Ronan M. T. Fleming

14.4k total citations · 4 hit papers
71 papers, 6.2k citations indexed

About

Ronan M. T. Fleming is a scholar working on Molecular Biology, Biomedical Engineering and Cellular and Molecular Neuroscience. According to data from OpenAlex, Ronan M. T. Fleming has authored 71 papers receiving a total of 6.2k indexed citations (citations by other indexed papers that have themselves been cited), including 60 papers in Molecular Biology, 16 papers in Biomedical Engineering and 6 papers in Cellular and Molecular Neuroscience. Recurrent topics in Ronan M. T. Fleming's work include Microbial Metabolic Engineering and Bioproduction (44 papers), Gene Regulatory Network Analysis (19 papers) and Bioinformatics and Genomic Networks (14 papers). Ronan M. T. Fleming is often cited by papers focused on Microbial Metabolic Engineering and Bioproduction (44 papers), Gene Regulatory Network Analysis (19 papers) and Bioinformatics and Genomic Networks (14 papers). Ronan M. T. Fleming collaborates with scholars based in Luxembourg, Netherlands and Iceland. Ronan M. T. Fleming's co-authors include Ines Thiele, Bernhard Ø. Palsson, Almut Heinken, Skarphéðinn Halldórsson, Rafael Gómez-Sjöberg, Edinson Lucumi, Jeffrey D. Orth, Allyn C. Howlett, Aarash Bordbar and Richard Que and has published in prestigious journals such as Nature Biotechnology, Bioinformatics and PLoS ONE.

In The Last Decade

Ronan M. T. Fleming

68 papers receiving 6.1k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

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

2011 1.3k citations Richard Que, Ronan M. T. Fleming et al. Nature Protocols profile →
Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices

2014 769 citations Skarphéðinn Halldórsson, Edinson Lucumi et al. Biosensors and Bioelectronics profile →
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

2016 522 citations Stefanía Magnúsdóttir, Almut Heinken et al. Nature Biotechnology profile →
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

2023 140 citations Almut Heinken, Johannes Hertel et al. Nature Biotechnology profile →

Peers

Countries citing papers authored by Ronan M. T. Fleming

Since Specialization

Citations

This map shows the geographic impact of Ronan M. T. Fleming's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Ronan M. T. Fleming with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Ronan M. T. Fleming more than expected).

Fields of papers citing papers by Ronan M. T. Fleming

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Ronan M. T. Fleming. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Ronan M. T. Fleming. The network helps show where Ronan M. T. Fleming may publish in the future.

Co-authorship network of co-authors of Ronan M. T. Fleming

This figure shows the co-authorship network connecting the top 25 collaborators of Ronan M. T. Fleming. A scholar is included among the top collaborators of Ronan M. T. Fleming based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Ronan M. T. Fleming. Ronan M. T. Fleming is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

#	Work	Indexed citations
1	KinForm: Kinetics Informed Feature Optimised Representation Models for Enzyme $k_{cat}$ and $K_{M}$ Prediction 2025 ·ArXiv.org ·(unknown), Ronan M. T. Fleming	0
2	mzQuality: An Open-Source Software Tool for Quality Monitoring and Reporting of Targeted Mass Spectrometry Measurements 2025 ·Journal of the American Society for Mass Spectrometry ·(unknown), (unknown), (unknown), Lieke Lamont, Ronan M. T. Fleming, Constance Bordes, Stéphanie Debette, Amy C. Harms, Thomas Hankemeier, Alida Kindt	1
3	XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models 2025 ·Nature Protocols ·German Preciat, (unknown), (unknown), Ines Thiele, Thomas Hankemeier, Ronan M. T. Fleming	0
4	Integration of proteomic data with genome‐scale metabolic models: A methodological overview 2024 ·Protein Science ·(unknown), Ronan M. T. Fleming	3
5	Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine breakdown → 2023 ·Nature Biotechnology ·Almut Heinken, Johannes Hertel, (unknown), Dmitry A. Ravcheev, (unknown), (unknown), (unknown), Stefanía Magnúsdóttir, Filippo Martinelli Boneschi, (unknown), German Preciat, Janaka N. Edirisinghe, Christopher S. Henry, Ronan M. T. Fleming, Ines Thiele	140
6	Local convergence of the Levenberg-Marquardt method under Hölder metric subregularity 2019 ·Data Archiving and Networked Services (DANS) ·Masoud Ahookhosh, Francisco J. Aragón Artacho, Ronan M. T. Fleming, (unknown), (unknown)	24
7	Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease 2019 ·Microbiome ·Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele	237
8	The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities 2018 ·Bioinformatics ·Federico Baldini, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele	94
9	Community-driven roadmap for integrated disease maps 2018 ·Briefings in Bioinformatics ·Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andreï Zinovyev, Uğur Doğrusöz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas Ligon, Anna Niarakis, David Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider	37
10	Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D 2017 ·Journal of Cheminformatics ·German Preciat, (unknown), Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir, Ronan M. T. Fleming	23
11	Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression 2017 ·Scientific Reports ·Ding Ma, Laurence Yang, Ronan M. T. Fleming, Ines Thiele, Bernhard Ø. Palsson, Michael A. Saunders	28
12	Conditions for duality between fluxes and concentrations in biochemical networks 2016 ·Journal of Theoretical Biology ·Ronan M. T. Fleming, Nikos Vlassis, Ines Thiele, Michael A. Saunders	11
13	Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota breakdown → 2016 ·Nature Biotechnology ·Stefanía Magnúsdóttir, Almut Heinken, (unknown), Dmitry A. Ravcheev, Eugen Bauer, Alberto Noronha, Kacy Greenhalgh, Christian Jäger, Joanna Bagińska, Paul Wilmes, Ronan M. T. Fleming, Ines Thiele	522
14	Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices breakdown → 2014 ·Biosensors and Bioelectronics ·Skarphéðinn Halldórsson, Edinson Lucumi, Rafael Gómez-Sjöberg, Ronan M. T. Fleming	769
15	Real-time optical pH measurement in a standard microfluidic cell culture system 2013 ·Biomedical Optics Express ·E. B. Magnusson, Skarphéðinn Halldórsson, Ronan M. T. Fleming, Kristján Leósson	36
16	Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage 2012 ·PLoS ONE ·Ines Thiele, Ronan M. T. Fleming, Richard Que, Aarash Bordbar, Dinh Diep, Bernhard Ø. Palsson	87
17	A systems biology approach to studying the role of microbes in human health 2012 ·Current Opinion in Biotechnology ·Ines Thiele, Almut Heinken, Ronan M. T. Fleming	76
18	Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction 2012 ·Biophysical Journal ·Hulda S. Haraldsdóttir, Ines Thiele, Ronan M. T. Fleming	37
19	Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole–time of flight mass spectrometry (UPLC–Q–ToF-MS) 2011 ·Analytical and Bioanalytical Chemistry ·Giuseppe Paglia, (unknown), Manuela Magnúsdóttir, Ronan M. T. Fleming, Steinunn Thorlacius, Bernhard Ø. Palsson, Ines Thiele	67
20	Nascent very low density lipoprotein particles and apoproteins of hepatocytic endoplasmic reticulum 1985 ·R. Hay, Ronan M. T. Fleming	2

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