Multiscale Systems Biology Collaboration
Papers
D. Ma, K. L. Judd, D. Orban and M. A. Saunders,
Stabilized optimization via an NCL algorithm,
pp 173191 in M. AlBaali et al. (eds.),
Numerical Analysis and Optimization. NAOIV, Muscat, Oman, January 2017,
Springer Proceedings in Mathematics & Statistics, Volume 235,
Springer International Publishing AG (2018);
doi:doi.org10.10079783319900261_8.
L. Yang, J. T. Yurkovich, C. J Lloyd, A. Ebrahim, M. A. Saunders,
and B. O. Palsson,
Principles of proteome allocation are revealed using proteomic data
and genomescale models,
Scientific Reports 6:36734 (2016).
N. W. Henderson, S. Kim, D. Ma, M. A. Saunders, Y. Sun, R. M. T. Fleming, and I. Thiele,
Conservation analysis of genomescale biochemical networks,
Bioinformatics, in preparation, Feb 2016.
D. Ma and M. A. Saunders,
Solving multiscale linear programs using the simplex method in quadruple precision,
pp. 223235 in M. AlBaali, L. Grandinetti, and A. Purnama (eds.),
Numerical Analysis and Optimization,
NAOIII, Muscat, Oman, January 2014,
Springer Proceedings in Mathematics and Statistics, Volume 134,
Springer International Publishing Switzerland 2015.
A. Ebrahim, E. Almaas, E. Bauer, A Bordbar, AP Burgard, RL Chang,
A. Drager, I. Famili, A. M. Feist, R. M. T. Fleming,
S. S. Fong, V. Hatzimanikatis, M. J. Herrgard, A. Holder,
M. Hucka, D. Hyduke, N. Jamshidi, S. Y. Lee, N. Le, Novere,
J. A. Lerman, N. E. Lewis, D. Ma, R. Mahadevan, C. Maranas,
H. Nagarajan, A. Navid, J. Nielsen, L. K. Nielsen, J. Nogales,
A. Noronha, C. Pal, B. O. Palsson, J. A. Papin, K. R. Patil,
N. D. Price, J. L. Reed, M. Saunders, R. S. Senger, N. Sonnenschein,
Y. Sun, and I. Thiele,
Do genomescale models need exact solvers or clearer standards?,
Molecular Systems Biology 11:831 (2015), 3 pp.
J. A. Lerman, D. R. Hyduke, H. Latif, V. A. Portnoy, N. E. Lewis, J. D. Orth,
A. C. SchrimpeRutledge, R. D. Smith, J. N. Adkins, K. A. Zengler, and B. O. Palsson,
In silico method for modelling metabolism and gene product expression at genome scale,
Nat. Commun. 3 (2012) 929.
