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Items: 1 to 50 of 167


Reply to "Challenges in modeling the human gut microbiome".

Magnúsdóttir S, Heinken A, Fleming RMT, Thiele I.

Nat Biotechnol. 2018 Aug 6;36(8):686-691. doi: 10.1038/nbt.4212. No abstract available.


Semiquantification Limitations: FMTVDM©℗ Demonstrates Quantified Tumor Response to Treatment with Both Regional Blood Flow and Metabolic Changes.

Fleming RM, Fleming MR, McKusick A, Chaudhuri TK.

J Nucl Med. 2018 Oct;59(10):1643-1644. doi: 10.2967/jnumed.118.217018. Epub 2018 Jul 20. No abstract available.


FMTVDM-TFM©℗: True quantification requires standardization of the tool being used to measure, with a known, unchanging standard to produce accurate, consistent and reproducible quantified measurements.

Fleming RM, Fleming MR, McKusick A, Chaudhuri T.

J Nucl Cardiol. 2018 Jun 19. doi: 10.1007/s12350-018-1343-3. [Epub ahead of print] No abstract available.


Community-driven roadmap for integrated disease maps.

Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R.

Brief Bioinform. 2018 Apr 23. doi: 10.1093/bib/bby024. [Epub ahead of print]


Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO.

Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19.


Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

Preciat Gonzalez GA, El Assal LRP, Noronha A, Thiele I, Haraldsdóttir HS, Fleming RMT.

J Cheminform. 2017 Jun 14;9(1):39. doi: 10.1186/s13321-017-0223-1.


A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines.

Aurich MK, Fleming RMT, Thiele I.

PLoS Comput Biol. 2017 Aug 14;13(8):e1005698. doi: 10.1371/journal.pcbi.1005698. eCollection 2017 Aug.


Embryonic development of selectively vulnerable neurons in Parkinson's disease.

Oliveira MAP, Balling R, Smidt MP, Fleming RMT.

NPJ Parkinsons Dis. 2017 Jun 26;3:21. doi: 10.1038/s41531-017-0022-4. eCollection 2017. Review.


DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia.

Heirendt L, Thiele I, Fleming RMT.

Bioinformatics. 2017 May 1;33(9):1421-1423. doi: 10.1093/bioinformatics/btw838.


Derivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells.

Monzel AS, Smits LM, Hemmer K, Hachi S, Moreno EL, van Wuellen T, Jarazo J, Walter J, Brüggemann I, Boussaad I, Berger E, Fleming RMT, Bolognin S, Schwamborn JC.

Stem Cell Reports. 2017 May 9;8(5):1144-1154. doi: 10.1016/j.stemcr.2017.03.010. Epub 2017 Apr 13.


CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.

Haraldsdóttir HS, Cousins B, Thiele I, Fleming RMT, Vempala S.

Bioinformatics. 2017 Jun 1;33(11):1741-1743. doi: 10.1093/bioinformatics/btx052.


Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression.

Ma D, Yang L, Fleming RM, Thiele I, Palsson BO, Saunders MA.

Sci Rep. 2017 Jan 18;7:40863. doi: 10.1038/srep40863.


ReconMap: an interactive visualization of human metabolism.

Noronha A, Daníelsdóttir AD, Gawron P, Jóhannsson F, Jónsdóttir S, Jarlsson S, Gunnarsson JP, Brynjólfsson S, Schneider R, Thiele I, Fleming RM.

Bioinformatics. 2017 Feb 15;33(4):605-607. doi: 10.1093/bioinformatics/btw667.


Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RM, Thiele I.

Nat Biotechnol. 2017 Jan;35(1):81-89. doi: 10.1038/nbt.3703. Epub 2016 Nov 28.


Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks.

Haraldsdóttir HS, Fleming RM.

PLoS Comput Biol. 2016 Nov 21;12(11):e1004999. doi: 10.1371/journal.pcbi.1004999. eCollection 2016 Nov.


MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models.

Aurich MK, Fleming RM, Thiele I.

Front Physiol. 2016 Aug 3;7:327. doi: 10.3389/fphys.2016.00327. eCollection 2016.


Conditions for duality between fluxes and concentrations in biochemical networks.

Fleming RMT, Vlassis N, Thiele I, Saunders MA.

J Theor Biol. 2016 Nov 21;409:1-10. doi: 10.1016/j.jtbi.2016.06.033. Epub 2016 Jun 23.


A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease.

Mao L, Nicolae A, Oliveira MA, He F, Hachi S, Fleming RM.

Comput Struct Biotechnol J. 2015 Sep 2;13:484-91. doi: 10.1016/j.csbj.2015.08.002. eCollection 2015. Review.


Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


Prediction of intracellular metabolic states from extracellular metabolomic data.

Aurich MK, Paglia G, Rolfsson Ó, Hrafnsdóttir S, Magnúsdóttir M, Stefaniak MM, Palsson BØ, Fleming RM, Thiele I.

Metabolomics. 2015;11(3):603-619. Epub 2014 Aug 14.


Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture.

Moreno EL, Hachi S, Hemmer K, Trietsch SJ, Baumuratov AS, Hankemeier T, Vulto P, Schwamborn JC, Fleming RM.

Lab Chip. 2015 Jun 7;15(11):2419-28. doi: 10.1039/c5lc00180c.


Long-term quality of life and risk factors for recurrence after laparoscopic repair of paraesophageal hernia.

Lidor AO, Steele KE, Stem M, Fleming RM, Schweitzer MA, Marohn MR.

JAMA Surg. 2015 May;150(5):424-31. doi: 10.1001/jamasurg.2015.25.


Modeling the effects of commonly used drugs on human metabolism.

Sahoo S, Haraldsdóttir HS, Fleming RM, Thiele I.

FEBS J. 2015 Jan;282(2):297-317. doi: 10.1111/febs.13128. Epub 2014 Nov 21.


Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices.

Halldorsson S, Lucumi E, Gómez-Sjöberg R, Fleming RMT.

Biosens Bioelectron. 2015 Jan 15;63:218-231. doi: 10.1016/j.bios.2014.07.029. Epub 2014 Jul 19. Review.


fastGapFill: efficient gap filling in metabolic networks.

Thiele I, Vlassis N, Fleming RM.

Bioinformatics. 2014 Sep 1;30(17):2529-31. doi: 10.1093/bioinformatics/btu321. Epub 2014 May 7.


Real-time optical pH measurement in a standard microfluidic cell culture system.

Magnusson EB, Halldorsson S, Fleming RM, Leosson K.

Biomed Opt Express. 2013 Aug 27;4(9):1749-58. doi: 10.1364/BOE.4.001749. eCollection 2013.


Robust flux balance analysis of multiscale biochemical reaction networks.

Sun Y, Fleming RM, Thiele I, Saunders MA.

BMC Bioinformatics. 2013 Jul 30;14:240. doi: 10.1186/1471-2105-14-240.


Consistent estimation of Gibbs energy using component contributions.

Noor E, Haraldsdóttir HS, Milo R, Fleming RM.

PLoS Comput Biol. 2013;9(7):e1003098. doi: 10.1371/journal.pcbi.1003098. Epub 2013 Jul 11.


Defining recurrence after paraesophageal hernia repair: correlating symptoms and radiographic findings.

Lidor AO, Kawaji Q, Stem M, Fleming RM, Schweitzer MA, Steele KE, Marohn MR.

Surgery. 2013 Aug;154(2):171-8. doi: 10.1016/j.surg.2013.03.015. Epub 2013 Jun 15.


A community-driven global reconstruction of human metabolism.

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ.

Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3.


A systems biology approach to studying the role of microbes in human health.

Thiele I, Heinken A, Fleming RM.

Curr Opin Biotechnol. 2013 Feb;24(1):4-12. doi: 10.1016/j.copbio.2012.10.001. Epub 2012 Oct 25. Review.


Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.

Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson BO.

PLoS One. 2012;7(9):e45635. doi: 10.1371/journal.pone.0045635. Epub 2012 Sep 28.


Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut.

Heinken A, Sahoo S, Fleming RM, Thiele I.

Gut Microbes. 2013 Jan-Feb;4(1):28-40. doi: 10.4161/gmic.22370. Epub 2012 Sep 28.


Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration.

Fleming RM, Thiele I.

J Theor Biol. 2012 Dec 7;314:173-81. doi: 10.1016/j.jtbi.2012.08.021. Epub 2012 Aug 28.


Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

Haraldsdóttir HS, Thiele I, Fleming RM.

Biophys J. 2012 Apr 18;102(8):1703-11. doi: 10.1016/j.bpj.2012.02.032.


A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm.

Sigurdsson G, Fleming RM, Heinken A, Thiele I.

PLoS One. 2012;7(4):e34337. doi: 10.1371/journal.pone.0034337. Epub 2012 Apr 16.


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, Hrafnsdóttir S, Magnúsdóttir M, Fleming RM, Thorlacius S, Palsson BØ, Thiele I.

Anal Bioanal Chem. 2012 Jan;402(3):1183-98. doi: 10.1007/s00216-011-5556-4. Epub 2011 Dec 13.


A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.

Fleming RM, Maes CM, Saunders MA, Ye Y, Palsson BØ.

J Theor Biol. 2012 Jan 7;292:71-7. doi: 10.1016/j.jtbi.2011.09.029. Epub 2011 Oct 5.


Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ.

Nat Protoc. 2011 Aug 4;6(9):1290-307. doi: 10.1038/nprot.2011.308.


A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D.

BMC Syst Biol. 2011 Jan 18;5:8. doi: 10.1186/1752-0509-5-8.


von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.

Fleming RM, Thiele I.

Bioinformatics. 2011 Jan 1;27(1):142-3. doi: 10.1093/bioinformatics/btq607. Epub 2010 Nov 28.


Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide.

Orth JD, Fleming RM, Palsson BØ.

EcoSal Plus. 2010 Sep;4(1). doi: 10.1128/ecosalplus.10.2.1.


Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.

Thiele I, Fleming RM, Bordbar A, Schellenberger J, Palsson BØ.

Biophys J. 2010 May 19;98(10):2072-81. doi: 10.1016/j.bpj.2010.01.060.


Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.

Fleming RM, Thiele I, Provan G, Nasheuer HP.

J Theor Biol. 2010 Jun 7;264(3):683-92. doi: 10.1016/j.jtbi.2010.02.044. Epub 2010 Mar 15.


Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli.

Fleming RM, Thiele I, Nasheuer HP.

Biophys Chem. 2009 Dec;145(2-3):47-56. doi: 10.1016/j.bpc.2009.08.007. Epub 2009 Sep 1.


Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.

Thiele I, Jamshidi N, Fleming RM, Palsson BØ.

PLoS Comput Biol. 2009 Mar;5(3):e1000312. doi: 10.1371/journal.pcbi.1000312. Epub 2009 Mar 13.


Safety of ephedra and related anorexic medications.

Fleming RM.

Expert Opin Drug Saf. 2008 Nov;7(6):749-59. doi: 10.1517/14740330802510915 . Review.


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