MEMOTE for standardized genome-scale metabolic model testing

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

KBase: The United States Department of Energy Systems Biology Knowledgebase

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COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-74 · Cited by 1,378

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

Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., Haraldsdóttir, H. S., Wachowiak, J., Keating, S., Vlasov, V., et al. (2019) · Nature Protocols · doi:10.1038/s41596-018-0098-2 · Cited by 1,222

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., Ebrahim, A., Palsson, B. O., & Lewis, N. E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1049 · Cited by 938

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

Magnúsdóttir, S., Heinken, A., Kutt, L., Ravcheev, D. A., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3703 · Cited by 798

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Machado, D., Andrejev, S., Tramontano, M., & Patil, K. R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky537 · Cited by 754

Minimum information requested in the annotation of biochemical models (MIRIAM)

Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622

OptFlux: an open-source software platform for in silico metabolic engineering

Rocha, I., Maia, P., Evangelista, P., Vilaça, P., Soares, S., Pinto, J. P., Nielsen, J., Patil, K. R., Ferreira, E. C., & Rocha, M. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-45 · Cited by 390

LibSBML: an API Library for SBML

Bornstein, B. J., Keating, S. M., Jouraku, A., & Hucka, M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn051 · Cited by 373

Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction

Sigmarsdóttir, Þ. B., McGarrity, S., Yurkovich, J. T., Rolfsson, Ó., & Sigurjónsson, Ó. E. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.642681 · Cited by 12

Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases

Jin, H., & Moseley, H. (2021) · Metabolites · doi:10.3390/metabo11070431 · Cited by 12

Multiomics metabolic and epigenetics regulatory network in cancer: A systems biology perspective

Wang, X., Dong, Y., Zheng, Y., & Chen, Y. (2021) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.05.008 · Cited by 13

Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor

López-López, N., León, D. S., de Castro, S., Díez‐Martínez, R., Iglesias-Bexiga, M., Camarasa, M., Menéndez, M., Nogales, J., & Garmendia, J. (2022) · mSystems · doi:10.1128/msystems.01459-21 · Cited by 12

Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis

Wendering, P., & Nikoloski, Z. (2022) · mSystems · doi:10.1128/msystems.01216-21 · Cited by 12

Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes

Caivano, A., van Winden, W. A., Dragone, G., & Mussatto, S. I. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.09.015 · Cited by 12

First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies

Renz, A., Widerspick, L., & Dräger, A. (2021) · Metabolites · doi:10.3390/metabo11040232 · Cited by 12

Recent advances in metabolic engineering–integration of in silico design and experimental analysis of metabolic pathways

Shimizu, H., & Toya, Y. (2021) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2021.08.002 · Cited by 12

Bacterial metabolism and pathogenesis intimate intertwining: time for metabolic modelling to come into action

Nogales, J., & Garmendia, J. (2021) · Microbial Biotechnology · doi:10.1111/1751-7915.13942 · Cited by 12

Proteomic analysis for the effects of non-saponin fraction with rich polysaccharide from Korean Red Ginseng on Alzheimer's disease in a mouse model

Kim, S., Nam, Y., Kim, M., Kwon, S., Jeon, J., Shin, S. J., Park, S., Chang, S., Kim, H. U., Lee, Y. Y., et al. (2022) · Journal of Ginseng Research · doi:10.1016/j.jgr.2022.09.008 · Cited by 12

Metabolic modeling predicts unique drug targets in Borrelia burgdorferi

Gwynne, P. J., Stocks, K.-L. K., Karozichian, E. S., Pandit, A., & Hu, L. T. (2023) · mSystems · doi:10.1128/msystems.00835-23 · Cited by 11

Genome‐Scale Metabolic Modeling of Halomonas elongata 153B Explains Polyhydroxyalkanoate and Ectoine Biosynthesis in Hypersaline Environments

Enuh, B. M., Çelik, P. A., & Angione, C. (2024) · Biotechnology Journal · doi:10.1002/biot.202400267 · Cited by 11

A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers

Hendry, J. I., Dinh, H. V., Sarkar, D., Wang, L., Bandyopadhyay, A., Pakrasi, H. B., & Maranas, C. D. (2021) · Metabolites · doi:10.3390/metabo11030168 · Cited by 11

Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria

Nazarshodeh, E., Marashi, S., & Gharaghani, S. (2021) · PLoS ONE · doi:10.1371/journal.pone.0261267 · Cited by 11

CobraMod: a pathway-centric curation tool for constraint-based metabolic models

Camborda, S., Weder, J.-N., & Töpfer, N. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac119 · Cited by 11

SALARECON connects the Atlantic salmon genome to growth and feed efficiency

Zakhartsev, M. V., Rotnes, F., Gulla, M., Øyås, O., van Dam, J. C. J., Diez, M. S., Grammes, F., Hafþórsson, R. A., van Helvoirt, W., Koehorst, J. J., et al. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010194 · Cited by 11

Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets

Tezcan, E. F., Demirtas, Y., Çakar, Z. P., & Ülgen, K. Ö. (2023) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2023.1121409 · Cited by 11

Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces

Czajka, J. J., Han, Y., Kim, J., Mondo, S. J., Hofstad, B. A., Robles, A. L., Haridas, S., Riley, R. W., LaButti, K. M., Pangilinan, J. L., et al. (2024) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2024.1356551 · Cited by 11

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines

Karimi, E., Geslain, E., Belcour, A., Frioux, C., Aïte, M., Siegel, A., Corre, E., & Dittami, S. M. (2021) · PeerJ · doi:10.7717/peerj.11344 · Cited by 11

Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology

Blinov, M. L., Gennari, J. H., Karr, J. R., Moraru, I. I., Nickerson, D. P., & Sauro, H. M. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.06.001 · Cited by 11

Whole‐genome sequencing and genome‐scale metabolic modeling of Chromohalobacter canadensis 85B to explore its salt tolerance and biotechnological use

Enuh, B. M., Yaman, B. N., Tarzi, C., Çelik, P. A., Mutlu, M. B., & Angione, C. (2022) · MicrobiologyOpen · doi:10.1002/mbo3.1328 · Cited by 11

Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts

Pettersen, J. P., Castillo, S., Jouhten, P., & Almaas, E. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05506-7 · Cited by 10

Shifts in carbon partitioning by photosynthetic activity increase terpenoid synthesis in glandular trichomes

Saadat, N. P., van Aalst, M., Brand, A., Ebenhöh, O., Tissier, A. F., & Matuszyńska, A. (2023) · The Plant Journal · doi:10.1111/tpj.16352 · Cited by 10

Host cell CRISPR genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of Plasmodium falciparum and related hemoparasites

Maurizio, M., Masid, M., Woods, K. L., Caldelari, R., Doench, J. G., Naguleswaran, A., Joly, D. A. H. L., Fernández, M. G., Zemp, J., Borteele, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50405-x · Cited by 10

The marine environmental microbiome mediates physiological outcomes in host nematodes

Xue, Y., Xie, Y., Cao, X., & Zhang, L. (2024) · BMC Biology · doi:10.1186/s12915-024-02021-w · Cited by 10

A bacterial signal coordinates plant-microbe fitness trade-off to enhance sulfur deficiency tolerance in plants

Mukherjee, A., Mazumder, M., Verma, A. K., Tikariha, H., Bhattacharya, R., Ooi, Q. E., & Swarup, S. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.09.007 · Cited by 10

An ecology-driven microbial consortium enhances plant growth and immunity while sustaining rhizospheric microbial balance

Mazumder, M., Tikariha, H., Sevugan, M., Majedi, S. M., Hamid, N. A. B. A., Mukhopadhyay, S., Pavagadhi, S., Selvaraj, P., Naqvi, N. I., & Swarup, S. (2025) · Plant Communications · doi:10.1016/j.xplc.2025.101665 · Cited by 10

A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility

He, B., Cai, C., McCubbin, T., Muriel, J. C., Sonnenschein, N., Hu, S., Yuan, Z., & Marcellin, E. (2022) · Metabolites · doi:10.3390/metabo12040314 · Cited by 10

Review of Current Human Genome-Scale Metabolic Models for Brain Cancer and Neurodegenerative Diseases

Kishk, A., Pacheco, M. P., Heurtaux, T., Sinkkonen, L., Pang, J., Fritah, S., Niclou, S. P., & Sauter, T. (2022) · Cells · doi:10.3390/cells11162486 · Cited by 10

Metabolic compatibility and the rarity of prokaryote endosymbioses

Libby, E., Kempes, C. P., & Okie, J. G. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2206527120 · Cited by 11

Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture

Potter, A. D., Baiocco, C. M., Papin, J. A., & Criss, A. K. (2023) · mSystems · doi:10.1128/msystems.01265-22 · Cited by 10

Cardinality optimization in constraint-based modelling: application to human metabolism

Fleming, R. M. T., Haraldsdóttir, H. S., Le, H. M., Vuong, P. T., Hankemeier, T., & Thiele, I. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad450 · Cited by 10

Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R

Neal, M., Thiruppathy, D., & Zengler, K. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011594 · Cited by 11

Systems Biology in ELIXIR: modelling in the spotlight

dos Santos, V. A. P. M., Anton, M., Szomolay, B., Ostaszewski, M., Arts, I. C. W., Benfeitas, R., Angel, V. D. D., Domínguez-Romero, E., Ferk, P., Fey, D., et al. (2022) · F1000Research · doi:10.12688/f1000research.126734.1 · Cited by 12

Development of a genome-scale metabolic model for the lager hybrid yeast S. pastorianus to understand the evolution of metabolic pathways in industrial settings

Timouma, S., Balarezo-Cisneros, L. N., Schwartz, J., & Delneri, D. (2024) · mSystems · doi:10.1128/msystems.00429-24 · Cited by 10

Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002

Vijayakumar, S., & Angione, C. (2021) · STAR Protocols · doi:10.1016/j.xpro.2021.100837 · Cited by 10

Insight into the biotechnology potential of Alicyclobacillus tolerans from whole genome sequence analysis and genome-scale metabolic network modeling.

Enuh, B. M., & Çelik, P. A. (2022) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2022.106459 · Cited by 10

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic ModelsPreprint

Raman, K., Kratochvíl, M., Olivier, B. G., König, M., Sengupta, P., Baskaran, D. K. K., Nguyen, T. V. N., Lobo, D., Wilken, S. E., Tiwari, K. K., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.24.614797 · Cited by 10

Genome‐scale metabolic models applied for human health and biopharmaceutical engineering

Li, F., Chen, Y., Gustafsson, J., Wang, H., Wang, Y., Zhang, C., & Xing, X. (2023) · Quantitative Biology · doi:10.1002/qub2.21 · Cited by 10

Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data

Lee, G., Lee, S. M., Lee, S., Jeong, C. W., Song, H., Lee, S. Y., Yun, H., Koh, Y., & Kim, H. U. (2024) · Genome biology · doi:10.1186/s13059-024-03208-8 · Cited by 9

Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities

Leonidou, N., Ostyn, L., Coenye, T., Crabbé, A., & Dräger, A. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.04006-23 · Cited by 9

Genome streamlining of Pseudomonas putida B6-2 for bioremediation

Fan, S., Ren, H., Fu, X., Kong, X., Wu, H., & Lv, Z. (2024) · mSystems · doi:10.1128/msystems.00845-24 · Cited by 9

Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms

Arend, M., Paulitz, E., Hsieh, Y. E., & Nikoloski, Z. (2025) · Metabolic Engineering · doi:10.1016/j.ymben.2025.02.015 · Cited by 9

Proteome trade-off between primary and secondary metabolism shapes acid stress induced bacterial exopolysaccharide production

Qiu, S., Yang, A., Yang, X., Ni, H., Li, W., Yang, Z., Zeng, H., & Wang, Y. (2025) · Metabolic Engineering · doi:10.1016/j.ymben.2025.05.002 · Cited by 9

Synthetic Microbial Cocultivation for Targeted Production of Odd-Chain Carboxylates and Alcohols from Carbon Monoxide

Olm, I. P., Benito-Vaquerizo, S., Dubaere, C., dos Santos, V. A. P. M., Diez, M. S., & Sousa, D. Z. (2025) · Environmental Science & Technology · doi:10.1021/acs.est.4c14794 · Cited by 9

Spontaneous immortalization of bovine fibroblasts following long-term expansion offers a non-transformed cell source for cultivated beef

Pasitka, L., Cohen, M., Regenbaum, S., Ehrlich, A., Gildor, B., Gold, A., & Nahmias, Y. (2025) · Nature Food · doi:10.1038/s43016-025-01255-3 · Cited by 13

Transmission of Klebsiella strains and plasmids within and between grey‐headed flying fox colonies

Vezina, B., Judd, L. M., McDougall, F. K., Boardman, W., Power, M. L., Hawkey, J., Brisse, S., Monk, J. M., Holt, K. E., & Wyres, K. L. (2022) · Environmental Microbiology · doi:10.1111/1462-2920.16047 · Cited by 9

A genome-scale metabolic model of parasitic whipworm

Bay, Ö. F., Hayes, K. S., Schwartz, J., Grencis, R. K., & Roberts, I. S. (2023) · Nature Communications · doi:10.1038/s41467-023-42552-4 · Cited by 9

Genome-scale flux balance analysis reveals redox trade-offs in the metabolism of the thermoacidophile Methylacidiphilum fumariolicum under auto-, hetero-and methanotrophic conditions

Saldivar, A., Ruiz‐Ruiz, P., Revah, S., & Zúñiga, C. (2024) · Frontiers in Systems Biology · doi:10.3389/fsysb.2024.1291612 · Cited by 9

Genome-scale metabolic models in translational medicine: the current status and potential of machine learning in improving the effectiveness of the models

Turanlı, B., Gülfidan, G., Aydogan, O. O., Kula, C., Selvaraj, G., & Arğa, K. Y. (2024) · Molecular Omics · doi:10.1039/d3mo00152k · Cited by 10

Executable Simulation Model of the Liver

König, M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11682-4 · Cited by 9

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

Leonidou, N., Renz, A., Mostolizadeh, R., & Dräger, A. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010903 · Cited by 9

Metabolic modelling: Insights into the machine room of plant metabolism

Machado, T. M., Töpfer, N., & Soltani, F. (2025) · Journal of Plant Physiology · doi:10.1016/j.jplph.2025.154584 · Cited by 8

Multi-omics integration in genome-scale metabolic models: a review of constraint-based approaches

Shahreen, N., Osinuga, A., Malla, S., Razmpour, T., Tabibian, M., & Saha, R. (2026) · Molecular Omics · doi:10.1093/molecular-omics/aaiag005 · Cited by 8

Metabolic modeling unveils potential probiotic roles of Flavonifractor plautii in reshaping the Western gut microbiota landscape

Scott, W. T., Nataya, E. D., Belzer, C., & Schaap, P. J. (2026) · ISME Communications · doi:10.1093/ismeco/ycag077 · Cited by 8

Programmatic modeling for biological systems

Lubbock, A. L. R., & Lopez, C. F. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.05.004 · Cited by 8

COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions

Wendering, P., & Nikoloski, Z. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009906 · Cited by 8

iNovo479: Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans

Linz, A. M., Ma, Y., Scholz, S., Noguera, D. R., & Donohue, T. J. (2022) · Metabolites · doi:10.3390/metabo12040366 · Cited by 8

Genome-scale metabolic model led engineering of Nothapodytes nimmoniana plant cells for high camptothecin production

Murali, S., Ibrahim, M., Rajendran, H., Shagun, S., Masakapalli, S. K., Raman, K., & Srivastava, S. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1207218 · Cited by 8

MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions

Thiele, I., Preciat, G., & Fleming, R. M. T. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac596 · Cited by 8

Systematic diet composition swap in a mouse genome-scale metabolic model reveals determinants of obesogenic diet metabolism in liver cancer

Clasen, F., Nunes, P. M., Bidkhori, G., Bah, N. K., Boeing, S., Shoaie, S., & Anastasiou, D. (2023) · iScience · doi:10.1016/j.isci.2023.106040 · Cited by 8

Modelling hCDKL5 Heterologous Expression in Bacteria

Fondi, M., Gonzi, S., Dziurzyński, M., Turano, P., Ghini, V., Calvanese, M., Colarusso, A., Lauro, C., Parrilli, E., & Tutino, M. L. (2021) · Metabolites · doi:10.3390/metabo11080491 · Cited by 8

Upgrading a cyanobacterial genome-scale model by inclusion of enzymatic constraints

Andrews, F., Scrutton, N. S., & Schwartz, J.-M. (2024) · Algal Research · doi:10.1016/j.algal.2024.103584 · Cited by 7

Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations

Scott, W. T., Rockx, S., Mariën, Q., Regueira, A., Candry, P., Ganigué, R., Koehorst, J. J., & Schaap, P. J. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.01.013 · Cited by 7

ThermOptCobra: Thermodynamically optimal construction and analysis of metabolic networks for reliable phenotype predictions

Kumar, S. P., & Bhatt, N. (2025) · iScience · doi:10.1016/j.isci.2025.113005 · Cited by 7

Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources

(2025) · doi:10.1128/msystems.00690-25 · Cited by 7

A synthetic biology toolkit for the plasmid-dependent and thermophilic methylotroph Bacillus methanolicus

Liu, P., Yuan, Q., Yang, X., Wang, Q., Chang, T., YaNing, B., Wu, P., Zhang, T., Yang, J., Guo, S., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116788 · Cited by 7

Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations

Dufault‐Thompson, K., Nie, C., Jian, H., Wang, F., & Zhang, Y. (2022) · mSystems · doi:10.1128/msystems.00588-22 · Cited by 7

ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization

Tamasco, G., Kumar, M., Zengler, K., Silva‐Rocha, R., & Silva, R. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-05056-4 · Cited by 7

Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12

Han, S., Kim, D., Kim, Y.-S., & Yoon, S. H. (2024) · BMC Genomics · doi:10.1186/s12864-023-09940-y · Cited by 7

mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers

Hari, A., Zarrabi, A., & Lobo, D. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae010 · Cited by 8

A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex

Cooper, H. B., Vezina, B., Hawkey, J., Passet, V., López-Fernández, S., Monk, J. M., Brisse, S., Holt, K. E., & Wyres, K. L. (2024) · Microbial Genomics · doi:10.1099/mgen.0.001206 · Cited by 7

Use of a neuron-glia genome-scale metabolic reconstruction to model the metabolic consequences of the Arylsulphatase a deficiency through a systems biology approach

Echeverri-Peña, O. Y., Salazar-Barreto, D., Rodríguez‐López, A., González, J., Alméciga-Díaz, C. J., Verano-Guevara, C. H., & Barrera, L. A. (2021) · Heliyon · doi:10.1016/j.heliyon.2021.e07671 · Cited by 7

Unveiling abundance-dependent metabolic phenotypes of microbial communities

Jiménez, N. E., Acuña, V., Cortés, M. P., Eveillard, D., & Maass, A. (2023) · mSystems · doi:10.1128/msystems.00492-23 · Cited by 7

Reconstruction of Eriocheir sinensis Y-organ Genome-Scale Metabolic Network and Differential Analysis After Eyestalk Ablation

Wang, B., Yang, J., Gao, C., Hao, T., Li, J., & Sun, J. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.532492 · Cited by 7

NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome

Gloeckler, M., Dräger, A., & Mostolizadeh, R. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.827024 · Cited by 7

A scalable method for modulating plant gene expression using a multispecies genomic model and protoplast-based massively parallel reporter assayPreprint

Jevtic, S., Drapek, C., Gaillochet, C., Brockman, A. I., Cadman, J., Flesch, T., & Kral, N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.05.626999 · Cited by 9

Niche-specific metabolic phenotypes can be used to identify antimicrobial targets in pathogens

Glass, E. M., Dillard, L. R., Kolling, G. L., Warren, A. S., & Papin, J. A. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002907 · Cited by 6

Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction

Jiang, B., Quinn-Bohmann, N., Diener, C., Nathan, V. B., Han-Hallett, Y., Reddivari, L., Gibbons, S. M., & Baloni, P. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013253 · Cited by 6

Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation

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pnnl-predictive-phenomics/csc040-gem

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