Citations¶
Publications that cited COBRA Toolbox¶
Rosina Nkuna, Nikwando Mohlomi, and Tonderayi S. Matambo. From omics to applications: how bioinformatics and multi-omics approaches are revolutionizing metal bioleaching. 16(1):56–56, 2026. [DOI].
Togo Yamada, Pamella Apriliana, Prihardi Kahar, Tomoya Kobayashi, Yutaro Mori, and Chiaki Ogino. Genome-scale modeling-guided metabolic engineering enables heterologous production of 3-amino-4-hydroxybenzoic acid in streptomyces thermoviolaceus. 12(2):108–108, 2026. [DOI].
Chunhao Gu, Ville Mustonen, and Paula Jouhten. <i>in silico</i> prediction of metabolic trait robustness in microbial cells. ():, 2026. [DOI].
Delphine Nègre, Abdelhalim Larhlimi, and Samuel Bertrand. A required sensitivity analysis for predictive reliability of genome–scale metabolic networks: probing biomass, nutrient conditions, and specialised metabolism with <i>penicillium rubens</i> as a case study. 123(5):1350–1363, 2026. [DOI].
Pratik Ramchandra Chaudhari, Alisha Zaffar, Muhil Raj Prabhakar, Balasubramanian Paramasivan, and Bikash Chandra Maharaj. Constraint-based mathematical model analysis reveals glycogen and cellulose storage competition during conversion of co2 to hyaluronic acid in chlorella vulgaris. ():, 2026. [DOI].
Bushra Dohai, Diana C. El Assal, Mina Kang, Ashish Jaiswal, Christophe Poulet, Sarah Daakour, David R. Nelson, Pascal Falter‐Braun, Jean‐Claude Twizere, and Kourosh Salehi‐Ashtiani. Conserved metabolic vulnerabilities across pathogenic coronaviruses nominate host-directed therapeutic targets. ():, 2026. [DOI].
Maria Elena Maccari, Christoph König, Geoffroy Andrieux, Patrick Küry, Sarah A. Berger, Jasmin Mann, Beth Kelly, Simon Völkl, Chenglong Huang, Martin Helmstädter, Simon Lagies, Marco Fischer, Francesc Baixauli, Oliver Gorka, Olaf Groß, Markus Hufnagel, Sarah Salou, Susan Farmand, Sabine Heine, V Schuster, W Willenbacher, Gregor Dückers, Bodo Grimbacher, Klaus Warnatz, Friedrich G. Kapp, Myriam Lorenz, Miriam Groß, Jens Wittner, Roland Elling, Luca Scorrano, Iwona A. Koenig, B Bengsch, Carsten Speckmann, Bernd Kammerer, M Börries, Klaus Schwarz, Johannes Hertel, Erika L. Pearce, Stephan Ehl, Ramon I. Klein Geltink, and Anne Rensing-Ehl. Fas-controlled t cells drive lymphoproliferation through glycolysis without effector differentiation. 2(4):e20250233–e20250233, 2026. [DOI].
Maziya Ibrahim and Karthik Raman. Constraint-based modeling of microbial communities for metabolite production. 3006():221–231, 2026. [DOI].
Jing Wui Yeoh, C. Pawan K. Patro, L L Wong, and Chueh Loo Poh. Comprehensive evaluation of llm capabilities for interpretation and analysis of genome-scale metabolic models in metabolic engineering. ():, 2026. [DOI].
Sania Rehman, Kaiser Iqbal Wani, M. Naeem, and Tariq Aftab. Introduction to systems biology in crop improvement. ():1–16, 2026. [DOI].
Marco Polo Castillo-Villalba. Topological environment in genetic and metabolic networks. ():, 2026. [DOI].
Michele Giovannini, Emanuele Bosi, Walter Vieri, Luana Presta, Elisa Viciani, Ilaria Bernabei, Giulia Nannini, Mark Stares, Hilary P. Browne, Trevor D. Lawley, Thomas Sauter, Elisabeth Letellier, Jessica Karta, Amedeo Amedei, R Fani, and Marco Fondi. Modelling fusobacterium lifestyles transitions by integrating transcriptomics and growth data. 10():100573–100573, 2026. [DOI].
Marjan M. Naeini, Mengyuan Pang, Neha Rohatgi, Sinem Kadioglu, Umesh Ghoshdastider, Renzo G. DiNatale, Roy Mano, A. Ari Hakimi, and A. Skanderup. Convergent genomic and molecular features predict risk of metachronous metastasis in clear cell renal cell carcinoma. 6(1):, 2026. [DOI].
Neema Jamshidi and Sanjay K. Nigam. Aryl hydrocarbon receptor in the kidney regulates metabolic cross-talk with the liver and gut microbiome. 16(1):, 2026. [DOI].
Zahra Ghasemi Naraghi, Ehsan Motamedian, and Seyed Abbas Shojaosadati. Enhancing electron generation in a microbial fuel cell using a regulated microbial community by systemic metabolic modeling. 566():148710–148710, 2026. [DOI].
Guangqi Shan, Yingqi Zhao, Haolin Han, Boyuan Xue, Shaojie Wang, and Haijia Su. Reprogramming xylose metabolism for sustainable cadaverine production in engineered escherichia coli. ():, 2026. [DOI].
Miguel Pacheco, Pedro Montenegro-Silva, Fernando Dourado, Miguel Gama, Lucı́lia Domingues, and Óscar Dias. Biology tools for optimizing bacterial cellulose production. ():25–52, 2026. [DOI].
Hayden Gallo and Vanni Bucci. Dynamical systems–constrained metabolic modeling enables forecasting of host-microbiome dynamics. ():, 2026. [DOI].
Sandra Itzel Gomez Romero, Mark Vigliotti, Victoria Ramirez Lopez, Kyle Nguyen, Valeria Marchitto, and Nanette Boyle. Issus3744: a genome-scale model-guided strategy for rational media design for cultivated pork. ():, 2026. [DOI].
Johan Nicolas Anzola, Diana Marcela Bernal Franco, Andrés Fernando González Barrios, and María Francisca Villegas Torres. Tissue-specific genome-scale metabolic models of erythroxylum novogranatense reveal distinct leaf-root metabolism beyond cocaine. ():, 2026. [DOI].
Thotagamuwe Widanage Nipuni Kasunika Perera. Uncovering extended functions of artificial intelligence in the mass production of microbial metabolites. ():49–108, 2026. [DOI].
Phillip R. Clauer, Angelina Nou, Tyler Toth, Qiguo Yu, Yonatan Chemla, Alice Boo, Kwan Yoon, and Christopher A. Voigt. Synthetic biology of plants and microbes for agriculture, environment, and future applications. 126(2):895–1109, 2026. [DOI].
Feng Xu, Hao Gao, Rong Ben, K.P. Hu, Yuan Wang, Ali Mohsin, Yuanxin Guo, Xu Li, HaiFeng Hang, Ju Chu, and Xiwei Tian. Systematic engineering of micromonospora echinospora cell factory for gentamicin c1a overproduction. 44(5):1397–1424, 2026. [DOI].
Nabia Shahreen, Abraham Osinuga, Sunayana Malla, Tahereh Razmpour, Masoud Tabibian, and Rajib Saha. Multi-omics integration in genome-scale metabolic models: a review of constraint-based approaches. 22(2):, 2026. [DOI].
Sophie Robertson, Himashree Ponrajan, Malvika Sharma, Loong‐Tak Lim, and Guneet Kaur. Bioprocess considerations and enabling technologies for high-efficiency precision fermentation. ():1–36, 2026. [DOI].
Simran Kaur Aulakh, Oliver Lemke, Łukasz Szyrwiel, Stephan Kamrad, Yu Chen, Johannes Hartl, Michael Muelleder, Jens Nielsen, and Markus Ralser. The molecular landscape of cellular metal ion biology. ():101677–101677, 2026. [DOI].
Yanjun Liu, Xi Luo, Samira Ranjbar, Johannes M. F. G. Aerts, Martijn van der Lienden, Andrea Dardis, and Ronan M. T. Fleming. Constraint-based modelling of metabolic dysregulation in gaucher disease: mitochondrial dysfunction and disrupted cholesterol homeostasis. 21(1):, 2026. [DOI].
Alvin Lu, Liam P. Kelley, Ilija Dukovski, and Daniel Segrè. Dynamic metabolic modelling of atp allocation during viral infection. 23(235):, 2026. [DOI].
Thomas A. Pugsley, Guy T. Hanke, and Christopher D. P. Duffy. Evaluating transcriptomic integration for cyanobacterial constraint-based metabolic modelling. 6():1715377–1715377, 2026. [DOI].
Junli Liu, Deyong Zeng, Bichun Hu, Weiping Wang, Shuaimin Hu, Alejandro Cifuentes, Guojian Liao, Mengfei Long, Haitian ZHAO, and Weihong Lu. Precision nutrition and food biomanufacturing for space missions: toward intelligent and bioregenerative life-support systems. 231(Pt 2):118803–118803, 2026. [DOI].
Yuke He, Suttavadee Junyakul, Nachon Raethong, Massalin Nakphaichit, Solange I. Mussatto, and Wanwipa Vongsangnak. Integrated growth physiology and transcriptome profiling uncover probiotic adaptability of limosilactobacillus fermentum kub-d18. 12(3):168–168, 2026. [DOI].
Pablo Di Giusto, Dong-Hyuk Choi, Athanasios Antonakoudis, Vikash Gokul Duraikannan, Pierrick Craveur, Nicholas Luke Cowie, Tejaswini Ganapathy, Kannan Ramesh, Santiago Benavidez-López, Camila A. Orellana, Natalia E. Jiménez, Leo Alexander Dworkin, James Morrissey, Igor Marín de Mas, Benjamin Strain, Norma A. Valdez‐Cruz, Mauricio A. Trujillo‐Roldán, Jannis Marzluf, Verónica S. Martínez, Leopold Zehetner, Claudia Altamirano, Ana María Vega-Letter, Bradley Priem, Haoyu Chris Cao, Martin Hold, Junyu Ma, Yi Fan Hong, Saratram Gopalakrishnan, Blaise Manga Enuh, Chaimaa Tarzi, Kuin Tian Pang, Claudio Angione, Jürgen Zanghellini, Cleo Kontoravdi, Hooman Hefzi, Michael J. Betenbaugh, Lars K. Nielsen, Meiyappan Lakshmanan, Dong-Yup Lee, Anne Richelle, and Nathan E. Lewis. A community reconstruction of chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free cho cells. 17(6):101574–101574, 2026. [DOI].
Luisella Spiga, Ryan T. Fansler, Alexandra Grote, Madison Langford-Butler, Asia K. Miller, M J Neal, Owen F. Hale, Yifan Wu, Deepanshu Singla, M. Wade Calcutt, Abigail E. Rose, Madeline M. Bresson, Alexandra C. Schrimpe‐Rutledge, Brittany Berdy, Simona G. Codreanu, M. Kay Washington, Benjamin P. Bratton, Stacy D. Sherrod, John A. McLean, Karsten Zengler, Cynthia L. Sears, Megan G. Behringer, Andreas Gnirke, Jonathan Livny, Danyvid Olivares–Villagómez, Ashlee M. Earl, Wenhan Zhu, and Wenhan Zhu. An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut. 189(13):3968–3990.e38, 2026. [DOI].
Alex Popinga, Jack R Forman, Dmitri Svetlov, Huy D. Vo, and Brian Munsky. The stochastic system identification toolkit (ssit) to model, fit, predict, and design experiments. ():, 2026. [DOI].
Bastien Nihant, Job A.J. Verdonschot, Sonia Balăn, Eva Thielecke, Joost Luiken, Miranda Nabben, Stéphane Heymans, Marian Breuer, and Michiel Adriaens. Metabolic task analysis reveals distinct metabotypes in end-stage dilated cardiomyopathy. ():e005366–e005366, 2026. [DOI].
Danni Guo, Yuanyuan Chen, Yahong Wu, Jingmin Cheng, Wenjie Lai, Wentao Ma, Hang Yang, Lianyi Han, Lan Ma, Haidong Jia, and Xiao Liu. Multi-omics characterization of the skin microbiota reveals the anti-aging roles of stenotrophomonas maltophilia. ():, 2026. [DOI].
B. Maruthi Shankar, Sarayu Murali, Shagun Shagun, Shyam Kumar Masakapalli, Karthik Raman, and Smita Srivastava. Genome-scale metabolic model guided metabolic flux analysis in the endophyte alternaria burnsii ncim1409. 49(6):1567–1578, 2026. [DOI].
M. Krishnamurthy, Harish P S, and Abhishek Subramanian. Naviflux: a visualization-centric platform for interactive analysis, refinement and design of genome-scale metabolic networks. ():, 2026. [DOI].
Melvin Li, Bradley Priem, Luke V. Loftus, M. Betenbaugh, Kenneth J. Pienta, and Sarah R. Amend. Drug-tolerant persister cells reallocate carbon sources to fuel antioxidant metabolism for survival. ():, 2026. [DOI].
Bram Nap, Bronson R. Weston, Annette Brandt, Maximilian F. Wodak, Ina Bergheim, and Ines Thiele. The nutrition toolbox permits <i>in silico</i> generation, analysis, and optimization of personalized diets through metabolic modelling. 6(1):vbaf325–vbaf325, 2026. [DOI].
Cyriel A.M. Huijer, Jiao Xiang, Yun Chen, and Rosemary Yu. Improved flux profiling in genome-scale modeling of human cell metabolism. 6(1):101275–101275, 2026. [DOI].
Jia Zhang, Wei Xing, Yannan Hou, Jianfeng Liu, Nanqi Ren, Hongwu Ma, Aijie Wang, Qianqian Yuan, and Cong Huang. Metabolic rewiring and osmoregulation in halotolerant oceanimonas sp. gk1 under salinity stress: insights from genome-scale modeling and transcriptomics for saline wastewater biotreatment. ():, 2026. [DOI].
Nachon Raethong, Preecha Patumcharoenpol, and Wanwipa Vongsangnak. Modeling diet-gut microbiome interactions and prebiotic responses in thai adults. 12(1):, 2026. [DOI].
Leon F. Toro-Navarro, Laura Pinilla-Mendoza, and Rigoberto Ríos‐Estepa. Dynamic metabolic modeling of streptomyces clavuligerus in complex medium highlights nutrient-dependent metabolic transitions associated with clavulanic acid biosynthesis. 21(2):e0342057–e0342057, 2026. [DOI].
Pablo Reina-Gonzalez, Müberra Fatma Cesur, Aiesha Anchan, Abdulla Abu-Salah, Tunahan Cakir, Emir Malovic, and Souvarish Sarkar. Comparative proteomic analysis of environmental and genetic models of parkinson’s disease highlights the role of purine metabolism. ():, 2026. [DOI].
Thummarat Paklao, Apichat Suratanee, and Kitiporn Plaimas. Igm: integrated gene-expression modeling for multi-condition flux-preserving genome-scale metabolic models. 21(2):e0342294–e0342294, 2026. [DOI].
Diego Alejandro Núñez Valderrama, Camila Krauss, Maria Gomes Fernandes, Judith M. Vlaar, Amy Cochrane, José Ricardo Pérez-Correa, Alejandro I. Maass, Eduardo Agosín, and S Cynthia Mendoza. A comprehensive genome-scale metabolic model for porcine cells as a tool for process optimization and design in the cultivated meat industry. ():, 2026. [DOI].
S W Lee, Yun-Jeong Kim, Seongmo Kang, Hyuk‐Jin Cha, and Hyun Ju Kim. Multi-omics analysis and metabolic modeling reveal bcl2l1- and cpt1a-driven fatty acid oxidation in culture-adapted human embryonic stem cells with implications for cell therapy safety. 531():174074–174074, 2026. [DOI].
Huiyuan Guo, Qing Liu, Hexing Han, Weichao Xu, Wansheng Shi, Mingxing Zhao, Xin Xiao, Jianwei Liu, and Tinggang Li. Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: multi-scale responses and energy partition. 294():125552–125552, 2026. [DOI].
Pınar Kocabaş. Advances in genome-scale metabolic modeling of bacillus subtilis. 48(2):, 2026. [DOI].
Aruldoss Immanuel, Subramaniyasharma Sivaraman, Ponnusami Venkatachalam, and Venkatasubramanian Ulaganathan. Integrated production of levan and hyaluronic acid in bacillus subtilis: metabolic bottleneck analysis using enzyme constraint genome-scale modeling and process economics. 34():102656–102656, 2026. [DOI].
Samyuktha Srinivasan, Karthik Raman, and Smita Srivastava. Investigating the impact of carbamazepine on tomato plant metabolism using genome-scale metabolic modelling. 16(1):, 2026. [DOI].
Zhenhao Fu, Jiamin Zheng, Lele Zhang, Jiansheng Jian, Zhonghu Bai, and Ye Li. Modular co-culture engineering of escherichia coli and saccharomyces cerevisiae for de novo biosynthesis of tryptophol from glucose. 449():134398–134398, 2026. [DOI].
Guido Zampieri, Viktor Sandner, Suraj Verma, Julia Kraemer, Christopher Lennon, Annalisa Occhipinti, Graham McCreath, and Claudio Angione. Bioprocess optimisation via joint machine learning and metabolic modelling. 96():113–128, 2026. [DOI].
Martha L Ascencio‐Galván, Víctor A López‐Agudelo, Andreas Dräger, Julio C Caicedo, David Gómez‐Ríos, Rodrigo Andler, and Howard Ramírez‐Malule. Integrating fed‐batch pulse feeding and flux balance analysis for <scp>phb</scp> production by <i>cupriavidus necator</i> from cassava‐based dextrose. 101(5):1011–1026, 2026. [DOI].
Merve Yarıcı and Muhammed Erkan Karabekmez. Systems biology of metabolic dysregulation in ankylosing spondylitis using scrna-seq data. 30(3):146–157, 2026. [DOI].
Satyajit Beura, Amit Kumar Das, and Amit Ghosh. Tissue‐specific differential flux analysis reveals metabolic insights into pancreatic β‐cell dysfunction in type 2 diabetes. 123(6):1558–1569, 2026. [DOI].
Maria Pacheco, Evelyn Gonzalez, and Thomas Sauter. Fastercc: accelerating flux consistency testing and context-specific reconstruction for large-scale metabolic network models. ():, 2026. [DOI].
Ravineet Yadav, Mohammed A. Qasim, and Sunil A. Patil. Assessment of different strategies for acetic acid production from gaseous co <sub>2</sub> and n <sub>2</sub> feedstock using <i>clostridium ljungdahlii</i>. 40(14):7446–7457, 2026. [DOI].
Alexander T Nguyen and Bryan A Nguyen. A reproducible dual-model constraint-based framework for exploring hepatic energy metabolism under stachys affinis-derived short-chain fatty acid scenarios. ():, 2026. [DOI].
Shanzhou Huang, Chang Li, Yuyuan Zhi, Zengling Su, Fei Ma, Congcong Shi, and S Li. Revealing the role of a novel ids gene mutation in mucpolysaccharidosis type ii: insights from computational analysis. 13():1734111–1734111, 2026. [DOI].
Xinchen Zhang, Ying Wang, Wenpei Huang, C.L. Wei, Meng Zhao, Yongjin J. Zhou, and Yingjin Yuan. Sulfur assimilation determines s-adenosyl-l-methionine flux for enhancing methylation efficiency in heterologous biosynthesis. ():, 2026. [DOI].
Daniel Fässler, Katharina Wittfeld, Stefan Frenzel, Sandra Van der Auwera, Ameneh Merhjerd, Maryam Gholizadeh, Stefan Simm, Lars Kaderali, Maximilien Franck, Malte Rühlemann, Corinna Bang, Andre Franke, Nele Friedrich, Matthias Nauck, Markus M. Lerch, Frank Ulrich Weiss, Uwe Völker, Robin Bülow, Henry Völzke, Kenneth Peuker, Sebastian Zeißig, Hans Jörgen Grabe, Fabian Frost, and Johannes Hertel. Bilophila wadsworthia is linked to basal ganglia atrophy in the general population. 136():106587–106587, 2026. [DOI].
Dilara Uzuner Odongo, Roxan A. Stephenson, Linling Cheng, Linda Yang, Priyanka Narayan, Tunahan Çakır, and Madhav Thambisetty. Genome-scale metabolic modeling uncovers cell-type specific signatures associated with apoe variants. 29(5):115638–115638, 2026. [DOI].
Pavan Kumar S, Subasree Sridhar, Noor Alsmadi, Radhakrishnan Mahadevan, and Nirav Bhatt. Generalist method to reconstruct metabolic networks from multi-omics data at large-scale. ():, 2026. [DOI].
Haibo Shen, Longlin Zhang, Xiaokang Ma, Yulong Yin, Jing Wang, and Bi’e Tan. Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications. 69(7):2230–2248, 2026. [DOI].
Nilesh Anantha Subramanian, S Pavan Kumar, Raghunathan Rengaswamy, Nirav Bhatt, and Manikandan Narayanan. Modeling and dissecting bidirectional feedback in gene-metabolite systems using the causalflux method. ():, 2026. [DOI].
Yuchen Zhang, Wenkai Lai, Meiling Wang, Shirong Lai, Qing Liu, Qi Luo, Zheng Chen, Da Zhao, Ziwei Wang, and F. Yang. Gut microbial metabolic disorder in depression: insights from computational modeling and mediation analysis. 26(1):, 2026. [DOI].
Anik Khan, Samuel Breselge, A. Kate O’Mahony, Órla O’Sullivan, Paul D. Cotter, Sinéad N McCarthy, Jennifer Mahony, and John Kenny. Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food. 12(1):, 2026. [DOI].
Melvin Li, Bradley Priem, Luke V. Loftus, Michael J. Betenbaugh, Kenneth J Pienta, and Sarah R. Amend. Polyploid cancer cells surviving cisplatin reallocate central carbon sources to fuel antioxidant metabolism for survival. 108():102370–102370, 2026. [DOI].
Abhishek Subramanian, M. Krishnamurthy, and P S Harish. Naviflux: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks. 42(5):, 2026. [DOI].
Ecehan Abdi̇k and Tunahan Çakır. Personalized metabolite biomarker predictions reveal heterogeneous characteristics of parkinson’s disease. 12(1):, 2026. [DOI].
Noushin Eftekhari, Suraj Verma, Aninda Saha, Guido Zampieri, Saladin Sawan, Annalisa Occhipinti, and Claudio Angione. Fusing imaging and metabolic modeling via multimodal deep learning in ovarian cancer. 17(6):101594–101594, 2026. [DOI].
Yue Zhang, Zhigang Wang, and Weihui Xu. Biofilm synergy by agrobacterium deltaense and bacillus velezensis in co-cultures indicates bacterial interspecific cooperation. 11():100364–100364, 2026. [DOI].
Faezeh Zalpour, Elham Iranmanesh, Mojtaba Mortazavi, and Shahryar Shakeri. Enhancing squalene production in aurantiochytrium ch25 via integrated optimization strategy and genome-scale metabolic modeling. 6(3):, 2026. [DOI].
Regan Odongo and Tunahan Çakır. Metabolite-centric identification of antimetabolite drug targets across cancer and neurodegenerative diseases. 22(3):, 2026. [DOI].
Okezie Emmanuel, Christopher C. Okonkwo, Stephen A. Akinola, Hasan K. Atiyeh, and Prof. Dr. Thaddeus C. Ezeji. Metabolic synergy of species growth, solvent, and gas production in cocultures of clostridium carboxidivorans and clostridium beijerinckii. 35():102802–102802, 2026. [DOI].
William T. Scott, Luz A. Puentes Jacome, Bart Nijsse, Jinsong Wang, Gerben R. Stouten, Jasper J. Koehorst, Hauke Smidt, Elizabeth A. Edwards, Peter J. Schaap, and Robbert Kleerebezem. Unraveling the metabolic interactions of a <i>dehalobacter</i> -containing anaerobic mixed culture for bioremediation. ():, 2026. [DOI].
Josh Loecker, Narayana Pujara, William Bryant, Bhanwar Lal Puniya, Prakash Packrisamy, Ahmed Hamed, and Tomas Helikar. Mechainistic: an llm-guided multi-agent system for reasoning over genome-scale constraint-based metabolic models. ():, 2026. [DOI].
Gun-Hwi Yeon, Du-Kyeong Kang, Hyun-Jin Koo, Daewon Go, Jungyeon Kim, and Bong Hyun Sung. Enhanced production of l-fuculose by escherichia coli engineered via genome-scale metabolic modeling. 21(5):e0349374–e0349374, 2026. [DOI].
Mohammad Tauqeer Alam. Metabolic robustness is an emergent property of hierarchical network organization in yeast. 11(6):e0027626–e0027626, 2026. [DOI].
Muhammad Naufal Hakim, Porntip Chiewchankaset, Saowalak Kalapanulak, Rattiya Waeonukul, Suratsawadee Tiangpook, and Treenut Saithong. Dynamic metabolic modeling uncovers systems-level strategies to simultaneously maximize levan yield and substrate efficiency in bacillus subtilis ly7.16. 22(5):e1014273–e1014273, 2026. [DOI].
Jordi Roma Pi and Almut Heinken. Personalized constraint-based modeling of microbial communities from metagenomic data. 3006():233–260, 2026. [DOI].
Satyajit Beura, Sayan Saha Roy, Amit Kumar Das, and Amit Kumar Ghosh. Constraint-based metabolic modeling approach for microbial communities. 3006():191–220, 2026. [DOI].
Ali Nawaz, Jessye L. Schaefer, and Florian Centler. Dynamic simulation of growth and cross-feeding in microbiomes with μbialsim. 3006():317–330, 2026. [DOI].
Isha Sharma, Sakshi Bharti, Swapnil Pandey, Saksham Gupta, Prakash S. Bisen, Naveen Kango, and Kaushal K. Sharma. Leveraging computational methodologies for probiotic research: unraveling host-microbiota interactions and therapeutic potential. 2(1):100067–100067, 2026. [DOI].
Emma Lee, Ashwin Koppayi, Almudena Veiga-Lopez, and Beatriz Peñalver Bernabé. A novel network approach to identify sample-specific context-informed metabolic signatures during developmental processes. ():, 2026. [DOI].
Ashwin Arulselvan, Mahdi Doostmohammadi, and Jose Alexander Vindel Garduno. A unified bi-level framework for gene-knockout strategies. 51(5):, 2026. [DOI].
Shuaihua Chen, Teng Chen, Z Xu, L Zhang, Bei Gao, and Jiali Mao. Cytogem-xai: a hypergraph neural network framework for genome-scale metabolic modeling and interpretable analysis. ():, 2026. [DOI].
Emma M. Glass, Glynis L. Kolling, and Jason A. Papin. Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics. 11(7):2034–2046, 2026. [DOI].
Esraa Gabal, Thi Kim Oanh Nguyen, Tetiana Kovalenko, Huanyao Gao, Noa Rappaport, Cory C. Funk, Priyanka Baloni, and Eugenia Trushina. Mitochondrial complex i modulator restores network resilience in advanced alzheimer’s disease through metabolic reprogramming. ():, 2026. [DOI].
Kate E. Meeson, Rachel Gaffney, Jean‐Marc Schwartz, and Magnus Rattray. Simoff: discovering the metabolic objective of the cell. ():, 2026. [DOI].
Hatice Büşra Lüleci̇, Attila Jones, Ryan Neff, David A. Bennett, Bin Zhang, Tunahan Çakır, and Madhav Thambisetty. Unraveling aberrant metabolic patterns in alzheimer’s disease subtypes: from perturbed metabolic pathways to candidate drug targets. 63(1):, 2026. [DOI].
Defne Cig Kabakcioglu and Ceyda Kasavi. Network-based multiomics integration reveals immunometabolic convergence between covid-19 and pulmonary arterial hypertension. 30(8):479–491, 2026. [DOI].
Ross P. Carlson, Tomáš Gedeon, Mauricio Garcia Benitez, Campbell Putnam, William R. Harcombe, R MAHADEVAN, and Ashley E. Beck. Cell geometry and membrane protein crowding constrain <i>escherichia coli</i> growth rate, overflow metabolism, respiration, and maintenance energy. ():, 2026. [DOI].
Lamiaa Ibrahim Ahmed, Eman M. Taher, Karima Mogahed Fahim, Walaa G. Nadi, Hanan S. Khalefa, Mona Shaban E. M. Badawy, and Ghada Abd‐Elmonsef Mahmoud. Ai implementation in bioreactor design and optimization of the fermentation conditions for microbial metabolite production. ():301–340, 2026. [DOI].
Muhammad Zohaib Anwar, Miguel Darío Prieto, and William W.L. Hsiao. Bioinformatics roadmap for characterizing the gut microbiome to study its interactions and associations with the gut mucosal immune system. ():100375–100375, 2026. [DOI].
Noah Hutchinson, Zeyang Pang, Collins Chimezie, Brian Hamp, Amber Haley, and J Li. Systems engineering of engineered live biotherapeutics: a discovery-to-translation framework for streamlining microbiome therapeutic development. 397():115160–115160, 2026. [DOI].
Igor Goryanin, Igor Goryanin, Leonid Slovianov, Irina V. Goryanin, Irina V. Goryanin, and Alexander Kel. Ehmn2026®t: a license-aware ai-qsp integration framework linking ehmn2026® with transfac®, transpath® and humanpsd™ for diagnostic-metabolite interpretation. 16(7):469–469, 2026. [DOI].
Huili Yuan, Yang Bai, and Xiongfei Fu. Dynamic constrained allocation flux balance analysis (dcafba). 3041():399–422, 2026. [DOI].
Aamir Faisal Ansari, Gayathri Sambamoorthy, Thrisha C. Alexander, Yugandhar B. S. Reddy, Janhavi Raut, and Narendra M. Dixit. Quartet: disentangling positive and negative components of microbial interactions. 22(7):e1014502–e1014502, 2026. [DOI].
Iqra Mariam, Ulrika Rova, Paul Christakopoulos, Λεωνίδας Μάτσακας, and Alok Patel. Data-driven synthetic microbes for sustainable future. 11(1):74–74, 2025. [DOI].
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Arianna Basile, Almut Heinken, Johannes Hertel, Larry Smarr, Weizhong Li, Laura Treu, Giorgio Valle, Stefano Campanaro, and Ines Thiele. Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics. 15(1):2226921–2226921, 2023. [DOI].
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Koray Malcı, Rodrigo Santibáñez, Nestor Jonguitud‐Borrego, Jorge H. Santoyo‐Garcia, Eduard J. Kerkhoven, and Leonardo Rios‐Solis. Improved production of taxol® precursors in s. cerevisiae using combinatorial in silico design and metabolic engineering. 22(1):243–243, 2023. [DOI].
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William T. Scott, David Henriques, Eddy J. Smid, Richard A. Notebaart, and Eva Balsa‐Canto. Dynamic genome‐scale modeling of <i>saccharomyces cerevisiae</i> unravels mechanisms for ester formation during alcoholic fermentation. 120(7):1998–2012, 2023. [DOI].
Marius Arend, David Zimmer, Rudan Xu, Frederik Sommer, Timo Mühlhaus, and Zoran Nikoloski. Proteomics and constraint-based modelling reveal enzyme kinetic properties of chlamydomonas reinhardtii on a genome scale. 14(1):4781–4781, 2023. [DOI].
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Christopher Riccardi, Marzia Calvanese, Veronica Ghini, Tania Alonso-Vásquez, Elena Perrin, Paola Turano, Giorgio Giurato, Alessandro Weisz, Ermenegilda Parrilli, Maria Luisa Tutino, and Marco Fondi. Metabolic robustness to growth temperature of a cold- adapted marine bacterium. 8(2):e0112422–e0112422, 2023. [DOI].
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Johannes Hertel, Almut Heinken, Daniel Fässler, and Ines Thiele. Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses. 3(10):100615–100615, 2023. [DOI].
Patrick E. Gelbach and Stacey D. Finley. Genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer. 26(9):107569–107569, 2023. [DOI].
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Naroa Barrena, Luis V. Valcárcel, Danel Olaverri-Mendizabal, Iñigo Apaolaza, and Francisco J. Planes. Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells. 9(1):32–32, 2023. [DOI].
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Matti Gralka. Searching for principles of microbial ecology across levels of biological organization. 63(6):1520–1531, 2023. [DOI].
Adrián Povo‐Retana, Marco Fariñas, Rodrigo Landauro‐Vera, Marina Mojena, Carlota Alvarez‐Lucena, Miguel Ángel Fernández‐Moreno, Antonio Castrillo, Juan Vladimir de la Rosa, Sergio Sánchez‐García, Carles Foguet, Francesc Mas, Silvia Marín, Marta Cascante, and Lisardo Boscá. Immunometabolic actions of trabectedin and lurbinectedin on human macrophages: relevance for their anti-tumor activity. 14():1211068–1211068, 2023. [DOI].
Yawen Li, Jingyi Qian, Jiacong Huang, Dong‐Sheng Guo, Zhi-Kui Nie, Chao Ye, and Tian‐Qiong Shi. Improving gibberellin ga<sub>3</sub> production with the construction of a genome-scale metabolic model of <i>fusarium fujikuroi</i>. 71(48):18890–18897, 2023. [DOI].
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Tamara Bintener, Maria Pires Pacheco, Demetra Philippidou, Christiane Margue, Ali Kishk, Greta Del Mistro, Luca Di Leo, María Moscardó Garcia, Rashi Halder, Lasse Sinkkonen, Daniela De Zio, Stephanie Kreis, Dagmar Kulms, and Thomas Sauter. Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma. 14(7):468–468, 2023. [DOI].
Garhima Arora, Mallar Banerjee, Jimpi Langthasa, Ramray Bhat, and Samrat Chatterjee. Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer. 26(11):108081–108081, 2023. [DOI].
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Shweta Shinde, Muhammed Hamdan, Prerna Bhalla, and Aravind Kumar Chandiran. Biocompatible cs<sub>2</sub>ptx<sub>6</sub> (x = cl, br, i) vacancy ordered perovskites and <i>shewanella oneidensis mr-1</i> bacteria hybrid for potential photocatalytic solar fuel production. 4(2):224–230, 2023. [DOI].
Himel Nahreen Khaleque, Hadi Nazem‐Bokaee, Yosephine Gumulya, Ross P. Carlson, and Anna H. Kaksonen. Simulating compatible solute biosynthesis using a metabolic flux model of the biomining acidophile, acidithiobacillus ferrooxidans atcc 23270. 175(1-2):104115–104115, 2023. [DOI].
Jing Yu, Xiaowei Wang, Qianqian Yuan, Jiaxin Shi, Jingyi Cai, Zhichao Li, and Hongwu Ma. Elucidating the impact of in vitro cultivation on nicotiana tabacum metabolism through combined in silico modeling and multiomics analysis. 14():1281348–1281348, 2023. [DOI].
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Nattharat Punyasu, Saowalak Kalapanulak, and Treenut Saithong. Co2 recycling by phosphoenolpyruvate carboxylase enables cassava leaf metabolism to tolerate low water availability. 14():1159247–1159247, 2023. [DOI].
Rafael Muñoz‐Tamayo, Mohsen Davoudkhani, Ibrahim Fakih, Carlos Eduardo Robles-Rodríguez, Francesco Rubino, Christopher J. Creevey, and Évelyne Forano. Review: towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies. 17():100984–100984, 2023. [DOI].
Yanhua Liu and Hans V. Westerhoff. Competitive, multi‐objective, and compartmented flux balance analysis for addressing tissue‐specific inborn errors of metabolism. 46(4):573–585, 2023. [DOI].
Darwin Carranza‐Saavedra, Jesús Torres‐Bacete, Blas Blázquez, Claudia Patricia Sánchez Henao, José E. Zapata, and Juan Nogales. System metabolic engineering of escherichia coli w for the production of 2-ketoisovalerate using unconventional feedstock. 11():1176445–1176445, 2023. [DOI].
Agris Pentjuss, Emīls Bolmanis, Anastasija Šuleiko, Elina Didrihsone, Artūrs Šuleiko, Konstantīns Dubencovs, Jānis Liepiņš, Andris Kazāks, and Juris Vanags. Pichia pastoris growth—coupled heme biosynthesis analysis using metabolic modelling. 13(1):15816–15816, 2023. [DOI].
Nunthaphan Vikromvarasiri, Shuhei Noda, Tomokazu Shirai, and Akihiko Kondo. Investigation of two metabolic engineering approaches for (r,r)-2,3-butanediol production from glycerol in bacillus subtilis. 17(1):3–3, 2023. [DOI].
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Delphine Nègre, Abdelhalim Larhlimi, and Samuel Bertrand. Reconciliation and evolution of penicillium rubens genome-scale metabolic networks–what about specialised metabolism? 18(8):e0289757–e0289757, 2023. [DOI].
Håvard Molversmyr, Ove Øyås, Filip Rotnes, and Jon Olav Vik. Extracting functionally accurate context-specific models of atlantic salmon metabolism. 9(1):19–19, 2023. [DOI].
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