Multiscale Systems Biology Collaboration

Papers

• See also
  UCSD Systems Biology Research Group publications,
  Ronan Fleming homepage,
  Ines Thiele homepage

• L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, …,
  Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0, Nature Protocols 14, 639-702 (2019).

• FJA Artacho, RMT Fleming, PT Vuong,
  Accelerating the DC algorithm for smooth functions, Mathematical Programming 169:1, 95-118 (2019).

• C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, …,
  Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite, BioRxiv 350991 (2019).

• L Heirendt, S Arreckx, C Trefois, Y Yarosz, M Vyas, VP Satagopam, …,
  ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software, arXiv preprint arXiv:1712.05236 (2019).

• HS Haraldsdottir, B Cousins, I Thiele, RMT Fleming, S Vempala,
  CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models, Bioinformatics 33:11, 1741-1743 (2018).

• GAP Gonzalez, LRP El Assal, A Noronha, I Thiele, HS Haraldsdottir, …,
  Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D, Journal of Cheminformatics 9:1, 39 (2018).

• L. Yang, A. Ebrahim, C. J. Lloyd, M. A. Saunders and B. O. Palsson,
  DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression, BMC Systems Biology 13:2 (2019).

• D. Ma, K. L. Judd, D. Orban and M. A. Saunders,
  Stabilized optimization via an NCL algorithm, pp 173-191 in M. Al-Baali et al. (eds.), Numerical Analysis and Optimization. NAO-IV, Muscat, Oman, January 2017, Springer Proceedings in Mathematics & Statistics, Volume 235, Springer International Publishing AG (2018);
  doi:doi.org10.1007978-3-319-90026-1_8.

• D. Ma, L. Yang, R. M. T. Fleming, I. Thiele, B. O. Palsson and M. A. Saunders, Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression, Sci. Rep. 7, Article number: 40863 (2017); doi:10.1038/srep40863.
  PDF.
  Supplementary information.

• 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 genome-scale models, Scientific Reports 6:36734 (2016).

• L. Yang, D. Ma, A. Ebrahim, C. J. Lloyd, M. A. Saunders, and B. O. Palsson, solveME: fast and reliable solution of nonlinear ME models, BMC Bioinformatics 17(1):391 (2016).

• R. M. T. Fleming, N. Vlassis, I. Thiele, and M. A. Saunders, Conditions for duality between fluxes and concentrations in biochemical networks, J. Theoretical Biology, 409 (2016), 1-10. PDF

• N. W. Henderson, S. Kim, D. Ma, M. A. Saunders, Y. Sun, R. M. T. Fleming, and I. Thiele, Conservation analysis of genome-scale biochemical networks, Bioinformatics, in preparation, Feb 2016.

• H. S. Haraldsdottir and R. M. T. Fleming, Identification of conserved moieties in metabolic networks by graph theoretical analysis of atom transition networks, submitted 2016.

• J. D. Lee, D. L. Sun, Y. Sun, and J. E. Taylor, Exact post-selection inference, with application to the lasso, Annals of Statistics, to appear.

• F. J. Aragon Artacho and R. M. T. Fleming, Globally convergent algorithms for finding zeros of duplomonotone mappings, Optimization Letters (2015), 3(3), 569584.

• D. Ma and M. A. Saunders, Solving multiscale linear programs using the simplex method in quadruple precision, pp. 223-235 in M. Al-Baali, L. Grandinetti, and A. Purnama (eds.), Numerical Analysis and Optimization, NAO-III, 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 genome-scale models need exact solvers or clearer standards?, Molecular Systems Biology 11:831 (2015), 3 pp.

• J. D. Lee, Y. Sun, and M. A. Saunders, Proximal Newton-type methods for minimizing composite functions, SIAM. J. Optim. 24:3 (2014) 1420–1443.

• I. Thiele, N. Vlassis, and R. M. T. Fleming, FastGapFill: Efficient gap filling in metabolic networks, Bioinformatics Advance Access, May 7, 2014.

• X. Meng, M. A. Saunders, and M. W. Mahoney, LSRN: a parallel iterative solver for strongly over- or underdetermined systems, SIAM J. Sci. Comput. 36:2 (2014) C95–C118.

• J. A. Lerman, Genome-scale Models of Metabolism and Gene Expression: Construction and Use for Growth Phenotype Prediction, PhD thesis, Bioinformatics and Systems Biology, University of California, San Diego, CA, 2014, 172 pp.

• E. J. O'Brien, J. A. Lerman, R. L. Chang, D. R. Hyduke, and B. O. Palsson, Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction, Molecular Systems Biology 9:693 (2013) 13 pp. Download pdf. Supplementary information.

• Y. Sun, R. M. T. Fleming, M. A. Saunders, and I. Thiele, Robust flux balance analysis of multiscale biochemical reaction networks, BMC Bioinformatics 14:240 (2013) 6pp. Download pdf.

• S. Akle, O. Dalal, R. M. T. Fleming, M. A. Saunders, N. A. Taheri, and Y. Ye, Existence of positive steady states for mass conserving and mass-action chemical reaction networks with a single terminal-linkage class, arXiv:1106:2359.

• I. Thiele, R. M. T. Fleming, R. Que, A. Bordbar, and B. O. Palsson, Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage, PLoS One 7(9):e45635 (2012).

• J. Nogales, S. Gudmundsson, E. M. Knight, B. O. Palsson, and I. Thiele, Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis, Proc. Natl. Acad. Sci. USA 109:7 (2012) 2678–2683.

• J. A. Lerman, D. R. Hyduke, H. Latif, V. A. Portnoy, N. E. Lewis, J. D. Orth, A. C. Schrimpe-Rutledge, 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.

• R. M. T. Fleming, C. M. Maes, M. A. Saunders, Y. Ye, and B. O. Palsson, A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks, J. Theor. Biol. 292 (2012) 71–77.