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

Reproducibility in systems biology modelling

Tiwari, K., Kananathan, S., Roberts, M. G., Meyer, J. P., Sharif Shohan, M. U., Xavier, A., Maire, M., Zyoud, A., Men, J., Ng, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.07.239855 · Cited by 131

Metabolic Modeling of Wine Fermentation at Genome Scale

Mendoza, S. N., Saa, P. A., Teusink, B., & Agosin, E. E. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-1831-8_16 · Cited by 5

Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium

Nev, O. A., Zamaraeva, E., Oliveira, R. D., Ryzhkov, I., Duvenage, L., Abou-Jaoudé, W., Ouattara, D. A., Hoving, J. C., Gudelj, I., & Brown, A. J. P. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012545 · Cited by 4

Insights into optimization of oleaginous fungi – genome-scale metabolic reconstruction and analysis of Umbelopsis sp. WA50703

Dziurzyński, M., Nowak, M. E., Furman, M., Okrasińska, A., Pawłowska, J., & Fondi, M. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.03.049 · Cited by 4

Genome-scale metabolic modeling of Ruminiclostridium cellulolyticum : a microbial cell factory for valorization of lignocellulosic biomass

Burgos, I. M. T., Øyås, O., Perret, S., Fierobe, H., & Machado, D. (2025) · mSystems · doi:10.1128/msystems.00960-25 · Cited by 4

Systematic engineering of Micromonospora echinospora cell factory for gentamicin C1a overproduction

Xu, F., Gao, H., Ben, R., Hu, K., Wang, Y., Mohsin, A., Guo, Y., Li, X., Hang, H., Chu, J., et al. (2026) · Trends in biotechnology · doi:10.1016/j.tibtech.2025.12.006 · Cited by 4

Pangenome-Scale Mathematical Modelling of ANAMMOX Bacteria Metabolism

Bielski, R. G., & Islam, M. A. (2024) · SynBio · doi:10.3390/synbio2010005 · Cited by 4

Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae

Paulay, A., Grimaud, G. M., Caballero, R., Laroche, B., Leclerc, M., Labarthe, S., & Maguin, E. (2024) · mSystems · doi:10.1128/msystems.00153-24 · Cited by 4

Data integration strategies for whole-cell modeling

Tummler, K., & Klipp, E. (2024) · FEMS Yeast Research · doi:10.1093/femsyr/foae011 · Cited by 4

AI-based automated construction of high-precision Geobacillus thermoglucosidasius enzyme constraint model

Zhang, M., Shi, H., Wang, X., Zhu, Y., Li, Z., Tu, L., Zheng, Y., Xia, M., Wang, M., & Wang, M. (2024) · Metabolic Engineering · doi:10.1016/j.ymben.2024.10.006 · Cited by 4

Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions

Leonidou, N., Renz, A., Winnerling, B., Grekova, A., Grein, F., & Dräger, A. (2025) · mSystems · doi:10.1128/msystems.00418-25 · Cited by 4

Genome-Scale Metabolic Modelling of the Drosophila Melanogaster Gut Microbial Community Uncovers Growth Promoting Metabolite Exchange

Schönborn, J. W., Stewart, F., Maas-Enriquez, K., Akhtar, I., Droste, A., Waschina, S., & Beller, M. (2021) · iScience · doi:10.1016/j.isci.2021.103216 · Cited by 5

A Beginner’s Guide to the COBRA Toolbox

Navid, A. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1585-0_15 · Cited by 4

Critical assessment of genome-scale metabolic models of Arabidopsis thaliana

Amirzakaria, J. Z., Marashi, S., Malboobi, M. A., Lohrasebi, T., & Forouzan, E. (2021) · Molecular Omics · doi:10.1039/d1mo00351h · Cited by 4

Unveiling metabolic pathways involved in the extreme desiccation tolerance of an Atacama cyanobacterium

Moore, R. A., Azúa-Bustos, A., González‐Silva, C., & Carr, C. E. (2023) · Scientific Reports · doi:10.1038/s41598-023-41879-8 · Cited by 4

Isolating structural errors in reaction networks in systems biology

Shin, W., & Hellerstein, J. L. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa720 · Cited by 4

Genome-scale reconstruction and metabolic modelling of the fast-growing thermophile Geobacillus sp. LC300

Ljungqvist, E., & Gustavsson, M. (2022) · Metabolic Engineering Communications · doi:10.1016/j.mec.2022.e00212 · Cited by 4

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

Tamasco, G. (2022) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/d.17.2022.tde-08112022-173558 · Cited by 4

Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic modelsPreprint

Vezina, B., Watts, S. C., Hawkey, J., Cooper, H. B., Judd, L. M., Jenney, A. W. J., Monk, J. M., Holt, K. E., & Wyres, K. L. (2023) · eLife · doi:10.7554/elife.87406.1 · Cited by 4

Unification of cell-scale metabolic activity with biofilm behavior by integration of advanced flow and reactive-transport modeling and microfluidic experimentsPreprint

Zhao, J., Zarabadi, M. P., Hall, D. M., Dahal, S., Greener, J., & Yang, L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.25.577134 · Cited by 4

Multi-omics analysis and genome-scale metabolic reconstruction of cattle Bos taurus for optimal production of cultured meatPreprint

Lee, J., Kim, J., Bae, H., Kim, M., Jung, B. K., Kim, J., Lee, S., & Kim, H. U. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.09.627468 · Cited by 4

Improving poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesis with the construction of a genome-scale metabolic model for Haloferax mediterranei

Gao, Q., Zhang, L., Huang, W., Zhang, Y., Hewage, R., Zhou, M., Xu, Y., Han, Y., Yu, J., Wang, Z., et al. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.146335 · Cited by 3

GEMsembler: consensus model assembly and structural comparison of genome-scale metabolic models across tools improve functional performance

Matveishina, E., Bartmanski, B. J., Benito-Vaquerizo, S., & Zimmermann‐Kogadeeva, M. (2025) · mSystems · doi:10.1128/msystems.00574-25 · Cited by 3

Health-associated key gut microbiota drives the variation in community metabolic interactions in non-human primates

Gao, S., Lan, L., Li, Y., Chen, T., & Fan, P. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116477 · Cited by 3

Genome‐scale Metabolic Modeling Guided Escherichia coli Engineering for De Novo Biosynthesis of Chrysanthemic Acid

Yu, J., Cheng, K., Qu, S., Wang, J., Wang, X., Zhao, C., & Li, W. (2025) · Advanced Science · doi:10.1002/advs.202512736 · Cited by 3

Proteome constrained metabolic modeling of Sus scrofa muscle stem cells for cultured meat production

Qiu, S., Kratochvilova, E., Huang, W. E., Cui, Z., Agnew, T., Yang, A., & Ye, H. (2026) · Metabolic Engineering · doi:10.1016/j.ymben.2026.01.001 · Cited by 3

2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction

Yepes-García, J., & Falquet, L. (2026) · mSystems · doi:10.1128/msystems.00844-25 · Cited by 3

Methanotroph-driven phosphorus recovery for sustainable wastewater management

Wang, Z. J., Li, H.-Z., Tang, Y., Gan, L., Wang, D., Yan, Y., He, P., Cai, H., Zhu, Y., Cui, L., et al. (2026) · Nature Sustainability · doi:10.1038/s41893-026-01807-w · Cited by 3

AI-driven discovery of probiotic gene modules and their functional impact in food and health

Alshatari, S. S., & Ziarno, M. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1870115 · Cited by 3

Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas

Kishk, A., Pacheco, M. P., Heurtaux, T., & Sauter, T. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae199 · Cited by 3

Exploring the resilience and stability of a defined human gut microbiota consortium: An isothermal microcalorimetric study

Kattel, A., Aro, V., Lahtvee, P., Kazantseva, J., Jõers, A., Nahku, R., & Belouah, I. (2024) · MicrobiologyOpen · doi:10.1002/mbo3.1430 · Cited by 3

Intratumoral Heterogeneity and Metabolic Cross-Feeding in a Three-Dimensional Breast Cancer Culture: An In Silico Perspective

Arellano-Villavicencio, J. E., Vázquez-Jiménez, A., Vázquez-Jiménez, A., Oropeza-Valdéz, J., Padrón-Manrique, C., Prado-Garcı́a, H., & Tovar, A. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252010894 · Cited by 3

MCC: automated mass and charge curation at the genome scale applied to C. tuberculostearicum

Mostolizadeh, R., Mier, F., & Dräger, A. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.03200-24 · Cited by 3

Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in Chlamydia trachomatis persistence

Chowdhury, N. B., Pokorzynski, N., Rucks, E. A., Ouellette, S. P., Carabeo, R. A., & Saha, R. (2024) · mSystems · doi:10.1128/msystems.00717-24 · Cited by 3

Genome reconstructions of metabolism of Plasmodium RBC and liver stages

Chiappino-Pepe, A., Pandey, V., & Billker, O. (2021) · Current Opinion in Microbiology · doi:10.1016/j.mib.2021.08.006 · Cited by 3

Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation

Nursimulu, N., Moses, A. M., & Parkinson, J. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010452 · Cited by 3

Overview: Standards for Modeling in Systems Medicine

Dräger, A., & Waltemath, D. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-816077-0.00001-7 · Cited by 3

Curating COBRA Models of Microbial Metabolism

Navid, A. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1585-0_14 · Cited by 3

Evaluating and deploying genome-scale metabolic models for microbial cell factories

Pham, N. (2021) · doi:10.18174/537210 · Cited by 3

A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plantsPreprint

Ginatt, A. A., Berihu, M., Castel, E., Medina, S., Carmi, G., Faigenboim‐Doron, A., Sharon, I., Tal, O., Droby, S., Somera, T. M., et al. (2024) · eLife · doi:10.7554/elife.94558 · Cited by 3

SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models

Shin, W., Hellerstein, J. L., Munarko, Y., Neal, M. L., Nickerson, D. P., Rampadarath, A. K., Sauro, H. M., & Gennari, J. H. (2021) · doi:10.1101/2021.10.09.463757 · Cited by 2

Constraints on Metabolic Network Analysis in Bacterial Physiology

Zim, M., Euler, C., & Scott, M. (2025) · PRX Life · doi:10.1103/prxlife.3.022001 · Cited by 2

Unraveling metabolic preferences and syntrophy in anaerobic methanogenesis under meso-thermophilic conditions through omics and flux balance analysis

Wu, H., Song, Y., Gong, Y., Shou, Y., Qin, Y., Chen, H., Gan, J., Wu, W., & Lü, Z. (2025) · Chemical Engineering Journal · doi:10.1016/j.cej.2025.166596 · Cited by 2

Predicting Strain-Specific Metabolic Capabilities in the Genus Pseudomonas with a Flux-to-AI Approach Reveals Hidden Cell Envelope Properties

Focil-Espinosa, C., Dalldorf, C., Martínez, D., Zepeda, A., & Zúñiga, C. (2026) · Computational and Structural Biotechnology Journal · doi:10.34133/csbj.0190 · Cited by 2

Metabolic network analysis of Crohn’s disease reveals sex- and age-specific cellular phenotypes

Moore, C. J., Batavia, M., Shao, W., Zulqarnain, F., Kolling, G. L., Greene, A., Matthews, J. D., Syed, S., & Papin, J. A. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101447 · Cited by 2

Evaluation of Genome-Scale Model Reconstruction Strategies for Lentilactobacillus kefiri DH5 and Deciphering Its Metabolic Network

Esembaeva, M. A., Kulyashov, M. A., Sokolova, T. V., Akberdin, I. R., & Sazonov, A. E. (2025) · Metabolites · doi:10.3390/metabo15120767 · Cited by 2

From Single Organisms to Communities: Modeling Methanotrophs and Their Satellites

Esembaeva, M. A., Melikhova, E. V., Kachnov, V. A., & Kulyashov, M. A. (2025) · Microorganisms · doi:10.3390/microorganisms14010003 · Cited by 2

Reconstruction of a genome-scale metabolic model for Streptococcus zooepidemicus: Comparison with Corynebacterium glutamicum to study hyaluronic acid production

Nikuiyan, Z., Tabandeh, F., Motamedian, E., Salehi, S., Talebi, M., & Ghale, R. A. (2025) · PLoS ONE · doi:10.1371/journal.pone.0335509 · Cited by 2

Triclosan induced restructuring of microbial communities and antibiotic resistance gene dynamics in activated sludge: insights and mitigation strategies

Yin, Y., Wu, H., French, C. E., & Lü, Z. (2026) · Water Research · doi:10.1016/j.watres.2026.125614 · Cited by 2

A multi-way SMILES-based hypergraph inference network for metabolic model reconstruction

Zhao, Y., Chen, Y., Yu, Y., Liu, X., Du, J., Wen, J., Liao, C., Sun, Q., Wang, R., & Chen, C. (2026) · Communications Biology · doi:10.1038/s42003-026-09761-1 · Cited by 2

Hybrid metabolic engineering enables xylose-driven co-production of polyhydroxybutyrate and violacein in Escherichia coli

Pham, K., & Lee, E. Y. (2026) · Journal of Biological Engineering · doi:10.1186/s13036-026-00653-w · Cited by 2

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Mueller, J., Krishnan, J., Wei, Q., Hefner, Y., Monk, J. M., Verkler, H., Tibocha‐Bonilla, J. D., Ayala, A., Palsson, B. Ø., Feist, A. M., et al. (2026) · mSystems · doi:10.1128/msystems.01594-25 · Cited by 2

Dietary Polysaccharides Modulate Interactions between Bacteroides and the Gut Microbiota: Gene-Level Mechanisms and Perspectives on Genome-Scale Metabolic Modeling for Community Simulation

Zhang, Y., Song, X., Ai, L., & Wang, G. (2026) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.6c03152 · Cited by 2

Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis

Gao, Y., Yuan, Q., Mao, Z., Liu, H., & Ma, H. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02357-1 · Cited by 2

Reconstruction of a Context-Specific Model Based on Genome-Scale Metabolic Simulation for Identification of Prochloraz Resistance Mechanisms in Penicillium digitatum

Zou, P., Zhang, Y., Nshimiyimana, J. B., Cao, Q., Yang, Y., Geng, H., & Li, X. (2020) · Microbial Drug Resistance · doi:10.1089/mdr.2020.0018 · Cited by 2

Conserved Virulence-Linked Metabolic Reprogramming in Clostridioides Difficile Identified Through Genome-Scale Metabolic Network AnalysisPreprint

Jenior, M. L., Leslie, J. L., Powers, D. A., Garrett, E. M., Walker, K. A., Dickenson, M. E., Petri, W. A., Tamayo, R., & Papin, J. A. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3773788 · Cited by 2

Genome‐Scale Models

Palsson, B. Ø. (2021) · Metabolic Engineering · doi:10.1002/9783527823468.ch2 · Cited by 2

Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic ModelsPreprint

Canto-Encalada, G., Armstrong, J., Focil-Espinosa, C., Ademikanra, A. F., Peeler, I., Gebbie, W., Nunez-Garcia, J., Saldivar, A., Martinez, D., & Zúñiga, C. (2023) · Preprints.org · doi:10.20944/preprints202311.0461.v1 · Cited by 2

Genome-Scale Metabolic Modeling for Diseases

Çakır, T., Abdi̇k, E., Uzuner, D., & Lüleci̇, H. B. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00227-x · Cited by 2

Integration of metabolic models in biorefinery designs using superstructure optimisation

der Hauwaert, L. V., Regueira, A., & Mauricio‐Iglesias, M. (2023) · Computer-aided chemical engineering/Computer aided chemical engineering · doi:10.1016/b978-0-443-15274-0.50358-9 · Cited by 1

Determination of the genome-scale metabolic network of Bartonella quintana str. Toulouse to optimize growth for its use as chassis for synthetic biology

Garrote-Sánchez, E., Moyá, A., & Gil, R. (2025) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2025.1527084 · Cited by 1

A survey of computational approaches for characterizing microbial interactions in microbial mats

Perillo, V. L., Nute, M., Sapoval, N., Curry, K. D., Golia, L., Yin, Y., Ogilvie, H. A., Nakhleh, L. K., Segarra, S., Bhaya, D., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03634-2 · Cited by 2

Reconstruction of a resource balance analysis model of Clostridium thermocellum examines the metabolic cost of glycolytic and cellulosome enzymes

Willis, T. C., Schroeder, W. L., Khana, D. B., Qian, X., Dahal, S., Amador‐Noguez, D., & Maranas, C. D. (2025) · Metabolic Engineering · doi:10.1016/j.ymben.2025.09.001 · Cited by 1

Mathematical models of the colonic microbiota: an evaluation of accuracy using in vitro fecal fermentation data

da Silva, V. G., Smith, N. W., Mullaney, J. A., Roy, N. C., Wall, C. R., & McNabb, W. C. (2025) · Frontiers in Nutrition · doi:10.3389/fnut.2025.1623418 · Cited by 1

In Silico Prediction and In Vitro Validation of Bacterial Interactions in the Plant Rhizosphere Using a Synthetic Bacterial Community

Mukherjee, A., Tan, B. H. K., & Swarup, S. (2025) · BIO-PROTOCOL · doi:10.21769/bioprotoc.5496 · Cited by 1

Spectroscopy reveals cooperation in bacterial biofilm resistance: Cross-Fed metabolites enable less-resistant species to dominate Cd immobilization

Chen, J., Qu, C., Wu, C., Xing, Y., Zhang, M., Wu, Y., Gao, C., Dai, K., Huang, Q., & Cai, P. (2025) · Soil & Environmental Health · doi:10.1016/j.seh.2025.100190 · Cited by 1

Co-Metabolic Network Reveals the Metabolic Mechanism of Host–Microbiota Interplay in Colorectal Cancer

Wang, H.-W., Li, W., Ma, Q.-J., Zhang, H.-Y., Quan, Y., & Zhu, Q. (2026) · Metabolites · doi:10.3390/metabo16010064 · Cited by 1

From Genome to Function: Metabolism-Wide Models of Lifecycle Stages of Parasites

Pinto, B. R., Montanaro, G. T., Alencar, M. B., Hoving, M., Haanstra, J. R., Silber, A. M., & Grigaitis, P. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5142-1_19 · Cited by 1

Cross-scale modeling of bacteria-contaminant spatiotemporal dynamics in 3D bioprinted hydrogel for dye biodegradation

Guo, W., Hou, Y., Xing, W., Xu, R., Ma, J., Wang, A.-J., Ren, N., & Huang, C. (2026) · Bioresource Technology · doi:10.1016/j.biortech.2026.134171 · Cited by 1

A Required Sensitivity Analysis for Predictive Reliability of Genome–Scale Metabolic Networks: Probing Biomass, Nutrient Conditions, and Specialised Metabolism With Penicillium rubens as a Case Study

Nègre, D., Larhlimi, A., & Bertrand, S. (2026) · Biotechnology and Bioengineering · doi:10.1002/bit.70181 · Cited by 1

Integrating fed‐batch pulse feeding and flux balance analysis for PHB production by Cupriavidus necator from cassava‐based dextrose

Ascencio-Galván, M. L., López-Agudelo, V. A., Dräger, A., Caicedo, J. C., Ríos, D. G., Andler, R., & Ramírez-Malule, H. (2026) · Journal of Chemical Technology & Biotechnology · doi:10.1002/jctb.70160 · Cited by 1

Enzyme-constrained genome-scale model of Yarrowia lipolytica predicts growth-phase specific metabolic engineering targets

Biaggi, J. S. D., Park, Y. K., Kerkhoven, E. J., Ledesma‐Amaro, R., & Lahtvee, P. (2026) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-026-13791-4 · Cited by 1

EHMN 2026: A Thermodynamically Refined, SBML-Standardised Human Metabolic Network for Genome-Scale Analysis and QSP Integration

Goryanin, I., Slovianov, L., Checkley, S., & Goryanin, I. (2026) · Metabolites · doi:10.3390/metabo16040236 · Cited by 1

Transcriptome-constrained genome-scale metabolic modeling reveals central carbon and amino acid metabolic reprogramming underlying colistin-sulbactam synergy in Acinetobacter baumannii

Bian, X., Zhu, Y., Liu, X., Li, X., Li, W., Zhao, J., Li, J., & Zhang, J. (2026) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01848-25 · Cited by 1

Incorporation of Cryptic Plasmid Energetics Improves Genome‐Scale Metabolic Predictions in Probiotic E. coli Nissle 1917

Corbín-Agustí, P., Arévalo-Lalanne, A., Álvarez, P., Enrique, M., Ramón, D., Peretó, J. G., & Tortajada, M. (2026) · Microbial Biotechnology · doi:10.1111/1751-7915.70361 · Cited by 1

Bioinformatics roadmap for characterizing the gut microbiome to study its interactions and associations with the gut mucosal immune system

Anwar, M. Z., Prieto, M. D., & Hsiao, W. (2026) · Mucosal Immunology · doi:10.1016/j.mucimm.2026.100375 · Cited by 1

Genome-scale metabolic modelling of the priority fungal pathogen Lichtheimia corymbifera

Dimitriew, W., Acosta-España, J. D., Krüger, T., Kniemeyer, O., Panagiotou, G., Schuster, S., Brakhage, A. A., Voigt, K., & Schäuble, S. (2026) · microLife · doi:10.1093/femsml/uqag025 · Cited by 1

The role of computational cellular models in industrial bioprocesses: From genetic engineering to plant design

Garcia, S. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.108962 · Cited by 1

Mycobacterial metabolic model development for drug target identification

Bannerman, B. P., Oarga, A., & Júlvez, J. (2023) · Gigabyte · doi:10.46471/gigabyte.80 · Cited by 1

Genome-Scale Metabolic Models in Fungal Pathogens: Past, Present, and Future

Fonseca-Fernández, A. L., Barrios, A. F. G., & Ramírez, A. M. C. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251910852 · Cited by 1

COmmunity and Single Microbe Optimisation System (COSMOS)

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