsen, Lars Keld, Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard O., Papin, Jason A., Patil, Kiran R., Poolman, Mark, Price, Nathan D., Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J., Schaap, Peter J., Malik Sheriff, Rahuman S., Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith A. H., Xavier, Joana C., Yuan, Qianqian, Zakhartsev, Maksim, Zhang, Cheng
Published in Nature biotechnology (01.03.2020)
Published in Nature biotechnology (01.03.2020)
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Journal Article
A community-driven global reconstruction of human metabolism
Thiele, Ines, Swainston, Neil, Fleming, Ronan M T, Hoppe, Andreas, Sahoo, Swagatika, Aurich, Maike K, Haraldsdottir, Hulda, Mo, Monica L, Rolfsson, Ottar, Stobbe, Miranda D, Thorleifsson, Stefan G, Agren, Rasmus, Bölling, Christian, Bordel, Sergio, Chavali, Arvind K, Dobson, Paul, Dunn, Warwick B, Endler, Lukas, Hala, David, Hucka, Michael, Hull, Duncan, Jameson, Daniel, Jamshidi, Neema, Jonsson, Jon J, Juty, Nick, Keating, Sarah, Nookaew, Intawat, Le Novère, Nicolas, Malys, Naglis, Mazein, Alexander, Papin, Jason A, Price, Nathan D, Selkov, Evgeni, Sigurdsson, Martin I, Simeonidis, Evangelos, Sonnenschein, Nikolaus, Smallbone, Kieran, Sorokin, Anatoly, van Beek, Johannes H G M, Weichart, Dieter, Goryanin, Igor, Nielsen, Jens, Westerhoff, Hans V, Kell, Douglas B, Mendes, Pedro, Palsson, Bernhard Ø
Published in Nature biotechnology (01.05.2013)
Published in Nature biotechnology (01.05.2013)
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Journal Article
Comparative Metabolic Systems Analysis of Pathogenic Burkholderia
Bartell, Jennifer A, Yen, Phillip, Varga, John J, Goldberg, Joanna B, Papin, Jason A
Published in Journal of Bacteriology (01.01.2014)
Published in Journal of Bacteriology (01.01.2014)
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Journal Article
Do genome‐scale models need exact solvers or clearer standards?
Ebrahim, Ali, Almaas, Eivind, Bauer, Eugen, Bordbar, Aarash, Burgard, Anthony P, Chang, Roger L, Dräger, Andreas, Famili, Iman, Feist, Adam M, Fleming, Ronan MT, Fong, Stephen S, Hatzimanikatis, Vassily, Herrgård, Markus J, Holder, Allen, Hucka, Michael, Hyduke, Daniel, Jamshidi, Neema, Lee, Sang Yup, Le Novère, Nicolas, Lerman, Joshua A, Lewis, Nathan E, Ma, Ding, Mahadevan, Radhakrishnan, Maranas, Costas, Nagarajan, Harish, Navid, Ali, Nielsen, Jens, Nielsen, Lars K, Nogales, Juan, Noronha, Alberto, Pal, Csaba, Palsson, Bernhard O, Papin, Jason A, Patil, Kiran R, Price, Nathan D, Reed, Jennifer L, Saunders, Michael, Senger, Ryan S, Sonnenschein, Nikolaus, Sun, Yuekai, Thiele, Ines
Published in Molecular systems biology (01.10.2015)
Published in Molecular systems biology (01.10.2015)
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Journal Article
Reconstruction of cellular signalling networks and analysis of their properties
Palsson, Bernhard O, Subramaniam, Shankar, Papin, Jason A, Hunter, Tony
Published in Nature reviews. Molecular cell biology (01.02.2005)
Published in Nature reviews. Molecular cell biology (01.02.2005)
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Journal Article
Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats
Pannala, Venkat R., Vinnakota, Kalyan C., Rawls, Kristopher D., Estes, Shanea K., O'Brien, Tracy P., Printz, Richard L., Papin, Jason A., Reifman, Jaques, Shiota, Masakazu, Young, Jamey D., Wallqvist, Anders
Published in Toxicology and applied pharmacology (01.06.2019)
Published in Toxicology and applied pharmacology (01.06.2019)
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Journal Article
Comparison of network-based pathway analysis methods
Papin, Jason A., Stelling, Joerg, Price, Nathan D., Klamt, Steffen, Schuster, Stefan, Palsson, Bernhard O.
Published in Trends in biotechnology (Regular ed.) (01.08.2004)
Published in Trends in biotechnology (Regular ed.) (01.08.2004)
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Journal Article
Genome-scale microbial in silico models: the constraints-based approach
Price, Nathan D, Papin, Jason A, Schilling, Christophe H, Palsson, Bernhard O
Published in Trends in biotechnology (Regular ed.) (01.04.2003)
Published in Trends in biotechnology (Regular ed.) (01.04.2003)
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Journal Article
Metabolic pathways in the post-genome era
Papin, Jason A., Price, Nathan D., Wiback, Sharon J., Fell, David A., Palsson, Bernhard O.
Published in Trends in biochemical sciences (Amsterdam. Regular ed.) (01.05.2003)
Published in Trends in biochemical sciences (Amsterdam. Regular ed.) (01.05.2003)
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Journal Article
Characterizing emergent properties of immunological systems with multi-cellular rule-based computational modeling
Chavali, Arvind K, Gianchandani, Erwin P, Tung, Kenneth S, Lawrence, Michael B, Peirce, Shayn M, Papin, Jason A
Published in Trends in immunology (01.12.2008)
Published in Trends in immunology (01.12.2008)
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