Peer-reviewed publications:
2024
"Integration of proteomic data with genome‐scale metabolic models: A methodological overview",
Zare, F., Fleming, R.M.T., Protein Science 33 (10), e5150 (2024).
"Identification of metabolites reproducibly associated with Parkinson’s Disease via meta-analysis and computational modelling", Luo, X., Liu, Y., Balck, A., Klein, C., Fleming, R.M.T., npj Parkinson's Disease 10 (1), 126 (2024).
2023
"Omics data integration suggests a potential idiopathic Parkinson’s disease signature.", Zagare, A., Preciat, G., Nickels, S.L., Luo, X., Monzel, A.S., Gomez-Giro, G., Robertson, G., Jaeger, C., Sharif, J., Koseki, H., Diederich, N.J., Glaab, E. , Fleming, R.M.T., Schwamborn, J.C., Communications Biology, 6(1), p.1179 (2023).
"Reconstruction of Glutathione Metabolism in the Neuronal Model of Rotenone-Induced Neurodegeneration Using Mass Isotopologue Analysis with Hydrophilic Interaction Liquid Chromatography-Zeno High-Resolution Multiple Reaction Monitoring", Huang, L., Drouin, N., Causon, J., Wegrzyn, A., Castro-Perez, J., Fleming, R.M.T., Harms, A., Hankemeier, T., Analytical Chemistry, 95 (6), 3255-3266 (2023).
"Cardinality optimisation in constraint-based modelling: Application to human metabolism", Fleming, R.M.T., Haraldsdottir, H.S., Le, H.M., Vuong, P.T., Hankemeier, T., Thiele, I., Bioinformatics, 39 (9), btad450 (2023).
"Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.", Heinken, A., Hertel, J., Acharya, G., Ravcheev, D. A., Nyga, M., Okpala, O. E., Hogan, M., Magnúsdóttir, S., Martinelli, F., Nap, B., Preciat, G., Edirisinghe, J. N., Henry, C. S., Fleming, R. M. T., Thiele, I., Nat Biotechnol (2023). https://doi.org/10.1038/s41587-022-01628-0
2022
"MetaboAnnotator: An efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions", Thiele, I., Preciat, G., Fleming, R.M.T., Bioinformatics, btac596 (2022).
"Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication.", Thiele, I., Fleming, R. M. T., Computational and Structural Biotechnology, 4098-4109 (2022).
2021
"DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations", Heinken, A., Magnusdottir, S., Fleming, R.M.T., Thiele, I., Bioinformatics, btab622 (2021).
2020
"Passive controlled flow for Parkinson"s disease neuronal cell culture in 3D microfluidic devices", Kane, K.I.W., Jarazo, J., Moreno, E.L., Fleming, R.M.T., Schwamborn, J.C., Organs-on-a-Chip, Volume 2 (2020)
"Phenotype-Agnostic Molecular Subtyping of Neurodegenerative Disorders: The Cincinnati Cohort Biomarker Program (CCBP)", Sturchio, A., Marsili, L., Vizcarra, J.A., Dwivedi, A.K., Kauffman, M.A., Duker, A.P., Lu, P., Pauciulo, M.W., Wissel, B.D., Hill, E.J., Stecher, B., Keeling, E.G., Vagal, A.S., Wang, L., Haslam, D.B., Robson, M.J., Tanner, C.M., Hagey, D.W., El Andaloussi, S., Ezzat, K., Fleming, R.M.T., Lu, L.J., Little, M.A., Espay, A.J., Front. Aging Neurosci., Volume 12 (2020)
"Structural conserved moiety splitting of a stoichiometric matrix", S. Ghaderi, H.S. Haraldsdóttir, M. Ahookhosh, S. Arreckx, R.M.T. Fleming, Journal of Theoretical Biology 499, 110276, (2020)
"MEMOTE for standardized genome-scale metabolic model testing", C. Lieven, M.E. Beber, B.G. Olivier, F.T. Bergmann, M. Ataman, P. Babaei, L.M. Blank, S. Chauhan, K. Correia, C. Diener, A, Drager, B.E. Ebert, J.N. Edirisinghe, J.P. Faria, A.M. Feist, G. Fengos, R.M.T. Fleming, B. Garcia-Jimenez, V. Hatzimanikatis, Wout Van Helvoirt, C. S. Henry, H. Hermjakob, M. J. Herrgård, A. Kaafarani, H. U. Kim, Z. King, S. Klamt, E. Klipp, J. J. Koehorst, M. König, M. Lakshmanan, D.Y. Lee, S. Y. Lee, S. Lee, N. E. Lewis, F. Liu, H. Ma, D. Machado, R. Mahadevan, P. Maia, A. Mardinoglu, G. L. Medlock, J. M. Monk, J. Nielsen, L. K. Nielsen, J. Nogales, I. Nookaew, B. O. Palsson, J. A. Papin, K. R. Patil, M. Poolman, N. D. Price, O. Resendis-Antonio, A. Richelle, I. Rocha, B. J. Sánchez, P. J. Schaap, R. S. M. Sheriff, S. Shoaie, N. Sonnenschein, B. Teusink, P. Vilaça, J. O. Vik, J. A.H. Wodke, J. C. Xavier, Q. Yuan, M. Zakhartsev, C. Zhang, Nature biotechnology 38 (3), 272-276, (2020)
"SBML Level 3: an extensible format for the exchange and reuse of biological models", S.M. Keating, D. Waltemath, M. König, F. Zhang, A. Dräger, C. Chaouiya, et.al., Molecular systems biology 16 (8), e9110, (2020)
"Personalized whole-body models integrate metabolism, physiology, and the gut microbiome", Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., Fleming, R.M.T., , Molecular Systems Biology, 16:e8982 (2020).
"Finding zeros of Hölder metrically subregular mappings via globally convergent Levenberg–Marquardt methods", M. Ahookhosh, R.M.T. Fleming, P.T. Vuong, Optimization Methods and Software, 1-37, (2020)
2019
"Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease", Hertel, J., Harms, A.C., Heinken, A., Baldini, F., Thinnes. C.C., Glaab, E., Vasco, D.A., Pietzner, M., Stewart, I.D., Wareham, N.J., Langenberg, C., Trenkwalder, C., Krüger, R., Hankemeier, T., Fleming, R.M.T., Mollenhauer, B., Ines Thiele, I., Cell Reports (2019).
"LC–MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide", C.C.W. Willacey, M. Naaktgeboren, E.L. Moreno, A.B. Wegrzyn, D. Van der Es, et. al., Journal of Chromatography a 1608, 460413, (2019)
"Local convergence of the Levenberg–Marquardt method under Hölder metric subregularity", M. Ahookhosh, F.J. Aragón Artacho, R.M.T. Fleming, P.T. Vuong, Advances in Computational Mathematics 45 (5), 2771-2806, (2019)
"Community-driven roadmap for integrated disease maps", M. Ostaszewski, S. Gebel, I. Kuperstein, A. Mazein, A. Zinovyev, U. Dogrusoz, et. al, Briefings in bioinformatics 20 (2), 659-670, (2019)
"The connectome is necessary but not sufficient for the spread of alpha-synuclein pathology in rats", M.A.P. Oliveira, S. Arreckx, D. Di Monte, G.A. Preciat, A. Ulusoy, R.M.T. Fleming, bioRxiv, 567222, (2019)
"3D cultures of Parkinson"s disease‐specific dopaminergic neurons for high content phenotyping and drug testing", S. Bolognin, M. Fossépré, X. Qing, J. Jarazo, J. Ščančar, E.L. Moreno, et. al, Advanced Science 6 (1), 1800927, (2019)
"Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease", Heinken, A., Ravcheev, D.A., Baldini, F., Heirendt, L., Fleming, R.M.T., Thiele, I., Microbiome, 7:75 (2019).
"Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer", N. Sompairac, J. Modamio, E. Barillot, R.M.T. Fleming, A. Zinovyev, et. al, BMC bioinformatics 20 (4), 1-14, (2019)
"Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0", Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S.N., Richelle, A., Heinken, A., Haraldsdottir, H.S., Keating, S.M., Vlasov, V., Wachowiak, J., Magnusdottir, S., Ng, C.Y., Preciat, G., Zagar, A., Chan, S.H.J., Aurich, M.K., Clancy, C.M., Modamio, J., Sauls, J.T., Noronha, A., Bordbar, A., Cousin, B., Guebila, M., Apaolaza, I., Kostromins, A., Le, H.M., Ma, D., Sun, Y., Valcarcel, L., Wang, L., Yurkovich, J.T., Vuong, P.T., El Assal, L.P., Hinton, S., Bryant, W.A., Artacho, F.J.A., Planes, F.J., Stalidzans, E., Maas, A., Vempala, S., Hucka, M., Saunders, M.A., Maranas, C.D., Lewis, N.E., Sauter, T., Palsson, B.O., Thiele, I., Fleming, R.M.T., Nature Protocol, 14, 639-702 (2019).
"Automated microfluidic cell culture of stem cell derived dopaminergic neurons", K.I.W. Kane, E.L. Moreno, S. Hachi, M. Walter, J. Jarazo, M.A.P. Oliveira, et. al., Scientific reports 9 (1), 1-12, (2019)
"The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease", Noronha, A., Modamio, J., Jarosz, Y., Sompairac, N., Gonzalez, G., DanÃielsdottir, A.D., Krecke, M., Merten, D., Haraldsdottir, H.S., , A., Heirendt, L., Magnusdottir, S., Ravcheev, D.A., Sahoo, S., Gawron, P., Guerard, E., Friscioni, L., Garcia, B., Prendergast, M., Rodrigues, M., Roy, A., Rouquaya, M., Wiltgen, L., Zagare, A., John, E., Krueger, M., Kuperstein, I., Zinovyev, A., Schneider, R., Fleming, R.M.T., Thiele, I., Nucleic Acids Research, 47(D1): D614-D624 (2019). Breakthrough Article.
2018
"The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities", Baldini, F., Heinken, A., Heirendt, L., Magnusdottir, S., Fleming, R.M.T., Thiele, I., Bioinformatics, bty941 (2018).
Reply to" Challenges in modeling the human gut microbiome", Magnusdottir, S., Heinken, A., Fleming, R.M.T., Thiele, I., Nature Biotechnology, 36(8): 686 (2018).
"Determination of the rheological properties of Matrigel for optimum seeding conditions in microfluidic cell cultures", K.I.W. Kane, E.L. Moreno, C.M. Lehr, S. Hachi, R. Dannert, R. Sanctuary, et. al., AIP Advances 8 (12), 125332, (2018)
"Accelerating the DC algorithm for smooth functions", F.J. Aragón Artacho, R.M.T. Fleming, P.T. Vuong, Mathematical programming 169 (1), 95-118, (2018)
"Recon3D enables a three-dimensional view of gene variation in human metabolism", Brunk, E., Sahoo, S., Zielinski, D., Altunkaya, A., Draeger, A., Mih, N., Gatto, F., Nilsson, A., Preciat, G., Aurich, M.K., Prlic, A., Sastry, A., Danielsdottir, A.D., Heinken, A., Noronha, A., Rose, P.W., Burley, S.K., Fleming, R.M.T., Nielsen, J., Thiele, I., Palsson, B.O., Nature Biotechnology, 36(3), 272-281 (2018).
2017
"A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines", Aurich, M K., Fleming, R.M.T., Thiele, I., PLoS Computational Biology, 13(8):e1005698 (2017).
"Quantitative systems pharmacology and the personalized drug-microbiota-diet axis", Thiele, I., Clancy, C.M., Heinken, A., Fleming, R.M.T., Current Opinion in Systems Biology, 4: 43-52 (2017).
"Comparative evaluation of atom mapping algorithms for metabolic reactions: application to Recon 3D", Preciat-Gonzalez, G.A., El Assal, L., Noronha, A., Thiele, I., Haraldsdottir, H.S., Fleming, R.M.T., Journal of Cheminformatics, 9:39 (2017).
"Reliable and efficient solution of genome-scale models of metabolism and macromolecular expression", Ma, D., Yang, L., Fleming, R.M.T., Thiele, I., Palsson, B.O.P., Saunders, M. A., Scientific Reports, 7:40863 (2017).
"Embryonic development of selectively vulnerable neurons in Parkinson’s disease", M.A.P. Oliveira, R. Balling, M.P. Smidt, R.M.T. Fleming, npj Parkinson"s Disease 3 (1), 1-13, (2017)
"Derivation of human midbrain-specific organoids from neuroepithelial stem cells", A.S. Monzel, L.M. Smits, K. Hemmer, S. Hachi, E.L. Moreno, T. van Wuellen, et. al., Stem cell reports 8 (5), 1144-1154, (2017)
"CHRR: Coordinate hit-and-run with rounding for uniform sampling of constraint-based models", Haraldsdottir, H.S., Cousins, B., Thiele, I., Fleming, R.M.T., Vempala, S., Bioinformatics, 33(11):1741-1743 (2017).
"DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia", Heirendt, L., Thiele, I., Fleming, R.M.T., Bioinformatics, 33(9):1421-1423 (2017).
"Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota", Magnusdottir, S., Heinken, A., Kutt, L., Ravcheev, D.A., Bauer, E., Noronha, A., Greenhalgh, K., Jaeger, C., Baginska, J., Wilmes, P., Fleming, R.M.T., Thiele, I., Nature Biotechnology, 35(1):81-89 (2017).
2016
"ReconMap: an interactive visualization of human metabolism", Noronha, A., Danielsdottir, A.D., Gawron, P., Johannsson, F., Jonsdottir, S., Jarlsson, S., Gunnarsson, J.P., Brynjolfsson, S., Schneider, R., Thiele, I., Fleming, R.M.T., Bioinformatics, 33(4):605-607 (2016).
"MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models", Aurich, M.K., Fleming, R.M.T., Thiele, I., Front Physiol, 7:327 (2016).
"Conditions for duality between fluxes and concentrations in biochemical networks", Fleming, R.M.T., Vlassis, N., Thiele, I., Saunders, M.A., Journal of Theoretical Biology, pii: S0022-5193(16)30167-9 (2016).
"Identification of conserved moieties in metabolic networks by graph theoretical analysis of atom transition networks", H.S. Haraldsdóttir, R.M.T. Fleming, PLOS Computational Biology 12 (11), e1004999, (2016)
2015
"Do genome-scale models need exact solvers or clearer standards?", Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A.P., Chang, R.L., Dräger, A., Famili, I., Feist, A.M., Fleming, R.M.T., Fong, S.S., Hatzimanikatis, V., Herrgård, M.J., Holder, A., Hucka, M., Hyduke, D., Jamshidi, N., Lee, S.Y.,Le Novère, N., Lerman, J.A., Lewis, N.E., Ma, D., Mahadevan, R., Maranas, C., Nagarajan, H., Navid, A., Nielsen, J., Nielsen, L.K., Nogales, J., Noronha, A., Pal, C., Palsson, B.O., Papin, J.A., Patil, K.R., Price, N.D., Reed, J.L., Saunders, M., Senger, R.S., Sonnenschein, N., Sun, Y., Thiele, I., Molecular Systems Biology, 11 (10), 831 (2015).
"Globally convergent algorithms for finding zeros of duplomonotone mappings", FJ Aragón Artacho, RMT Fleming, Optimization Letters 9 (3), 569-584, 2015
"Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices", S Halldorsson, E Lucumi, R Gómez-Sjöberg, RMT Fleming, Biosensors and Bioelectronics 63, 218–231, 2015
"A constraint-based modelling approach to metabolic dysfunction in Parkinson"s disease" L Mao, A Nicolae, MAP Oliveira, F He, S Hachi, RMT Fleming Computational and structural biotechnology journal 13, 484-491, 2015
"Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture" EL Moreno, S Hachi, K Hemmer, SJ Trietsch, AS Baumuratov, T Hankemeier, P Vulto, JC Schwamborn, RMT Fleming, Lab on a Chip 15 (11), 2419-2428, 2015
"Modeling the effects of commonly used drugs on human metabolism", Sahoo, S., Haraldsdottir, H., Fleming, R.M.T., Thiele, I., FEBS Journal, 282 (2), 297-317 (2015).
"Prediction of intracellular metabolic states from extracellular metabolomic data", Aurich, M.K., Paglia, G., Rolfsson, O., Hrafnsdottir, S., Magnusdottir, M., Stefaniak, M.K., Palsson, B.O., Fleming, R.M.T., Thiele, I., Metabolomics, 11 (3), 603-619 (2015).
2014
"FASTGAPFILL: Efficient gap filling in metabolic networks", Thiele, I. , Vlassis, N., Fleming, R.M.T, Bioinformatics, 30(17):2529-31 (2014).
"Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2", Haraldsdottir, H.S., Thiele, I., Fleming, R.M.T., Journal of Cheminformatics, 6(2) (2014).
2013
"Robust flux balance analysis of multiscale biochemical reaction networks", Sun, Y., Fleming, R.M.T., Thiele, I., Saunders, M.A., BMC Bioinformatics, 14:420 (2013).
"Real-time optical pH measurement in a standard microfluidic cell culture system", EB Magnusson, S Halldorsson, RMT Fleming, K Leosson, Biomedical Optics Express 4 (9), 1749-1758, 2013
"Consistent estimation of Gibbs energy using component contributions", E Noor, HS Haraldsdóttir, R Milo, RMT Fleming, PLoS computational biology 9 (7), e1003098, 2013
"A community-driven global reconstruction of human metabolism", Thiele, I., Swainston, N., Fleming, R.M.T., Hoppe, A., Sahoo, S., Aurich, M.K., Haraldsdottir, H., Mo, M.L., Rolfsson, O., Stobbe, M.D., Thorleifsson, S.G., Agren, R., Boelling, C., Bordel, S., Chavali, A.K., Dobson, P., Dunn, W.B., Endler, L., Hala, D., Hucka, M., Hull, D., Jameson, D., Jamshidi, N., Jonsson, J.J., Juty, N., Keating, S., Nookaew, I., Le Novere, N., Malys, N., Mazein, A., Papin, J.A., Price, N.D., Selkov Sr., E, Sigurdsson, M.I., Simeonidis, E., Sonnenschein, N., Smallbone, K., Sorokin, A., van Beek, J.H.G.M., Weichart, D., Goryanin, I., Nielsen, J., Westerhoff, H.V., Kell, D.B., Mendes, P., Palsson, B.O., Nature Biotechnology, 31(5):419-25 (2013).
"Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut.", Heinken, A., Sahoo, S., Fleming, R.M.T., Thiele, I., Gut Microbes, 4(1):1-13 (2013).
"A systems biology approach to studying the role of microbes in human health", Thiele, I., Heinken, A., Fleming, R.M.T., Current Opinions in Biotechnology, 24(1):4-12 (2013).
2012
"Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage", Thiele, I., Fleming, R.M.T., Que, R., Bordbar, A., Diep, D., Palsson, B.O., PLoS One, 7(9):e45635 (2012).
"Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration", Fleming, R.M.T., Thiele, I., Journal of Theoretical Biology, 314:173-181 (2012).
"Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration", Fleming, R.M.T., Thiele, I., Journal of Theoretical Biology, 314:173-181 (2012).
"A systems biology approach to drug targets in Pseudomonas aeruginosa Biofilm", Sigurdsson, G., Fleming, R.M.T., Heinken, A., Thiele, I., PLoS One, 7(4): e34337 (2012).
"Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction: Recon 1", Haraldsdottir, H., Thiele, I., Fleming, R.M.T., Biophysical Journal, 102(8):1703-1711 (2012).
"A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks", RMT Fleming, CM Maes, MA Saunders, Y Ye, BØ Palsson, Journal of theoretical biology 292, 71-77, 2012
"Monitoring metabolites consumption and secretion in cultured cells using Ultra Performance Liquid Chromatography Quadrupole-Time of Flight Mass Spectrometry (UPLC-Q-ToF-MS)", Paglia, G., Hrafnsdottir, S., Magnusdottir, M., Fleming, R.M.T., Thorlacius, S., Palsson, B.O., Thiele, I., Anal Bioanal Chem, 402(3):1183-98 (2012).
2011
"Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.", Schellenberger, J., Que, R., Fleming, R.M.T., Thiele, I., Orth, J.D., Feist, A.M., Zielinski, D.C., Bordbar, A., Lewis, N.E.R., Kang, J., Hydruke, D., Palsson, B.O., Nature Protocols, 6, 1290-1307 (2011).
"A community effort towards a knowledge-base, mathematical model of the human pathogen Salmonella typhimurium LT2", Thiele, I., Hyduke, D.R., Steeb, B., Fankam, G., Allen, D.K., Bazzani, S., Charusanti, P., Chen, F.C., Fleming, R.M.T., Hsiung, C.A., De Keersmaecker, S.C., Liao, Y. C. , Marchal, K., Mo, M. L., Ozdemir, E., Raghunathan, A., Reed, J.L., Shin, S.I., Sigurbjornsdottir, S., Steinmann, J., Sudarsan, S., Swainston, N., Thijs, I.M., Zengler, K., Palsson, B.O., Adkins, J.N., , D., BMC Systems Biology, 5:8 (2011). Bumann
"von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models", Fleming, R.M.T., Thiele, I., Bioinformatics, 27(1):142-3 (2011).
2010
"Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism ", Fleming, R.M.T, Thiele, I., Provan, G., Nasheuer, H.P., Journal of Theoretical Biology, 264 (3): 683-692 (2010).
"Functional characterization of multiple equivalent states of Escherichia coli "s transcriptional and translational machinery.", Thiele, I., Fleming, M.T., Bordbar, A., Palsson, B.O., Biophysical Journal, 98(10): 2072-2081 (2010).
"A protocol for generating a high-quality genome-scale metabolic reconstruction.", Thiele, I. , Palsson, B.O., Nature Protocols, 5(1): 93 - 121 (2010).
"Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide", JD Orth, RMT Fleming, BØ Palsson, EcoSal plus 4 (1), 2010
"An annotated English translation of Kinetics of stationary reactions", [MI Temkin, Dolk. Akad. Nauk SSSR. 152, 156 (1963)] VV Levchenko, R Fleming, H Qian, DA Beard, arXiv preprint arXiv:1001.2861, 2010
2009
"Quantitative assignment of reaction directionality in constraint-based models of metabolism.", Fleming, R.M.T., Thiele, I., Nasheuer, H.P., Biophysical Chemistry, 145(2-3):47-56 (2009).
"Reconstruction and use of microbial metabolic networks: the core metabolic model as an Educational Guide" JD Orth, RMT Fleming, B Palsson, Bock A., editor. EcoSal–Escherichia coli and Salmonella: Cellular and …, 2009
"Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-base, its mathematical formulation, and its functional characterization.", Thiele, I., Jamshidi, N., Fleming, R.M.T., Palsson, B.O., PLoS Comput Biol, 5(3): e1000312 (2009).
