Constraint-based simulation of multiple interactive elemental cycles in biogeochemical systems
暂无分享,去创建一个
Clemente Izurieta | Geoffrey C. Poole | Emily S. Bernhardt | Ashley M. Helton | Ann Marie Reinhold | E. Bernhardt | A. Helton | G. Poole | C. Izurieta | A. Reinhold
[1] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.
[2] D. Fell,et al. Is maximization of molar yield in metabolic networks favoured by evolution? , 2008, Journal of theoretical biology.
[3] Jérémie Bourdon,et al. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems , 2017, PloS one.
[4] J. Vallino,et al. The Thermodynamics of Marine Biogeochemical Cycles: Lotka Revisited. , 2016, Annual review of marine science.
[5] Peter E. Thornton,et al. Parameterization and Sensitivity Analysis of the BIOME–BGC Terrestrial Ecosystem Model: Net Primary Production Controls , 2000 .
[6] E. Bernhardt,et al. A generalized optimization model of microbially driven aquatic biogeochemistry based on thermodynamic, kinetic, and stoichiometric ecological theory , 2014 .
[7] E. Bernhardt,et al. Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns. , 2015, Ecology letters.
[8] M. Kaspari,et al. Biogeochemistry and Geographical Ecology: Embracing All Twenty-Five Elements Required to Build Organisms* , 2016, The American Naturalist.
[9] C. Chen,et al. Stoichiometry of carbon, hydrogen, nitrogen, sulfur and oxygen in the particulate matter of the western North Pacific marginal seas , 1996 .
[10] J. J. Morgan,et al. Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters , 1970 .
[11] Brian P. Kennedy,et al. THERMODYNAMIC CONSTRAINTS ON NITROGENTRANSFORMATIONS AND OTHER BIOGEOCHEMICALPROCESSES AT SOIL–STREAM INTERFACES , 1998 .
[12] Brian P. Kennedy,et al. THERMODYNAMIC CONSTRAINTS ON NITROGEN TRANSFORMATIONS AND OTHER BIOGEOCHEMICAL PROCESSES AT SOIL-STREAM INTERFACES , 1998 .
[13] W. Schlesinger,et al. Introduction to coupled biogeochemical cycles , 2011 .
[14] Wendy H. Yang,et al. Beyond carbon and nitrogen: how the microbial energy economy couples elemental cycles in diverse ecosystems , 2011 .
[15] Orkun S. Soyer,et al. Challenges in microbial ecology: building predictive understanding of community function and dynamics , 2016, The ISME Journal.
[16] Costas D. Maranas,et al. OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities , 2012, PLoS Comput. Biol..
[17] Davey L. Jones,et al. Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? , 2016, Front. Microbiol..
[18] E. D. Schneider,et al. Complexity and thermodynamics: Towards a new ecology , 1994 .
[19] James H. Brown,et al. Linking the global carbon cycle to individual metabolism , 2005 .
[20] P. Visscher,et al. Anaerobic Metabolism: Linkages to Trace Gases and Aerobic Processes , 2003 .
[21] Yanan Shen,et al. The antiquity of microbial sulfate reduction , 2004 .
[22] Sven E. Jørgensen,et al. A New Ecology: Systems Perspective , 2007 .
[23] B. Palsson,et al. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.
[24] F. Mackenzie,et al. C, N, P, S Global Biogeochemical Cycles and Modeling of Global Change , 1993 .
[25] K. Rogers,et al. Energetics of chemolithoautotrophy in the hydrothermal system of Vulcano Island, southern Italy , 2003 .
[26] Brian D. Fath,et al. Application of thermodynamic principles in ecology , 2004 .
[27] Adam M. Feist,et al. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.
[28] B. Palsson,et al. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth , 2002, Nature.
[29] W. Parton,et al. Dynamics of C, N, P and S in grassland soils: a model , 1988 .
[30] C. Field,et al. Ecosystem constraints to symbiotic nitrogen fixers: A simple model and its implications , 1999 .
[31] J. Galloway,et al. An Earth-system perspective of the global nitrogen cycle , 2008, Nature.
[32] Abraham Lerman,et al. Geochemical Processes: Water and Sediment Environments , 1979 .
[33] J. Vallino. Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.
[34] E. Rastetter. Modeling coupled biogeochemical cycles , 2011 .
[35] E. Delong,et al. The Microbial Engines That Drive Earth's Biogeochemical Cycles , 2008, Science.
[36] M. Scheffer,et al. Predicting microbial nitrogen pathways from basic principles. , 2011, Environmental microbiology.
[37] D. Schrag,et al. Limitations on Limitation , 2018 .
[38] Jeffrey D Orth,et al. What is flux balance analysis? , 2010, Nature Biotechnology.
[39] Claes Wohlin,et al. Experimentation in Software Engineering , 2012, Springer Berlin Heidelberg.
[40] Ali R. Zomorrodi,et al. d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. , 2014, ACS synthetic biology.
[41] Peter E. Thornton,et al. Modeling and measuring the effects of disturbance history and climate on carbon and water budgets in evergreen needleleaf forests , 2002 .
[42] J. Benstead,et al. Ecological stoichiometry in freshwater benthic systems: recent progress and perspectives , 2005 .