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

por Du, Bin, Zielinski, Daniel C., Palsson, Bernhard O.
Publicado 2017

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

por Heckmann, David, Zielinski, Daniel C., Palsson, Bernhard O.
Publicado 2018

The quantitative metabolome is shaped by abiotic constraints

por Akbari, Amir, Yurkovich, James T., Zielinski, Daniel C., Palsson, Bernhard O.
Publicado 2021

Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways

por Mattei, Gianluca, Gan, Zhuohui, Ramazzotti, Matteo, Palsson, Bernhard O., Zielinski, Daniel C.
Publicado 2023

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

por Haiman, Zachary B., Zielinski, Daniel C., Koike, Yuko, Yurkovich, James T., Palsson, Bernhard O.
Publicado 2021

Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism

por Zielinski, Daniel C., Jamshidi, Neema, Corbett, Austin J., Bordbar, Aarash, Thomas, Alex, Palsson, Bernhard O.
Publicado 2017

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

por Dalldorf, Christopher, Rychel, Kevin, Szubin, Richard, Hefner, Ying, Patel, Arjun, Zielinski, Daniel C., Palsson, Bernhard O.
Publicado 2023

Empowering drug off-target discovery with metabolic and structural analysis

por Chowdhury, Sourav, Zielinski, Daniel C., Dalldorf, Christopher, Rodrigues, Joao V., Palsson, Bernhard O., Shakhnovich, Eugene I.
Publicado 2023

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

por Dräger, Andreas, Zielinski, Daniel C, Keller, Roland, Rall, Matthias, Eichner, Johannes, Palsson, Bernhard O, Zell, Andreas
Publicado 2015

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

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

A multi-scale expression and regulation knowledge base for Escherichia coli

por Lamoureux, Cameron R, Decker, Katherine T, Sastry, Anand V, Rychel, Kevin, Gao, Ye, McConn, John Luke, Zielinski, Daniel C, Palsson, Bernhard O
Publicado 2023

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

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

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

por Zielinski, Daniel C., Filipp, Fabian V., Bordbar, Aarash, Jensen, Kasper, Smith, Jeffrey W., Herrgard, Markus J., Mo, Monica L., Palsson, Bernhard O.
Publicado 2015

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

por Du, Bin, Zielinski, Daniel C., Kavvas, Erol S., Dräger, Andreas, Tan, Justin, Zhang, Zhen, Ruggiero, Kayla E., Arzumanyan, Garri A., Palsson, Bernhard O.
Publicado 2016

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

por Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O.
Publicado 2018

Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

por Phaneuf, Patrick V., Zielinski, Daniel C., Yurkovich, James T., Johnsen, Josefin, Szubin, Richard, Yang, Lei, Kim, Se Hyeuk, Schulz, Sebastian, Wu, Muyao, Dalldorf, Christopher, Ozdemir, Emre, Lennen, Rebecca M., Palsson, Bernhard O., Feist, Adam M.
Publicado 2021

Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

por Hirose, Yujiro, Poudel, Saugat, Sastry, Anand V., Rychel, Kevin, Lamoureux, Cameron R., Szubin, Richard, Zielinski, Daniel C., Lim, Hyun Gyu, Menon, Nitasha D., Bergsten, Helena, Uchiyama, Satoshi, Hanada, Tomoki, Kawabata, Shigetada, Palsson, Bernhard O., Nizet, Victor
Publicado 2023

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

por 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.
Publicado 2018

Recon 2.2: from reconstruction to model of human metabolism

por 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
Publicado 2016