Search Results - "Beber, Moritz E"

eQuilibrator 3.0: a database solution for thermodynamic constant estimation by Beber, Moritz E, Gollub, Mattia G, Mozaffari, Dana, Shebek, Kevin M, Flamholz, Avi I, Milo, Ron, Noor, Elad

“…Abstract eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a…”
Get full text

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes by 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

“…Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or…”
Get full text

Community standards to facilitate development and address challenges in metabolic modeling by Carey, Maureen A, Dräger, Andreas, Beber, Moritz E, Papin, Jason A, Yurkovich, James T

“…Standardization of data and models facilitates effective communication, especially in computational systems biology. However, both the development and…”
Get full text

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes by 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

Get full text

Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB by Beber, Moritz E, Muskhelishvili, Georgi, Hütt, Marc-Thorsten

“…RegulonDB is a database storing the biological information behind the transcriptional regulatory network (TRN) of the bacterium Escherichia coli. It is one of…”
Get full text

Interplay of digital and analog control in time-resolved gene expression profiles by Beber, Moritz E., Sobetzko, Patrick, Muskhelishvili, Georgi, Hütt, Marc-Thorsten

“…Background Measuring the agreement between a gene expression profile and a known transcriptional regulatory network is an important step in the functional…”
Get full text

MEMOTE for standardized genome-scale metabolic model testing by 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

“…Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organism’s metabolism under different conditions…”
Get full text

eQuilibrator 3.0: a database solution for thermodynamic constant estimation by Beber, Moritz E., Gollub, Mattia G., Mozaffari, Dana, Shebek, Kevin M., Flamholz, Avi I, Milo, Ron, Noor, Elad

“…Abstract eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a…”
Get full text

TAXPASTA: TAXonomic Profile Aggregation and STAndardisation by Beber, Moritz E., Borry, Maxime, Stamouli, Sofia, Yates, James A. Fellows

Get full text

BioSimulators: a central registry of simulation engines and services for recommending specific tools by 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

“…Abstract Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and…”
Get full text

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing by 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

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
Get full text

eQuilibrator 3.0 -- a platform for the estimation of thermodynamic constants by Beber, Moritz E, Gollub, Mattia G, Mozaffari, Dana, Shebek, Kevin M, Noor, Elad

“…eQuilibrator (equilibrator.weizmann.ac.il) is a calculator for biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based…”
Get full text

BioSimulators: a central registry of simulation engines and services for recommending specific tools by 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

“…Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse…”
Get full text