Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

द्वारा Du, Bin, Zielinski, Daniel C., Palsson, Bernhard O.
में प्रकाशित PLoS One (2017)

Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

द्वारा Heckmann, David, Zielinski, Daniel C., Palsson, Bernhard O.
में प्रकाशित Nat Commun (2018)

The quantitative metabolome is shaped by abiotic constraints

द्वारा Akbari, Amir, Yurkovich, James T., Zielinski, Daniel C., Palsson, Bernhard O.
में प्रकाशित Nat Commun (2021)

Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice

द्वारा Du, Bin, Zielinski, Daniel C., Monk, Jonathan M., Palsson, Bernhard O.
में प्रकाशित Proc Natl Acad Sci U S A (2018)

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

द्वारा Haiman, Zachary B., Zielinski, Daniel C., Koike, Yuko, Yurkovich, James T., Palsson, Bernhard O.
में प्रकाशित PLoS Comput Biol (2021)

A systematic evaluation of methods for tailoring genome-scale metabolic models

द्वारा Opdam, Sjoerd, Richelle, Anne, Kellman, Benjamin, Li, Shanzhong, Zielinski, Daniel C., Lewis, Nathan E.
में प्रकाशित Cell Syst (2017)

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method

द्वारा Du, Bin, Zhang, Zhen, Grubner, Sharon, Yurkovich, James T., Palsson, Bernhard O., Zielinski, Daniel C.
में प्रकाशित Biophys J (2018)

Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism

द्वारा Zielinski, Daniel C., Jamshidi, Neema, Corbett, Austin J., Bordbar, Aarash, Thomas, Alex, Palsson, Bernhard O.
में प्रकाशित Sci Rep (2017)

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

द्वारा Dräger, Andreas, Zielinski, Daniel C, Keller, Roland, Rall, Matthias, Eichner, Johannes, Palsson, Bernhard O, Zell, Andreas
में प्रकाशित BMC Syst Biol (2015)

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

द्वारा Feist, Adam M., Zielinski, Daniel C., Orth, Jeffrey D., Schellenberger, Jan, Herrgard, Markus J., Palsson, Bernhard Ø.
प्रकाशित 2009

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

द्वारा Nam, Hojung, Campodonico, Miguel, Bordbar, Aarash, Hyduke, Daniel R., Kim, Sangwoo, Zielinski, Daniel C., Palsson, Bernhard O.
प्रकाशित 2014

Predicting outcomes of steady-state (13)C isotope tracing experiments using Monte Carlo sampling

द्वारा Schellenberger, Jan, Zielinski, Daniel C, Choi, Wing, Madireddi, Sunthosh, Portnoy, Vasiliy, Scott, David A, Reed, Jennifer L, Osterman, Andrei L, Palsson, Bernhard ∅
प्रकाशित 2012

Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis

द्वारा Zielinski, Daniel C., Filipp, Fabian V., Bordbar, Aarash, Jensen, Kasper, Smith, Jeffrey W., Herrgard, Markus J., Mo, Monica L., Palsson, Bernhard O.
में प्रकाशित Nat Commun (2015)

Evaluation of rate law approximations in bottom-up kinetic models of metabolism

द्वारा Du, Bin, Zielinski, Daniel C., Kavvas, Erol S., Dräger, Andreas, Tan, Justin, Zhang, Zhen, Ruggiero, Kayla E., Arzumanyan, Garri A., Palsson, Bernhard O.
में प्रकाशित BMC Syst Biol (2016)

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

द्वारा Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O.
में प्रकाशित Nat Commun (2018)

Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks

द्वारा 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.
में प्रकाशित J Biol Chem (2017)

Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions

द्वारा Zuñiga, Cristal, Li, Chien-Ting, Huelsman, Tyler, Levering, Jennifer, Zielinski, Daniel C., McConnell, Brian O., Long, Christopher P., Knoshaug, Eric P., Guarnieri, Michael T., Antoniewicz, Maciek R., Betenbaugh, Michael J., Zengler, Karsten
में प्रकाशित Plant Physiol (2016)

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

द्वारा Schellenberger, Jan, Que, Richard, Fleming, Ronan M. T., Thiele, Ines, Orth, Jeffrey D., Feist, Adam M., Zielinski, Daniel C., Bordbar, Aarash, Lewis, Nathan E., Rahmanian, Sorena, Kang, Joseph, Hyduke, Daniel R., Palsson, Bernhard Ø.
प्रकाशित 2011

Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism

द्वारा Brunk, Elizabeth, Sahoo, Swagatika, Zielinski, Daniel C., Altunkaya, Ali, Dräger, Andreas, Mih, Nathan, Gatto, Francesco, Nilsson, Avlant, Gonzalez, German Andres Preciat, Aurich, Maike Kathrin, Prlić, Andreas, Sastry, Anand, Danielsdottir, Anna D., Heinken, Almut, Noronha, Alberto, Rose, Peter W., Burley, Stephen K., Fleming, Ronan M.T., Nielsen, Jens, Thiele, Ines, Palsson, Bernhard O.
में प्रकाशित Nat Biotechnol (2018)

Recon 2.2: from reconstruction to model of human metabolism

द्वारा 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
में प्रकाशित Metabolomics (2016)