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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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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Journal Article
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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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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Journal Article
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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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
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
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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Journal Article
Publisher Correction: 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., Sheriff, Rahuman S. Malik, 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 (01.04.2020)
Published in Nature biotechnology (01.04.2020)
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Journal Article
eQuilibrator 3.0 -- a platform for the estimation of thermodynamic constants
Beber, Moritz E, Gollub, Mattia G, Mozaffari, Dana, Shebek, Kevin M, Noor, Elad
Year of Publication 28.02.2021
Year of Publication 28.02.2021
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Journal Article
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, Hellerstein, Joseph L, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, 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, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R
Year of Publication 13.03.2022
Year of Publication 13.03.2022
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Journal Article
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, Azraf Anwar, Beber, Moritz E, Bergmann, Frank T, Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, G Bard Ermentrout, Faeder, James R, Freiburger, Andrew P, Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H, Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hellerstein, Joseph L, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, 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, Ankita Priya, Rampadarath, Anand K, Rohwer, Johann M, Saglam, Ali S, Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J, David van Niekerk, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R
Published in arXiv.org (13.03.2022)
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Published in arXiv.org (13.03.2022)
Paper
The ModelSEED 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, Jose P, Edirisinghe, Janaka, Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E, Best, Aaron A, Dejongh, Matthew, Kimbrel, Jeffrey A, D'haeseleer, Patrik, Wood-Charlson, Elisha M, Cottingham, Robert W, Arkin, Adam P, Henry, Christopher S
Published in bioRxiv (01.04.2020)
Published in bioRxiv (01.04.2020)
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Paper
Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite
Lieven, Christian, Moritz Emanuel Beber, Olivier, Brett G, Bergmann, Frank T, Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A, Blank, Lars M, Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Andreas Dr ger, Ebert, Birgitta Elisabeth, Edirisinghe, Janaka N, Faria, Jose P, Feist, Adam, Fengos, Georgios, Fleming, Ronan M T, Garcia-Jimenez, Beatriz, Hatzimanikatis, Vassily, Wout Van Helvoirt, Henry, Christopher, Hermjakob, Henning, Herrgard, Markus J, Kim, Hyun Uk, King, Zachary, Jasper Jan Koehorst, Klamt, Steffen, Klipp, Edda, Lakshmanan, Meiyappan, Nicolas Le Novere, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Greg L, Monk, Jonathan, Nielsen, Jens, Nielsen, Lars K, Nogales, Juan, Nookaew, Intawat, Resendis, Osbaldo, Palsson, Bernhard, Papin, Jason A, Patil, Kiran Raosaheb, Poolman, Mark, Price, Nathan D, Richelle, Anne, Rocha, Isabel, Sanchez, Benjamin, Schaap, Peter, Rahuman S Malik Sheriff, Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaca, Paulo, Vik, Jon Olav, Wodke, Judith A, Xavier, Joana C, Yuan, Qianqian, Zakhartsev, Maksim, Zhang, Cheng
Published in bioRxiv (11.07.2018)
Published in bioRxiv (11.07.2018)
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