The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Seaver, Samuel M D, Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P, Edirisinghe, Janaka N, Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E, Best, Aaron A, DeJongh, Matthew, Kimbrel, Jeffrey A, D’haeseleer, Patrik, McCorkle, Sean R, Bolton, Jay R, Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M, Cottingham, Robert W, Arkin, Adam P, Henry, Christopher S
Published in Nucleic acids research (08.01.2021)
Published in Nucleic acids research (08.01.2021)
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eQuilibrator 3.0: a database solution for thermodynamic constant estimation
Beber, Moritz E, Gollub, Mattia G, Mozaffari, Dana, Shebek, Kevin M, Flamholz, Avi I, Milo, Ron, Noor, Elad
Published in Nucleic acids research (07.01.2022)
Published in Nucleic acids research (07.01.2022)
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Community standards to facilitate development and address challenges in metabolic modeling
Carey, Maureen A, Dräger, Andreas, Beber, Moritz E, Papin, Jason A, Yurkovich, James T
Published in Molecular systems biology (01.08.2020)
Published in Molecular systems biology (01.08.2020)
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A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
Lu, Hongzhong, Li, Feiran, Sánchez, Benjamín J, Zhu, Zhengming, Li, Gang, Domenzain, Iván, Marcišauskas, Simonas, Anton, Petre Mihail, Lappa, Dimitra, Lieven, Christian, Beber, Moritz Emanuel, Sonnenschein, Nikolaus, Kerkhoven, Eduard J, Nielsen, Jens
Published in Nature communications (08.08.2019)
Published in Nature communications (08.08.2019)
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Journal Article
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Seaver, Samuel M D, Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P, Edirisinghe, Janaka N, Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E, Best, Aaron A, DeJongh, Matthew, Kimbrel, Jeffrey A, D’haeseleer, Patrik, McCorkle, Sean R, Bolton, Jay R, Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M, Cottingham, Robert W, Arkin, Adam P, Henry, Christopher S
Published in Nucleic acids research (08.01.2021)
Published in Nucleic acids research (08.01.2021)
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Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial
Ankersen, Dorit Vedel, Weimers, Petra, Bennedsen, Mette, Haaber, Anne Birgitte, Fjordside, Eva Lund, Beber, Moritz Emanuel, Lieven, Christian, Saboori, Sanaz, Vad, Nicolai, Rannem, Terje, Marker, Dorte, Paridaens, Kristine, Frahm, Suzanne, Jensen, Lisbeth, Rosager Hansen, Malte, Burisch, Johan, Munkholm, Pia
Published in Journal of medical Internet research (14.12.2021)
Published in Journal of medical Internet research (14.12.2021)
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Interplay of digital and analog control in time-resolved gene expression profiles
Beber, Moritz E., Sobetzko, Patrick, Muskhelishvili, Georgi, Hütt, Marc-Thorsten
Published in EPJ nonlinear biomedical physics (22.08.2016)
Published in EPJ nonlinear biomedical physics (22.08.2016)
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Author Correction: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
Lu, Hongzhong, Li, Feiran, Sánchez, Benjamín J., Zhu, Zhengming, Li, Gang, Domenzain, Iván, Marcišauskas, Simonas, Anton, Petre Mihail, Lappa, Dimitra, Lieven, Christian, Beber, Moritz Emanuel, Sonnenschein, Nikolaus, Kerkhoven, Eduard J., Nielsen, Jens
Published in Nature communications (22.10.2020)
Published in Nature communications (22.10.2020)
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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
eQuilibrator 3.0: a database solution for thermodynamic constant estimation
Beber, Moritz E., Gollub, Mattia G., Mozaffari, Dana, Shebek, Kevin M., Flamholz, Avi I, Milo, Ron, Noor, Elad
Published in Nucleic acids research (29.11.2021)
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Published in Nucleic acids research (29.11.2021)
Journal Article
dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python
Tourigny, David, Muriel, Jorge, Beber, Moritz
Published in Journal of open source software (31.08.2020)
Published in Journal of open source software (31.08.2020)
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TAXPASTA: TAXonomic Profile Aggregation and STAndardisation
Beber, Moritz E., Borry, Maxime, Stamouli, Sofia, Yates, James A. Fellows
Published in Journal of open source software (11.07.2023)
Published in Journal of open source software (11.07.2023)
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BioSimulators: a central registry of simulation engines and services for recommending specific tools
Shaikh, Bilal, Smith, Lucian P, Vasilescu, Dan, Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran, Agnew, Henry, Andrews, Steven S, Anwar, Azraf, Beber, Moritz E, Bergmann, Frank T, Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, Ermentrout, G Bard, Faeder, James R, Freiburger, Andrew P, Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H, Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hasenauer, Jan, Hellerstein, Joseph L, Hermjakob, Henning, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Sheriff, Rahuman S Malik, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung V N, Nickerson, David P, Olivier, Brett G, Patoliya, Drashti, Paulevé, Loïc, Petzold, Linda R, Priya, Ankita, Rampadarath, Anand K, Rohwer, Johann M, Saglam, Ali S, Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J, van Niekerk, David, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P, Schaff, James C, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R
Published in Nucleic acids research (05.07.2022)
Published in Nucleic acids research (05.07.2022)
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Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
Cardoso, João G. R, Jensen, Kristian, Lieven, Christian, Lærke Hansen, Anne Sofie, Galkina, Svetlana, Beber, Moritz, Özdemir, Emre, Herrgård, Markus J, Redestig, Henning, Sonnenschein, Nikolaus
Published in ACS synthetic biology (20.04.2018)
Published in ACS synthetic biology (20.04.2018)
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Artefacts in statistical analyses of network motifs: general framework and application to metabolic networks
Beber, Moritz Emanuel, Fretter, Christoph, Jain, Shubham, Sonnenschein, Nikolaus, Müller-Hannemann, Matthias, Hütt, Marc-Thorsten
Published in Journal of the Royal Society interface (07.12.2012)
Published in Journal of the Royal Society interface (07.12.2012)
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