Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

Autor: Edward J O'Brien, Joshua A Lerman, Roger L Chang, Daniel R Hyduke, Bernhard Ø Palsson

Publikováno v: Molecular Systems Biology, Vol 9, Iss 1, Pp 1-13 (2013)

Abstract Growth is a fundamental process of life. Growth requirements are well‐characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive of events at the molecular scale an

Externí odkaz: https://doaj.org/article/d2339f0bc6e74f0e9897c0a874ad4033

A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

Autor: Hojung Nam, Miguel Campodonico, Aarash Bordbar, Daniel R Hyduke, Sangwoo Kim, Daniel C Zielinski, Bernhard O Palsson

Publikováno v: PLoS Computational Biology, Vol 10, Iss 9, p e1003837 (2014)

Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH), succ

Externí odkaz: https://doaj.org/article/04a38c5545694958a010207816f363fe

SBML Level 3: an extensible format for the exchange and reuse of biological models

Autor: Edda Klipp, Marco Antoniotti, Frank Bergmann, James C. Schaff, Peter D. Karp, Daniel Lucio, Kedar Nath Natarajan, Thomas M. Hamm, Leandro Watanabe, Henning Hermjakob, David Tolnay, John Wagner, Joerg Stelling, Alida Palmisano, Falk Schreiber, Yukiko Matsuoka, Harold F. Gómez, Huaiyu Mi, Carole J. Proctor, Ulrike Wittig, Neil Swainston, Jan Červený, Denis Thieffry, Piero Dalle Pezze, Julio Saez-Rodriguez, Maciej J. Swat, Bin Hu, Martina Kutmon, Thomas Pfau, Bas Teusink, Sarah M. Keating, Fedor A. Kolpakov, Andreas Dräger, Pedro Mendes, Martin Scharm, Emek Demir, Ioannis Xenarios, Christoph Flamm, Axel von Kamp, Darren J. Wilkinson, Nick Juty, Fengkai Zhang, Leonard A. Harris, Michael Schubert, Dagmar Waltemath, Lucian P. Smith, Steffen Klamt, Herbert M. Sauro, Ali Ebrahim, Wolfram Liebermeister, Christian Knüpfer, Nicolas Rodriguez, Tramy Nguyen, Naoki Tanimura, Christopher Cox, Stuart C. Sealfon, Nicholas Alexander Allen, Clemens Wrzodek, Bastian R. Angermann, Martin Meier-Schellersheim, Anna Zhukova, Jean-Baptiste Pettit, Hovakim Grabski, Devin P. Sullivan, Claudine Chaouiya, Michael L. Blinov, John Doyle, Ilya Kiselev, Roman Schulte, Alex Gutteridge, Mélanie Courtot, Eric Mjolsness, Finja Wrzodek, Rahuman S Malik-Sheriff, Ronan M. T. Fleming, Bruce E. Shapiro, Kimberly Begley, Leslie M. Loew, Colin S. Gillespie, Ibrahim Vazirabad, Michael Hucka, Akira Funahashi, Bernhard O. Palsson, Hamid Bolouri, Tomáš Helikar, Camille Laibe, William S. Denney, Chris T. Evelo, Florian Mittag, William S. Hlavacek, Ron Henkel, Harish Dharuri, Julien Dorier, Karthik Raman, Martina Fröhlich, Conor Lawless, Rainer Machné, Falko Krause, Damon Hachmeister, Matthias König, Clifford A. Shaffer, Benjamin D. Heavner, Douglas B. Kell, Jonathan R. Karr, Mihai Glont, Lukas Endler, Melanie I. Stefan, Robert Phair, Lu Li, Henning Schmidt, Dirk Drasdo, Johan Elf, Allyson L. Lister, Hiroaki Kitano, Richard R. Adams, Oliver A. Ruebenacker, Roland Keller, Sven Sahle, Ion I. Moraru, Gary D. Bader, Poul M. F. Nielsen, Johann M. Rohwer, Johannes Eichner, Daniel R. Hyduke, James R. Faeder, Stefan Hoops, Emanuel Gonçalves, Yuichiro Inagaki, Aurélien Naldi, Koichi Takahashi, Sylvain Soliman, Brett G. Olivier, Kieran Smallbone, Stuart L. Moodie, Pedro T. Monteiro, Chris J. Myers, Martin Golebiewski, Tomas Radivoyevitch, Jeremy Zucker, Hidde de Jong, Andrew Finney

Publikováno v: Molecular Systems Biology
Molecular Systems Biology, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Molecular systems biology, vol 16, iss 8
Molecular Systems Biology, EMBO Press, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Keating, S M, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, F T, Finney, A, Gillespie, C S, Helikar, T, Hoops, S, Malik-Sheriff, R S, Moodie, S L, Moraru, I I, Myers, C J, Naldi, A, Olivier, B G, Sahle, S, Schaff, J C, Smith, L P, Swat, M J, Thieffry, D, Watanabe, L, Wilkinson, D J, Blinov, M L, Begley, K, Faeder, J R, Gómez, H F, Hamm, T M, Inagaki, Y, Liebermeister, W, Lister, A L, Lucio, D, Mjolsness, E, Proctor, C J, Raman, K, Rodriguez, N, Shaffer, C A, Shapiro, B E, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier-Schellersheim, M, Sauro, H M, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, J C, Hucka, M, Adams, R R, Allen, N A, Angermann, B R, Antoniotti, M, Bader, G D, Červený, J, Courtot, M, Cox, C D, Dalle Pezze, P, Demir, E, Denney, W S, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, C T, Flamm, C, Fleming, R M T, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, L A, Heavner, B D, Henkel, R, Hlavacek, W S, Hu, B, Hyduke, D R, de Jong, H, Juty, N, Karp, P D, Karr, J R, Kell, D B, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, L M, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, P T, Natarajan, K N, Nielsen, P M F, Nguyen, T, Palmisano, A, Pettit, J B, Pfau, T, Phair, R D, Radivoyevitch, T, Rohwer, J M, Ruebenacker, O A, Saez-Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, S C, Smallbone, K, Soliman, S, Stefan, M I, Sullivan, D P, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, von Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A & Zucker, J 2020, ' SBML Level 3 : an extensible format for the exchange and reuse of biological models ', Molecular Systems Biology, vol. 16, no. 8, e9110, pp. 1-21 . https://doi.org/10.15252/msb.20199110
MOLECULAR SYSTEMS BIOLOGY
Molecular Systems Biology, Vol 16, Iss 8, Pp n/a-n/a (2020)

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aa48af775634bdfd1c248e236b20ef61
http://hdl.handle.net/10281/282956

Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs

Autor: Roland Frötschl, Jiri Aubrecht, Heidrun Ellinger-Ziegelbauer, Andrew Williams, Heng-Hong Li, Renxiang Chen, Albert J. Fornace, Raegan O’Lone, Carole L. Yauk, Daniel R. Hyduke

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America

Significance Standard in vitro assays to assess genotoxicity frequently generate positive results that are subsequently found to be irrelevant for in vivo carcinogenesis and human cancer risk assessment. Currently used follow-up methods, such as anim

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e8ec003d8ac5c6cd165ef3207b1b8249
https://doi.org/10.1073/pnas.1714109114

Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells

Autor: Pamela L. Heard, Albert J. Fornace, Heng-Hong Li, Daniel R. Hyduke, Carole L. Yauk, Jiri Aubrecht, Renxiang Chen

Publikováno v: Environmental and Molecular Mutagenesis. 56:505-519

The development of in vitro molecular biomarkers to accurately predict toxicological effects has become a priority to advance testing strategies for human health risk assessment. The application of in vitro transcriptomic biomarkers promises increase

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::d74b1891784f77c5b2a627ac58888770
https://doi.org/10.1002/em.21941