Publications

2017

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See detailA systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines
Aurich, Maike Kathrin; Thiele, Ines; Fleming, Ronan MT

in PLoS Computational Biology (2017)

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See detailCHRR: Coordi- nate hit-and-run with rounding for uniform sampling of constraint-based models
Haraldsdottir, Hulda; Cousin, B; Thiele, Ines; Fleming, Ronan MT; Vempala, S

in Bioinformatics (2017)

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See detailDistributedFBA.jl: High-level, high-performance flux balance analysis in Julia.
Heirendt, Laurent; Thiele, Ines; Fleming, Ronan MT

in Bioinformatics (2017)

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See detailReliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Ma, Ding; Yang, Laurence; Fleming, Ronan MT; Thiele, Ines; Palsson, Bernhard; Saunders, Michael

in Scientific Reports (2017)

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See detailDerivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells
Monzel, Anna Sophia; Smits, Lisa; Hemmer, Kathrin; Hachi, Siham; Lucumi Moreno, Edinson; Van Wüllen, Thea Maria; Jarazo, Javier; Walter, Jonas; Werthschulte, Inga; Boussaad, Ibrahim; Berger, Emanuel; Fleming, Ronan MT; Bolognin, Silvia; Schwamborn, Jens Christian

in Stem Cell Reports (2017)

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See detailEmbryonic development of selectively vulnerable neurons in Parkinson’s disease
Oliveira, Miguel; Balling, Rudi; Smidt, Marten; Fleming, Ronan MT

in NPJ Parkinson's Disease (2017), 3

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See detailComparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
Preciat Gonzalez, German Andres; El Assal, Lemmer; Noronha, Alberto; Thiele, Ines; Haraldsdottir, Hulda; Fleming, Ronan MT

in Journal of Cheminformatics (2017)

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See detailQuantitative systems pharmacology and the personalized drug–microbiota–diet axis
Thiele, Ines; Clancy, Catherine; Heinken, Almut Katrin; Fleming, Ronan MT

in Current Opinion in Systems Biology (2017), 4

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2016

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See detailMetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models
Aurich, Maike Kathrin; Fleming, Ronan MT; Thiele, Ines

in Frontiers in Physiology (2016)

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See detailConditions for duality between fluxes and concentrations in biochemical networks
Fleming, Ronan MT; Vlassis, Nikos; Thiele, Ines; Saunders, Michael

in Journal of Theoretical Biology (2016), 409(21), 1-10

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See detailGeneration of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Magnusdottir, Stefania; Heinken, Almut Katrin; Kutt, Laura; Ravcheev, Dmitry; Bauer, Eugen; Noronha, Alberto; Greenhalgh, Kacy; Jäger, Christian; Baginska, Joanna; Wilmes, Paul; Fleming, Ronan MT; Thiele, Ines

in Nature Biotechnology (2016)

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See detailReconMap: An interactive visualisation of human metabolism
Noronha, Alberto; Danielsdóttir, Anna Dröfn; Jóhannsson, Freyr; Jónsdóttir, Soffia; Jarlsson, Sindri; Gunnarsson, Jón Pétur; Brynjólfsson, Sigurður; Gawron, Piotr; Schneider, Reinhard; Thiele, Ines; Fleming, Ronan MT

in Bioinformatics (2016)

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2015

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See detailGlobally convergent algorithms for finding zeros of duplomonotone mappings
Aragón Artacho, Francisco Javier; Fleming, Ronan MT

in Optimization Letters (2015), 3(3), 569584

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See detailAccelerating the DC algorithm for smooth functions
Aragón Artacho, Francisco Javier; Fleming, Ronan MT; Phan, Vuong

E-print/Working paper (2015)

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See detailPrediction of intracellular metabolic states from extracellular metabolomic data
Aurich, Maike Kathrin; Paglia, Guiseppe; Rolfsson, Ottar; Hrafnsdottir, Sigrun; Magnusdottir, Manuela; Stefaniak, Madgalena K.; Palsson, Bernhard O.; Fleming, Ronan MT; Thiele, Ines

in Metabolomics : Official journal of the Metabolomic Society (2015), 11(3), 603-619

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See detailDo Genome-scale Models Need Exact Solvers or Clearer Standards?
Ebrahim, Ali; Almaas, Eivind; Bauer, Eugen; Bordbar, Aarash; Burgard, Anthony P.; Chang, Roger L.; Dräger, Andreas; Famili, Iman; Feist, Adam M.; Fleming, Ronan MT; Fong, Stephen S.; Hatzimanikatis, Vassily; Herrgård, Markus J.; Holder, Allen; Hucka, Michael; Hyduke, Daniel; Jamshidi, Neema; Lee, Sang Yup; Le Novère, Nicolas; Lerman, Joshua A.; Lewis, Nathan E.; Ma, Ding; Mahadevan, Radhakrishnan; Maranas, Costas; Nagarajan, Harish; Navid, Ali; Nielsen, Jens; Nielsen, Lars K.; Nogales, Juan; Noronha, Alberto; Pal, Csaba; Palsson, Bernhard O.; Papin, Jason A.; Patil, Kiran R.; Price, Nathan D.; Reed, Jennifer L.; Saunders, Michael; Senger, Ryan S.; Sonnenschein, Nikolaus; Sun, Yuekai; Thiele, Ines

in Molecular Systems Biology (2015), 11(10), 1

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See detailAdvantages and challenges of microfluidic cell culture in polydimethylsiloxane devices
Halldórsson, Skarphédinn; Lucumi Moreno, Edinson; Gómez-Sjöberg, Rafael; Fleming, Ronan MT

in Biosensors and Bioelectronics (2015), 63

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See detailDifferentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture
Lucumi Moreno, Edinson; Hachi, Siham; Hemmer, Kathrin; Trietsch, Sebastian; Baumuratov, Aidos; Hankemeier, Thomas; Vulto, Paul; Schwamborn, Jens Christian; Fleming, Ronan MT

in Lab on a Chip - Miniaturisation for Chemistry & Biology (2015), 15

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See detailA constraint-based modelling approach to metabolic dysfunction in Parkinson's disease
Mao, Longfei; Nicolae, Averina; Oliveira, Miguel; He, Feng; Hachi, Siham; Fleming, Ronan MT

in Computational and Structural Biotechnology Journal (2015), 13

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2014

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See detailModeling the effects of commonly used drugs on human metabolism
Sahoo, Swagatika; Haraldsdottir, Hulda; Fleming, Ronan MT; Thiele, Ines

in FEBS Journal (2014)

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See detailFASTGAPFILL: Efficient gap filling in metabolic networks
Thiele, Ines; Vlassis, Nikos; Fleming, Ronan MT

in Bioinformatics (2014), 30(17), 2529-2531

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2013

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See detailExistence of Positive Steady States for Mass Conserving and Mass-Action Chemical Reaction Networks with a Single Terminal-Linkage Class
Fleming, Ronan MT; Akle, Santiago; Dalal, Onkar; Saunders, Michael; Taheri, Nicole; Ye, Yinyu

in arXiv preprint arXiv:1105.2359 (2013)

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See detailSystems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut.
Heinken, Almut Katrin; Sahoo, Swagatika; Fleming, Ronan MT; Thiele, Ines

in Gut microbes (2013), 4(1), 28-40

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See detailReal-time optical pH measurement in a standard microfluidic cell culture system
Magnusson, E. B.; Halldorsson, S.; Fleming, Ronan MT; Leosson, K.

in Biomedical Optics Express (2013), 4(9), 1749-1758

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See detailConsistent Estimation of Gibbs Energy Using Component Contributions
Noor, Elad; Haraldsdottir, Hulda; Milo, Ron; Fleming, Ronan MT

in PLoS Computational Biology (2013), 9(7), 1003098

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See detailRobust flux balance analysis of multi- scale biochemical reaction networks
Sun, Y; Fleming, Ronan MT; Thiele, Ines; Saunders, MA

in BMC Bioinformatics (2013), 1(14), 240

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See detailA systems biology approach to studying the role of microbes in human health.
Thiele, Ines; Heinken, Almut Katrin; Fleming, Ronan MT

in Current Opinion in Biotechnology (2013), 24(1), 4-12

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See detailA community-driven global reconstruction of human metabolism.
Thiele, Ines; Swainston, N.; Fleming, Ronan MT; Hoppe, A.; Sahoo, Swagatika; Aurich, Maike Kathrin; Haraldsdottir, Hulda; Mo, M. L.; Rolfsson, O.; Stobbe, M. D.; Thorleifsson, S. G.; Agren, R.; Bölling, 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 Novère, N.; Malys, N.; Mazein, A.; Papin, J. A.; Price, N. D.; Selkov, E. Sr; Sigurdsson, M. I.; Simeonidis, Evangelos; Sonnenschein, N.; Smallbone, K.; Sorokin, A.; van Beek, J. H.; Weichart, D.; Goryanin, I.; Nielsen, J.; Westerhoff, H. V.; Kell, D. B.; Mendes, P.; Palsson, B. O.

in Nature Biotechnology (2013), 31

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2012

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See detailA variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks
Fleming, Ronan MT; Maes, C. M.; Saunders, M. A.; Ye, Y.; Palsson, B. O.

in Journal of Theoretical Biology (2012), 292

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See detailMultiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.
Thiele, Ines; Fleming, Ronan MT; Que, Richard; Bordbar, Aarash; Diep, Dinh; Palsson, Bernhard O.

in PLoS ONE (2012), 7(9), 45635

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2010

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See detailIdentification of novel inhibitors of dietary lipid absorption using zebrafish.
Clifton, Justin D.; Lucumi Moreno, Edinson; Myers, Michael C.; Napper, Andrew; Hama, Kotaro; Farber, Steven A.; Smith, Amos B. Rd; Huryn, Donna M.; Diamond, Scott L.; Pack, Michael

in PloS one (2010), 5(8), 12386

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See detailDiscovery of potent small-molecule inhibitors of multidrug-resistant Plasmodium falciparum using a novel miniaturized high-throughput luciferase-based assay.
Lucumi Moreno, Edinson; Darling, Claire; Jo, Hyunil; Napper, Andrew D.; Chandramohanadas, Rajesh; Fisher, Nicholas; Shone, Alison E.; Jing, Huiyan; Ward, Stephen A.; Biagini, Giancarlo A.; DeGrado, William F.; Diamond, Scott L.; Greenbaum, Doron C.

in Antimicrobial agents and chemotherapy (2010), 54(9), 3597-604

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2007

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See detailMixing two differently labeled substrates in one immobilized metal assay for phosphochemicals assay to improve data quality.
Jezequel-Sur, Sylvie; Murray, Justin; Lucumi Moreno, Edinson; Ferrer, Marc; Zuck, Paul

in Analytical biochemistry (2007), 360(2), 312-4

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See detailDiscovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening.
Nicola, George; Smith, Colin A.; Lucumi Moreno, Edinson; Kuo, Mack R.; Karagyozov, Luchezar; Fidock, David A.; Sacchettini, James C.; Abagyan, Ruben

in Biochemical and biophysical research communications (2007), 358(3), 686-91

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2006

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See detailSynthesis and biological activity of diaryl ether inhibitors of malarial enoyl acyl carrier protein reductase. Part 2: 2'-substituted triclosan derivatives.
Freundlich, Joel S.; Yu, Min; Lucumi Moreno, Edinson; Kuo, Mack; Tsai, Han-Chun; Valderramos, Juan-Carlos; Karagyozov, Luchezar; Jacobs, William R. Jr; Schiehser, Guy A.; Fidock, David A.; Jacobus, David P.; Sacchettini, James C.

in Bioorganic & Medicinal Chemistry Letters (2006), 16(8), 2163-9

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2005

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See detailSynthesis, biological activity, and X-ray crystal structural analysis of diaryl ether inhibitors of malarial enoyl acyl carrier protein reductase. Part 1: 4'-substituted triclosan derivatives.
Freundlich, Joel S.; Anderson, John W.; Sarantakis, Dimitri; Shieh, Hong-Ming; Yu, Min; Valderramos, Juan-Carlos; Lucumi Moreno, Edinson; Kuo, Mack; Jacobs, William R. Jr; Fidock, David A.; Schiehser, Guy A.; Jacobus, David P.; Sacchettini, James C.

in Bioorganic & Medicinal Chemistry Letters (2005), 15(23), 5247-52

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