A community-driven global reconstruction of human metabolism

What is flux balance analysis?

Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060

DrugBank: a knowledgebase for drugs, drug actions and drug targets

Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B., & Hassanali, M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm958 · Cited by 2,896

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

Wikoff, W. R., Anfora, A. T., Liu, J., Schultz, P. G., Lesley, S. A., Peters, E. C., & Siuzdak, G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812874106 · Cited by 2,677

Towards a knowledge-based Human Protein Atlas

Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt1210-1248 · Cited by 2,440

HMDB: a knowledgebase for the human metabolome

Wishart, D. S., Knox, C., Guo, A. C., Eisner, R., Young, N., Gautam, B., Hau, D., Psychogios, N., Dong, E., Bouatra, S., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn810 · Cited by 1,874

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., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835

A protocol for generating a high-quality genome-scale metabolic reconstruction

Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789

Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation

Jain, M., Nilsson, R., Sharma, S., Madhusudhan, N., Kitami, T., Souza, A. L., Kafri, R., Kirschner, M. W., Clish, C. B., & Mootha, V. K. (2012) · Science · doi:10.1126/science.1218595 · Cited by 1,403

Global reconstruction of the human metabolic network based on genomic and bibliomic data

Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., & Palsson, B. Ø. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610772104 · Cited by 1,374

Taking Bioinformatics to Systems Medicine

van Kampen, A. H. C., & Moerland, P. D. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3283-2_2 · Cited by 17

Personalized Computational Models as Biomarkers

Kölch, W., & Fey, D. (2017) · Journal of Personalized Medicine · doi:10.3390/jpm7030009 · Cited by 17

Identification of metabolism-associated genes and pathways involved in different stages of clear cell renal cell carcinoma

Li, H., Li, W., Dai, S., Guo, Y., Zheng, J., Liu, J., Wang, Q., Chen, B., Li, G., & Huang, J. (2017) · Oncology Letters · doi:10.3892/ol.2017.7567 · Cited by 17

Horizon Scanning: How Will Metabolomics Applications Transform Food Science, Bioengineering, and Medical Innovation in the Current Era of Foodomics?

Bayram, M., & Gökırmaklı, Ç. (2018) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2017.0203 · Cited by 17

Current Status and Future Prospects of Clinically Exploiting Cancer-specific Metabolism—Why Is Tumor Metabolism Not More Extensively Translated into Clinical Targets and Biomarkers?

Muthu, M., & Nordström, A. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20061385 · Cited by 16

Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine

Sigmarsdóttir, Þ. B., McGarrity, S., Rolfsson, Ó., Yurkovich, J. T., & Sigurjónsson, Ó. E. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00239 · Cited by 18

Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer

Trilla‐Fuertes, L., Gámez‐Pozo, A., López‐Camacho, E., Prado-Vázquez, G., Zapater‐Moros, A., López‐Vacas, R., Arevalillo, J. M., Díaz‐Almirón, M., Navarro, H., Maı́n, P., et al. (2020) · BMC Cancer · doi:10.1186/s12885-020-06764-x · Cited by 17

Nutrient Sensing by Histone Marks: Reading the Metabolic Histone Code Using Tracing, Omics, and Modeling

Campit, S., Meliki, A., Youngson, N. A., & Chandrasekaran, S. (2020) · BioEssays · doi:10.1002/bies.202000083 · Cited by 17

CASMI—The Small Molecule Identification Process from a Birmingham Perspective

Allwood, J. W., Weber, R. J. M., Zhou, J., He, S., Viant, M. R., & Dunn, W. B. (2013) · Metabolites · doi:10.3390/metabo3020397 · Cited by 17

MetDisease—connecting metabolites to diseases via literature

Duren, W. L., Weymouth, T. E., Hull, T., Omenn, G. S., Athey, B. D., Burant, C., & Karnovsky, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu179 · Cited by 17

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

Sompairac, N., Modamio, J., Barillot, E., Fleming, R. M. T., Zinovyev, A. Y., & Kuperstein, I. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2682-z · Cited by 18

Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary diseasePreprint

Bassler, K. E., Fujii, W., Kapellos, T. S., Horne, A., Reiz, B., Dudkin, E., Luecken, M. D., Reusch, N., Osei-Sarpong, C., Warnat‐Herresthal, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.28.121541 · Cited by 16

Spatial hepatocyte plasticity of gluconeogenesis during the metabolic transitions between fed, fasted and starvation states

Okada, J., Landgraf, A., Xiaoli, A. M., Liu, L. P., Horton, M., Schuster, V. L., Yang, F., Sidoli, S., Qiu, Y., Kurland, I. J., et al. (2025) · Nature Metabolism · doi:10.1038/s42255-025-01269-y · Cited by 19

Metabolic Modeling to Interrogate Microbial Disease: A Tale for Experimentalists

Jean-Pierre, F., Henson, M. A., & O’Toole, G. A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.634479 · Cited by 16

Pharmacophore-Based Discovery of Substrates of a Novel Drug/Proton-Antiporter in the Human Brain Endothelial hCMEC/D3 Cell Line

Smirnova, M., Goracci, L., Cruciani, G., Federici, L., Declèves, X., Chapy, H., & Cisternino, S. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics14020255 · Cited by 16

Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501

Babaei, P., Marashi, S., & Asad, S. (2015) · Molecular BioSystems · doi:10.1039/c5mb00086f · Cited by 16

Towards high resolution analysis of metabolic flux in cells and tissues

Sims, J. K., Manteiga, S., & Lee, K. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2013.07.001 · Cited by 16

An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models

Røkke, G. B., Hohmann‐Marriott, M. F., & Almaas, E. (2020) · PLoS ONE · doi:10.1371/journal.pone.0229408 · Cited by 16

Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epi-thelial cells with metabolic and protein-protein interaction networks

Karakurt, H. U., & Pir, P. (2020) · TURKISH JOURNAL OF BIOLOGY · doi:10.3906/biy-2005-115 · Cited by 16

Importance of the biomass formulation for cancer metabolic modeling and drug prediction

Garcia, M. M., Pacheco, M. P., Bintener, T., Presta, L., & Sauter, T. (2021) · iScience · doi:10.1016/j.isci.2021.103110 · Cited by 15

Automated pathway and reaction prediction facilitates in silico identification of unknown metabolites in human cohort studies

Quell, J. D., Römisch‐Margl, W., Colombo, M., Krumsiek, J., Evans, A. M., Mohney, R. P., Salomaa, V. V., Fairé, U. D., Groop, L., Agakov, F. V., et al. (2017) · Journal of Chromatography B · doi:10.1016/j.jchromb.2017.04.002 · Cited by 16

Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines

Węglarz‐Tomczak, E., Mondeel, T. D. G. A., Piebes, D. G. E., & Westerhoff, H. V. (2021) · Biomolecules · doi:10.3390/biom11040490 · Cited by 16

A Systematic Assessment Of Current Genome-Scale Metabolic Reconstruction ToolsPreprint

Mendoza, S. N., Olivier, B. G., Douwe Molenaar, B., & Teusink, B. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/558411 · Cited by 16

Applications of genome-scale metabolic models to the study of human diseases: A systematic review

Cortese, N., Procopio, A., Merola, A., Zaffino, P., & Cosentino, C. (2024) · Computer Methods and Programs in Biomedicine · doi:10.1016/j.cmpb.2024.108397 · Cited by 17

Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks

Krumholz, E. W., & Libourel, I. G. L. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.634121 · Cited by 15

In-Silico Prediction of Key Metabolic Differences between Two Non-Small Cell Lung Cancer Subtypes

Rezola, A., Pey, J., Rubio, Á., & Planes, F. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0103998 · Cited by 15

Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches

Basler, G. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2398-4_12 · Cited by 15

Integration of metabolic, regulatory and signaling networks towards analysis of perturbation and dynamic responses

Chiappino-Pepe, A., Pandey, V., Ataman, M., & Vassily Hatzimanikatis, A. (2017) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.01.007 · Cited by 15

Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

de Mas, I. M., Torrents, L., Bedia, C., Nielsen, L. K., Cascante, M., & Tauler, R. (2019) · BMC Genomics · doi:10.1186/s12864-019-5979-4 · Cited by 15

Compartment and hub definitions tune metabolic networks for metabolomic interpretations

Waller, T. C., Berg, J. A., Lex, A., Chapman, B. E., & Rutter, J. P. (2020) · GigaScience · doi:10.1093/gigascience/giz137 · Cited by 15

Towards the routine use of in silico screenings for drug discovery using metabolic modelling

Bintener, T., Pacheco, M. P., & Sauter, T. (2020) · Biochemical Society Transactions · doi:10.1042/bst20190867 · Cited by 17

Non-coding RNAs, metabolic stress and adaptive mechanisms in cancer

Liu, X., Feng, S., Zhang, X. D., Li, J., Zhang, K., Wu, M., & Thorne, R. F. (2020) · Cancer Letters · doi:10.1016/j.canlet.2020.06.024 · Cited by 15

Advances in Astrocyte Computational Models: From Metabolic Reconstructions to Multi-omic Approaches

González, J., Pinzón, A. M., Angarita-Rodríguez, A., Aristizábal-Pachón, A. F., Barreto, G. E., & Martín-Jiménez, C. (2020) · Frontiers in Neuroinformatics · doi:10.3389/fninf.2020.00035 · Cited by 15

Leveraging genome-scale metabolic models for human health applications

Chowdhury, S., & Fong, S. S. (2020) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2020.08.017 · Cited by 14

Characterization and comparison of gene-centered human interactomes

Mosca, E., Bersanelli, M., Matteuzzi, T., Nanni, N. D., Castellani, G., Milanesi, L., & Remondini, D. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab153 · Cited by 17

Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data

Gawthrop, P. J., Pan, M., & Crampin, E. J. (2021) · Journal of The Royal Society Interface · doi:10.1098/rsif.2021.0478 · Cited by 15

Deducing Intracellular Distributions of Metabolic Pathways from Genomic Data

Gruber, A., & Kroth, P. G. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-661-0_12 · Cited by 16

Mitochondrial responses to extreme environments: insights from metabolomics

O’Brien, K. A., Griffin, J. L., Murray, A. J., & Edwards, L. M. (2015) · Extreme Physiology & Medicine · doi:10.1186/s13728-015-0026-9 · Cited by 15

Genome-wide metabolic model to improve understanding of CD4+ T cell metabolism, immunometabolism and application in drug design

Han, F., Li, G., Dai, S., & Huang, J. (2015) · Molecular BioSystems · doi:10.1039/c5mb00480b · Cited by 14

Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method

Tobalina, L., Pey, J., Rezola, A., & Planes, F. J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0154583 · Cited by 13

Influence of agricultural activities in the structure and metabolic functionality of paramo soil samples in Colombia studied using a metagenomics analysis in dynamic state

Álvarez-Yela, A. C., Silva, M. C. A., Restrepo, S., Husserl, J., Zambrano, M. M., Danies, G., Gómez, J. M., & Barrios, A. F. G. (2017) · Ecological Modelling · doi:10.1016/j.ecolmodel.2017.02.010 · Cited by 17

Metabopolis: scalable network layout for biological pathway diagrams in urban map style

Wu, H., Nöllenburg, M., Sousa, F. L., & Viola, I. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2779-4 · Cited by 15

Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges

Chen, Y., Li, G., & Nielsen, J. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9736-7_19 · Cited by 16

A scalable method for parameter-free simulation and validation of mechanistic cellular signal transduction network models

Romers, J. C., Thieme, S., Münzner, U., & Krantz, M. (2020) · npj Systems Biology and Applications · doi:10.1038/s41540-019-0120-5 · Cited by 15

Non-targeted Tracer Fate Detection

Weindl, D., Wegner, A., & Hiller, K. (2015) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2015.04.003 · Cited by 15

Control of metabolite efflux in microbial cell factories: current advances and future prospectsPreprint

Kell, D. B. (2018) · OSF Preprints (OSF Preprints) · doi:10.31219/osf.io/xg9jh · Cited by 15

Cisplatin-Induced Metabolic Responses Measured with Raman Spectroscopy in Cancer Cells, Spheroids, and Canine-Derived Organoids

Kothadiya, S., Cutshaw, G., Uthaman, S., Hassan, N. A., Sahoo, D. K., Wickham, H., Quam, E., Allenspach, K., Mochel, J. P., & Bardhan, R. (2024) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.4c08629 · Cited by 14

Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors

Sundqvist, N., Grankvist, N., Watrous, J. D., Jain, M., Nilsson, R., & Cedersund, G. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009999 · Cited by 15

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery

Bessell, B., Loecker, J., Zhao, Z., Aghamiri, S. S., Mohanty, S., Amin, R., Helikar, T., & Puniya, B. L. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad387 · Cited by 14

Quantitative computational models of molecular self-assembly in systems biology

Thomas, M., & Schwartz, R. S. (2017) · Physical Biology · doi:10.1088/1478-3975/aa6cdc · Cited by 15

Multi-Species Network Inference Improves Gene Regulatory Network Reconstruction for Early Embryonic Development in Drosophila

Joshi, A., Beck, Y., & Michoel, T. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2014.0290 · Cited by 15

eNutrition - The next dimension for eHealth?

Boland, M., & Bronlund, J. E. (2019) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2019.08.001 · Cited by 15

Elucidating the metabolic characteristics of pancreatic β-cells from patients with type 2 diabetes (T2D) using a genome-scale metabolic modeling

Paul, A., Azhar, S., Das, P. N., Bairagi, N., & Chatterjee, S. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105365 · Cited by 14

The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome

Diener, C., Muñoz-Gonzalez, F., Encarnación‐Guevara, S., & Reséndis-Antonio, O. (2016) · Scientific Reports · doi:10.1038/srep28415 · Cited by 16

Metabolic systems biology: a brief primer

Edwards, L. M. (2016) · The Journal of Physiology · doi:10.1113/jp272275 · Cited by 16

Genome-scale metabolic model of the rat liver predicts effects of diet restriction

Baloni, P., Sangar, V., Yurkovich, J. T., Robinson, M., Taylor, S., Karbowski, C. M., Hamadeh, H. K., He, Y. D., & Price, N. D. (2019) · Scientific Reports · doi:10.1038/s41598-019-46245-1 · Cited by 14

Transcriptome analysis reveals gender-specific differences in overall metabolic response of male and female patients in lung adenocarcinoma

Li, Y., He, C., Li, W., Zhang, R., & Duan, Y. (2020) · PLoS ONE · doi:10.1371/journal.pone.0230796 · Cited by 13

Novel Approaches in Astrocyte Protection: from Experimental Methods to Computational Approaches

Garzón, D., Cabezas, R., Vega-Vela, N. E., Ávila-Rodriguez, M., González, J., Gómez, R. M., Echeverrı́a, V., Aliev, G., & Barreto, G. E. (2016) · Journal of Molecular Neuroscience · doi:10.1007/s12031-016-0719-6 · Cited by 15

Convergent evolution of monocyte differentiation in adult skin instructs Langerhans cell identity

Appios, A., Davies, J., Sirvent, S., Henderson, S. R., Trzebanski, S., Schroth, J., Law, M. L., Boal‐Carvalho, I., Pinto, M. M., Carvalho, C., et al. (2024) · Science Immunology · doi:10.1126/sciimmunol.adp0344 · Cited by 14

Graph databases in systems biology: a systematic review

Mazein, I., Rougny, A., Mazein, A., Henkel, R., Gütebier, L., Michaelis, L., Ostaszewski, M., Schneider, R., Satagopam, V., Jensen, L. J., et al. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae561 · Cited by 15

Multiple pathways through which the gut microbiota regulates neuronal mitochondria constitute another possible direction for depression

Zhao, H., Qiu, X., Wang, S., Wang, Y., Xie, L., Xia, X., & Li, W. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1578155 · Cited by 14

Toward genome-scale models of the Chinese hamster ovary cells: incentives, status and perspectives

Kaas, C. S., Fan, Y., Weilguny, D., Kristensen, C., Kildegaard, H. F., & Andersen, M. R. (2014) · Pharmaceutical Bioprocessing · doi:10.4155/pbp.14.54 · Cited by 13

Consensus and conflict cards for metabolic pathway databases

Stobbe, M. D., Swertz, M. A., Thiele, I., Rengaw, T., van Kampen, A. H. C., & Moerland, P. D. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-50 · Cited by 13

Temporal transcriptomic analysis of metabolic genes in maternal organs and placenta during murine pregnancy†

Paquette, A. G., Baloni, P., Holloman, A. B., Nigám, S. K., Bammler, T. K., Mao, Q., & Price, N. D. (2018) · Biology of Reproduction · doi:10.1093/biolre/ioy148 · Cited by 13

Revealing the metabolic characteristics of human embryonic stem cells by genome‐scale metabolic modeling

He, Y., Wang, Y., Zhang, B., Li, Y., Diao, L., Lu, L., Yao, J., Liu, Z., Li, D., & He, F. (2018) · FEBS Letters · doi:10.1002/1873-3468.13255 · Cited by 15

Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation

Poupin, N., Corlu, A., Cabaton, N. J., Dubois‐Pot‐Schneider, H., Canlet, C., Person, E., Bruel, S., Frainay, C., Vinson, F., Maurier, F., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00524 · Cited by 15

Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma

Sahoo, S., Kumar, R. R., Nicolay, B., Mohite, O. S., Sivaraman, K., Khetan, V., Rishi, P., Ganesan, S., Subramanyan, K., Raman, K., et al. (2018) · FEBS Letters · doi:10.1002/1873-3468.13294 · Cited by 13

Modeling strategies to study metabolic pathways in progression to type 1 diabetes – Challenges and opportunities

Marinković, T., & Orešič, M. (2015) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2015.08.011 · Cited by 13

Predicting internal cell fluxes at sub-optimal growth

Schultz, A., & Qutub, A. A. (2015) · BMC Systems Biology · doi:10.1186/s12918-015-0153-3 · Cited by 13

An argument for mechanism-based statistical inference in cancer

Geman, D., Ochs, M. F., Price, N. D., Tomasetti, C., & Laurent Younes, B. (2014) · Human Genetics · doi:10.1007/s00439-014-1501-x · Cited by 13

Investigating Host–Pathogen Behavior and Their Interaction Using Genome-Scale Metabolic Network Models

Sadhukhan, P. P., & Raghunathan, A. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1115-8_29 · Cited by 13

Thermodynamic Constraints Improve Metabolic Networks

Krumholz, E. W., & Libourel, I. G. L. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.06.018 · Cited by 12

Logical versus kinetic modeling of biological networks: applications in cancer research

Calzone, L., Barillot, E., & Zinovyev, A. Y. (2018) · Current Opinion in Chemical Engineering · doi:10.1016/j.coche.2018.02.005 · Cited by 13

Systems biology as an emerging paradigm in transfusion medicine

Yurkovich, J. T., Bordbar, A., Sigurjónsson, Ó. E., & Palsson, B. O. (2018) · BMC Systems Biology · doi:10.1186/s12918-018-0558-x · Cited by 14

Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism

Occhipinti, A., Hamadi, Y., Kugler, H., Wintersteiger, C. M., Yordanov, B., & Angione, C. (2020) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2020.2973386 · Cited by 13

Human genes with a greater number of transcript variants tend to show biological features of housekeeping and essential genes

Ryu, J. Y., Kim, H. U., & Lee, S. Y. (2015) · Molecular BioSystems · doi:10.1039/c5mb00322a · Cited by 13

Ethical issues in personalized medicine

CHADWICK, R. F. (2013) · Drug Discovery Today Therapeutic Strategies · doi:10.1016/j.ddstr.2013.05.001 · Cited by 12

Genome scale metabolic network modelling for metabolic profile predictions

Cooke, J., Delmas, M., Wieder, C., Rodríguez-Mier, P., Frainay, C., Vinson, F., Ebbels, T. M. D., Poupin, N., & Jourdan, F. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011381 · Cited by 12

Computational approaches for understanding energy metabolism

Shestov, A. A., Barker, B., Gu, Z., & Locasale, J. W. (2013) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1238 · Cited by 14

Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota

Phalak, P., & Henson, M. A. (2019) · Processes · doi:10.3390/pr7020097 · Cited by 12

Intelligent host engineering for metabolic flux optimisation in biotechnology

Munro, L. J., & Kell, D. B. (2021) · Biochemical Journal · doi:10.1042/bcj20210535 · Cited by 12

Systems Biology and Cytokines Potential Role in Lung Cancer Immunotherapy Targeting Autophagic Axis

Khilwani, R., & Singh, S. (2023) · Biomedicines · doi:10.3390/biomedicines11102706 · Cited by 12

Network-based discovery through mechanistic systems biology. Implications for applications – SMEs and drug discovery: where the action is

Benson, N. (2015) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2015.07.003 · Cited by 12

A Method for Modeling Growth of Organs and Transplants Based on the General Growth Law: Application to the Liver in Dogs and Humans

Shestopaloff, Y. K., & Sbalzarini, I. F. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099275 · Cited by 12

Computational Approaches in Precision Medicine

Enríquez, J. E., Mejía-Pedroza, R. A., & Lemus, E. H. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-809411-2.00013-1 · Cited by 12

Proliferation inhibition of cisplatin‐resistant ovarian cancer cells using drugs screened by integrating a metabolic model and transcriptomic data

Motamedian, E., Taheri, E., & Bagheri, F. (2017) · Cell Proliferation · doi:10.1111/cpr.12370 · Cited by 12

Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics

Yugi, K., Ohno, S., Krycer, J. R., James, D. E., & Kuroda, S. (2019) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2019.04.005 · Cited by 11

Integration of metabolomics with genomics: Metabolic gene prioritization using metabolomics data and genomic variant (CADD) scores

Bongaerts, M., Bonte, R., Demirdas, S., Huidekoper, H. H., Langendonk, J. G., Wilke, M., de Valk, W. G., Blom, H. J., Reinders, M. J. T., & Ruijter, G. J. G. (2022) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2022.05.002 · Cited by 12

Melanoma proteomics suggests functional differences related to mutational status

Trilla‐Fuertes, L., Gámez‐Pozo, A., Prado-Vázquez, G., Zapater‐Moros, A., Díaz‐Almirón, M., Fortes, C., Ferrer-Gómez, M., López‐Vacas, R., Blanco, V. P., Márquez‐Rodas, I., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-43512-z · Cited by 12

Cofactors revisited – Predicting the impact of flavoprotein-related diseases on a genome scale

Wegrzyn, A. B., Stolle, S., Rienksma, R. A., dos Santos, V. A. P. M., Bakker, B. M., & Diez, M. S. (2018) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2018.10.021 · Cited by 13

Modeling Red Blood Cell Metabolism in the Omics Era

Key, A., Haiman, Z. B., Palsson, B. Ø., & D’Alessandro, A. (2023) · Metabolites · doi:10.3390/metabo13111145 · Cited by 11

Towards personalized genome-scale modeling of inborn errors of metabolism for systems medicine applications

Heinken, A., Kouche, S. E., Guéant‐Rodriguez, R., & Guéant, J. (2023) · Metabolism · doi:10.1016/j.metabol.2023.155738 · Cited by 13

NMR-based metabolomics: Where are we now and where are we going?

Gowda, G. A. N., Wentao, Z., & Raftery, D. (2025) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2025.101564 · Cited by 11

Metabolic reprogramming and functional crosstalk within the tumor microenvironment (TME) and A Multi-omics anticancer approach

Mir, R., Javid, J., Ullah, M. F., Alrdahe, S. S., Albalawi, I. A., Mustafa, S. K., Jalal, M. M., Altayar, M. A., Albalawi, A. D., Abunab, M. K., et al. (2025) · Medical Oncology · doi:10.1007/s12032-025-02945-5 · Cited by 12

Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes

Chénard, T., Guénard, F., Vohl, M., Carpentier, A. C., Tchernof, A., & Najmanovich, R. (2017) · BMC Systems Biology · doi:10.1186/s12918-017-0438-9 · Cited by 11

Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition

Sinha, N., Diez, M. S., van Schothorst, E. M., Keijer, J., dos Santos, V. A. P. M., & Hooiveld, G. J. E. J. (2017) · Scientific Reports · doi:10.1038/s41598-017-07350-1 · Cited by 11

Cancer Recurrence and Omics: Metabolic Signatures of Cancer Dormancy Revealed by Transcriptome Mapping of Genome-Scale Networks

Kutay, M., Gözüaçık, D., & Çakır, T. (2022) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2022.0008 · Cited by 11

Competitive, multi‐objective, and compartmented Flux Balance Analysis for addressing tissue‐specific inborn errors of metabolism

Liu, Y., & Westerhoff, H. V. (2023) · Journal of Inherited Metabolic Disease · doi:10.1002/jimd.12603 · Cited by 13

A contribution of metabolic engineering to addressing medical problems: Metabolic flux analysis

Lee, G., Lee, S. M., & Kim, H. U. (2023) · Metabolic Engineering · doi:10.1016/j.ymben.2023.04.008 · Cited by 12

Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer

Çubuk, C., Loucera, C., Peña-Chilet, M., & Dopazo, J. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24087450 · Cited by 12

Recon 2.2: from reconstruction to model of human metabolism

Swainston, N., Smallbone, K., Hefzi, H., Dobson, P. D., Brewer, J., Hanscho, M., Zielinski, D. C., Ang, K. S., Gardiner, N. J., Gutierrez, J. M., et al. (2016) · Metabolomics · doi:10.1007/s11306-016-1051-4 · Cited by 285

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

Swainston, N., Mendes, P., & Kell, D. B. (2013) · Metabolomics · doi:10.1007/s11306-013-0564-3 · Cited by 42

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

Brunk, E., Sahoo, S., Zielinski, D. C., Altunkaya, A., Dräger, A., Mih, N., Gatto, F., Nilsson, A., Preciat, G., Aurich, M. K., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4072 · Cited by 763

Reconstruction of genome-scale human metabolic models using omics data

Ryu, J. Y., Kim, H. U., & Lee, S. Y. (2015) · Integrative Biology · doi:10.1039/c5ib00002e · Cited by 58

ReconXKG: an open workspace for human metabolic network reconstruction

Mehl, F., Moretti, S., McGoldrick, J., Niknejad, A., Aimo, L., Bridge, A. J., Fleming, R. M. T., & Pagni, M. (2026) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.22769005