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Ronan M. T. Fleming

Ronan M. T. Fleming

D-Index & Metrics

Computer Science

D-Index
40
Citations
12679
World Ranking
9062
National Ranking
157

Overview

Ronan M. T. Fleming is affiliated with Leiden University in the Netherlands. Their research focuses primarily on the field of Biochemistry, Genetics, and Molecular Biology, with a strong emphasis on Molecular Biology as a subfield. Additional subfields include Neurology, Physiology, Biomedical Engineering, and Biological Psychiatry.

The scientist's work encompasses various specialized topics such as:

  • Microbial Metabolic Engineering and Bioproduction
  • Metabolomics and Mass Spectrometry Studies
  • Bioinformatics and Genomic Networks
  • Gut microbiota and health
  • Parkinson's Disease Mechanisms and Treatments
  • Gene Regulatory Network Analysis
  • Tryptophan and brain disorders

Among their recent papers are the following publications:

  • MEMOTE for standardized genome-scale metabolic model testing, 2020, Nature Biotechnology
  • SBML Level 3: an extensible format for the exchange and reuse of biological models, 2020, Molecular Systems Biology
  • Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine, 2023, Nature Biotechnology
  • Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions, 2020, BMC Biology
  • Personalized whole-body models integrate metabolism, physiology, and the gut microbiome, 2020, Molecular Systems Biology

Frequent co-authors collaborating with Fleming include:

  • Ines Thiele (18 papers)
  • Thomas Hankemeier (10 papers)
  • German Preciat (8 papers)
  • Amy C. Harms (8 papers)
  • Almut Heinken (7 papers)

Fleming's work has been published extensively across several venues. The most frequent publication outlets include:

  • bioRxiv (Cold Spring Harbor Laboratory) with 11 publications
  • Nature Biotechnology with 3 publications
  • Bioinformatics with 3 publications
  • Molecular Systems Biology with 2 publications
  • arXiv (Cornell University) with 2 publications

Best Publications

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

    Jan Schellenberger;Richard Que;Ronan M T Fleming;Ines Thiele

  • Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

    Laurent Heirendt;Sylvain Arreckx;Thomas Pfau;Sebastián N. Mendoza

  • A community-driven global reconstruction of human metabolism

    Ines Thiele;Neil Swainston;Ronan M T Fleming;Andreas Hoppe

  • Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices.

    Skarphedinn Halldorsson;Edinson Lucumi;Rafael Gómez-Sjöberg;Ronan M.T. Fleming

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

    Stefania Magnusdottir;Almut Katrin Heinken;Laura Kutt;Dmitry Ravcheev

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

    Elizabeth Brunk;Elizabeth Brunk;Swagatika Sahoo;Daniel C. Zielinski;Ali Altunkaya;Ali Altunkaya

  • MEMOTE for standardized genome-scale metabolic model testing

    Christian Lieven;Moritz Emanuel Beber;Brett G. Olivier;Frank T. Bergmann

  • The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.

    Alberto Noronha;Jennifer Modamio;Yohan Jarosz;Elisabeth Guerard

  • Consistent estimation of Gibbs energy using component contributions

    Elad Noor;Hulda S. Haraldsdóttir;Ron Milo;Ronan M. T. Fleming

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

    Jeffrey D. Orth;R. M. T. Fleming;Bernhard Ø. Palsson

  • Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.

    Almut Katrin Heinken;Dmitry Ravcheev;Federico Baldini;Laurent Heirendt

  • SBML Level 3: an extensible format for the exchange and reuse of biological models

    Sarah M. Keating;Sarah M. Keating;Dagmar Waltemath;Matthias König;Fengkai Zhang

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

    Ines Thiele;Neema Jamshidi;Ronan M. T. Fleming;Bernhard Ø. Palsson

  • Personalized whole-body models integrate metabolism, physiology, and the gut microbiome.

    Ines Thiele;Swagatika Sahoo;Almut Heinken;Johannes Hertel;Johannes Hertel

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

    Ines Thiele;Daniel R Hyduke;Benjamin Steeb;Guy Fankam

  • Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease

    Johannes Hertel;Johannes Hertel;Johannes Hertel;Amy C. Harms;Almut Heinken;Almut Heinken;Federico Baldini

  • The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

    Federico Baldini;Almut Katrin Heinken;Laurent Heirendt;Stefania Magnusdottir

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

    Ines Thiele;Ines Thiele;Ronan M. T. Fleming;Richard Que;Aarash Bordbar

  • fastGapFill: efficient gap filling in metabolic networks

    Ines Thiele;Nikos Vlassis;Ronan M. T. Fleming

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

    Ines Thiele;Almut Katrin Heinken;Ronan Mt Fleming

  • Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0.

    Laurent Heirendt;Sylvain Arreckx;Thomas Pfau;Sebastián N. Mendoza

Frequent Co-Authors

Ines Thiele
Ines Thiele University of Galway
Bernhard O. Palsson
Bernhard O. Palsson University of California, San Diego
Michael A. Saunders
Michael A. Saunders Stanford University
Jens Nielsen
Jens Nielsen Chalmers University of Technology
Nathan E. Lewis
Nathan E. Lewis University of California, San Diego
Adam M. Feist
Adam M. Feist University of California, San Diego
Sang Yup Lee
Sang Yup Lee Korea Advanced Institute of Science and Technology
Intawat Nookaew
Intawat Nookaew University of Arkansas for Medical Sciences
Lars K. Nielsen
Lars K. Nielsen University of Queensland
Andrei Zinovyev
Andrei Zinovyev Institute Curie

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