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].
Chunhao Gu, Ville Mustonen, and Paula Jouhten. in silico prediction of metabolic trait robustness in microbial cells. ():, 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].
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 penicillium rubens as a case study. ():, 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].
M. Marconcini M. Giovannini, Emanuele Bosi, Walter Vieri, Luana Presta, Elisa Viciani, Ilaria Bernabei, Giulia Nannini, Mark Stares, Hilary P. Browne, Kaede V. Sullivan, Thilo 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. ():, 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].
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 in silico 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].
S. Han, Wei Xing, Yannan Hou, Jianfeng Liu, Nanqi Ren, Hai Bo Li, 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].
Feng Xu, Hao Gao, Rong Ben, K.P. Hu, Yuan Wang, Ali Mohsin, Sheng Cai, Xu Li, HaiFeng Hang, Ju Chu, and Xiwei Tian. Systematic engineering of micromonospora echinospora cell factory for gentamicin c1a overproduction. ():, 2026. [DOI].
Yanjun Liu, Xi Luo, Samira Ranjbar, Marc Johannes, 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. ():, 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].
A.Y. 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].
Pablo Reina-Gonzalez, Muberra Fatma J 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].
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].
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].
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].
Pınar Kocabaş. Advances in genome-scale metabolic modeling of bacillus subtilis. 48(2):, 2026. [DOI].
Junli Liu, Deyong Zeng, Bichun Hu, Weiwei 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].
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. ():, 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. ():, 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 cupriavidus necator from cassava‐based dextrose. ():, 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].
Nick Quinn-Bohmann, Alex V. Carr, Christian Diener, and Sean M. Gibbons. Moving from genome-scale to community-scale metabolic models for the human gut microbiome. 10(5):1055–1066, 2025. [DOI].
Deepanwita Banerjee, Javier Menasalvas, Yan Chen, Jennifer Gin, Edward E. K. Baidoo, Christopher J. Petzold, Thomas Eng, and Aindrila Mukhopadhyay. Addressing genome scale design tradeoffs in pseudomonas putida for bioconversion of an aromatic carbon source. 11(1):8–8, 2025. [DOI].
Sílvia Àvila-Cabré, Joan Albiol, and Pau Ferrer. Metabolic engineering of komagataella phaffii for enhanced 3-hydroxypropionic acid (3-hp) production from methanol. 19(1):19–19, 2025. [DOI].
Zahra Negahban, Valerie C. A. Ward, Anne Richelle, Chris McCready, and Hector Budman. Hybrid dynamic flux balance modeling approach for bioprocesses: an e. coli case study. 48(5):841–856, 2025. [DOI].
Daniel Alejandro Caballero Cerbon and Dirk Weuster‐Botz. Exchange of the l-cysteine exporter after in-vivo metabolic control analysis improved the l-cysteine production process with engineered escherichia coli. 24(1):95–95, 2025. [DOI].
Isamar-Maydeth Vidal-Silva, Antonio Loza, and Rosa-María Gutiérrez-Ríos. Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation. 41(10):384–384, 2025. [DOI].
Érica Mangaravite, Christina Cleo Vinson, Eduardo Luís Menezes de Almeida, and Thomas Christopher Rhys Williams. Genome-scale metabolic models in plant stress physiology: implications for future climate resilience. 199(2):, 2025. [DOI].
Mariam Mohagheghi, Ali Navid, Thomas Mossington, Congwang Ye, Matthew A. Coleman, and Steven Hoang-Phou. Developing a media formulation to sustain ex vivo chloroplast function. 13():1560200–1560200, 2025. [DOI].
Xavier Benedicto, Åsmund Flobak, Miguel Ponce-de-León, and Alfonso Valencia. Using constraint-based metabolic modeling to elucidate drug-induced metabolic changes in a cancer cell line. ():, 2025. [DOI].
Alexis L. Marsh, Myra B. Cohen, and Robert W. Cottingham. A tale from the trenches: applying metamorphic and differential testing to bioinformatics software. ():553–564, 2025. [DOI].
Delphine Nègre, Larhlimi Abdelhalim, and Samuel Bertrand. 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. ():, 2025. [DOI].
Albert Fina, Pierre Millard, Cécilia Bergès, Pau Ferrer, Joan Albiol, and Stéphanie Heux. High-throughput stationary 13c-based metabolic flux analysis of pichia pastoris strains. 2697():153–170, 2025. [DOI].
Xavier Benedicto, Åsmund Flobak, Miguel Ponce-de-León, and Alfonso Valencia. Constraint based modeling of drug induced metabolic changes in a cancer cell line. 11(1):111–111, 2025. [DOI].
Anna Procopio, Elvira Immacolata Parrotta, Stefania Scalise, Paolo Zaffino, R. Granata, Francesco Amato, Giovanni Cuda, and Carlo Cosentino. Hipscgem01: a genome-scale metabolic model for fibroblast-derived human ipscs. 12(10):1128–1128, 2025. [DOI].
Edda Klipp. Simulation and modeling of metabolic networks. ():, 2025. [DOI].
Lokesh Venkatesh Babu and Pramod P. Wangikar. Constraint‐based metabolic modeling of synechococcus elongatus pcc 11801 and pcc 11802 for photosynthetic biomanufacturing. ():, 2025. [DOI].
Artai R. Moimenta, Diego Troitiño-Jordedo, David Henriques, Alba Contreras-Ruíz, Romain Minebois, Miguel Morard, Eladio Barrio, Amparo Querol, and Eva Balsa‐Canto. An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the saccharomyces genus. 10(2):e0161524–e0161524, 2025. [DOI].
M. K. Weldon and Christian Euler. Physiology-informed use of cupriavidus necator in biomanufacturing: a review of advances and challenges. 24(1):30–30, 2025. [DOI].
W.S. Verwoerd and Longfei Mao. The fba solution space kernel: introduction and illustrative examples. 26(1):182–182, 2025. [DOI].
Manish Kumar, Ballamoole Krishna Kumar, Veena Shetty, R. Shyama Prasad Rao, and Pavan Gollapalli. Perspective on integrated multi-omics approaches and constraint-based modeling to explore metabolic functionality on the evolution of bacterial antibiotic resistance. 208():107999–107999, 2025. [DOI].
L S Lin, Francesco Lapi, Bruno G. Galuzzi, Marco Vanoni, Lilia Alberghina, and C. Damiani. Mechanistically informed machine learning links non-canonical tca cycle activity to warburg metabolism and hallmarks of malignancy. 21(12):e1013384–e1013384, 2025. [DOI].
Xianghua Wen, Xin Sun, and Xingyu Liu. Synergizing mechanistic and ai models for deeper insights into algal-bacterial systems in sustainable wastewater treatment. 76():108169–108169, 2025. [DOI].
Ying Zhang, Zhihao Liu, Jingmin Hu, Qing Yao, Hongfei Xu, Qing Zhang, Shouwen Chen, and Y.Y. Wang. Elucidating metabolic mechanisms underlying the influence of specific growth rate on alkaline protease synthesis in bacillus licheniformis through combined omics and computational modeling analysis. 434():132762–132762, 2025. [DOI].
Esraa Gabal, Marwah Azaizeh, and Priyanka Baloni. Investigating lipid and energy dyshomeostasis induced by per- and polyfluoroalkyl substances (pfas) congeners in mouse model using systems biology approaches. 15(8):499–499, 2025. [DOI].
Sébastien Moretti, Anne Niknejad, Marco Pagni, and Florence Mehl. Metanetx: a bridge between metabolic resources for enhanced curation and multi-omics data harmonization. 54(D1):D617–D622, 2025. [DOI].
Mohammad Zim, Christian Euler, and Matthew P. Scott. Constraints on metabolic network analysis in bacterial physiology. 3(2):, 2025. [DOI].
Ruijian Shao, Zhe Huang, Su Sun, Hongbo Yu, Shangxian Xie, and Fuying Ma. Constructing metabolic pathway of lignin monomers and their derivatives based on metabolic recombination models and yield models. 434():132786–132786, 2025. [DOI].
Joseph Zavorskas, Penny Vlahos, Kristina Wagstrom, and Ranjan Srivastava. Dynamic flux balance analysis reveals climate‐driven shifts in arctic diatom succession and bloom dynamics. 31(7):e70339–e70339, 2025. [DOI].
Alvaro R. Lara, Marie B. Andersen, Anna Madsen, Kathrine Gravlund Fønss, Marta Irla, Hilal Taymaz‐Nikerel, Luz María Martínez, Max Daniel Dicke, Marcel Mann, Jørgen Barsett Magnus, and Guillermo Gosset. Biomanufacturing potential of streamlined cells. 122(12):3309–3318, 2025. [DOI].
P. M. Priyadarshan and Rodomiro Ortíz. Voyage of plant breeding to 2050. ():3–78, 2025. [DOI].
Sumit Tiwari, Lumbini Devi Darapu, and Prateek Gupta. Systems biology approach for plant breeding. ():637–657, 2025. [DOI].
María Masid, Ioanna A. Rota, David Barras, Flavia De Carlo, Pierpaolo Ginefra, Matthieu Desbuisson, Yaquelin Ortiz-Miranda, Dmitriy Zamarin, Sohrab P. Shah, Nicola Vannini, George Coukos, Denarda Dangaj-Laniti, and Vassily Hatzimanikatis. Computational inference of metabolic programs: a case study analyzing the effect of brca1 loss. ():, 2025. [DOI].
Qiannan Peng, Cheng Zhao, Xiaopeng Wang, Kai Cheng, Congcong Wang, Xihui Xu, and Lu Lin. Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium. 16(1):639–639, 2025. [DOI].
Xiaowei Li, Yanyan Wang, Xin Chen, Leon Eisentraut, Chunjun Zhan, Jens Nielsen, and Yun Chen. Modular deregulation of central carbon metabolism for efficient xylose utilization in saccharomyces cerevisiae. 16(1):4551–4551, 2025. [DOI].
Biki Bapi Kundu, Jayanth Krishnan, Richard Szubin, Arjun Patel, Bernhard Ø. Palsson, Daniel C. Zielinski, and Caroline M. Ajo‐Franklin. Extracellular respiration is a latent energy metabolism in escherichia coli. 188(11):2907–2924.e23, 2025. [DOI].
Anthony L. Shiver, Jiawei Sun, Rebecca N. Culver, Arvie Violette, Coral Wynter, Marta Nieckarz, Samara Paula Mattiello, Prabhjot Kaur Sekhon, Francesca Bottacini, Lisa Friess, Hans K. Carlson, Daniel P.G.H. Wong, Steven K. Higginbottom, Meredith Weglarz, Weigao Wang, Benjamin D. Knapp, Emma R. Guiberson, Juan M. Sánchez, Po‐Hsun Huang, Paulo Alonso Gaona-García, Cullen Buie, Benjamin H. Good, Brian C. DeFelice, Felipe Cava, Joy Scaria, Justin L. Sonnenburg, Douwe van Sinderen, Adam M. Deutschbauer, and Kerwyn Casey Huang. Genome-scale resources in the infant gut symbiont bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions. 188(7):2003–2021.e19, 2025. [DOI].
Lijuan Liao, Mengjun Xie, Xiaoshan Zheng, Zhou Zhao, Zixin Deng, and Jiangtao Gao. Molecular insights fast-tracked: ai in biosynthetic pathway research. 42(5):911–936, 2025. [DOI].
Diego Tec-Campos, Juan D. Tibocha‐Bonilla, Chunguo Jiang, Anurag Passi, Deepan Thiruppathy, Cristal Zúñiga, Camila Posadas, Alejandro Zepeda, and Karsten Zengler. A genome-scale metabolic model for the denitrifying bacterium thauera sp. mz1t accurately predicts degradation of pollutants and production of polymers. 21(1):e1012736–e1012736, 2025. [DOI].
Jun Feng, Qingke Wang, Xiaolong Guo, Jialei Hu, Geng Wang, Li Lü, Zhen Qin, Hongxin Fu, Jufang Wang, and Shang‐Tian Yang. Metabolic engineering of clostridium tyrobutyricum for high-yield n-butanol production by increasing intracellular reducing equivalent with nadph-dependent 3-hydroxybutyryl-coa dehydrogenase. 14(6):2341–2353, 2025. [DOI].
Simran Kaur Aulakh, Oliver Lemke, Łukasz Szyrwiel, Stephan Kamrad, Yu Chen, Johannes Hartl, Michael Mülleder, Jens Nielsen, and Markus Ralser. The molecular landscape of cellular metal ion biology. 16(7):101319–101319, 2025. [DOI].
Jintao Lu, Beining Wang, Xiqiang Liu, Jung‐Kul Lee, Vipin Chandra Kalia, and Chunjie Gong. Revolutionizing caffeic acid production: advanced microbial metabolic engineering and synthetic biology approaches. 20(8):e70091–e70091, 2025. [DOI].
Juan Pablo Molina Ortiz, Dale D. McClure, Andrew Holmes, Stuart A. Rice, Mark Read, and Erin R. Shanahan. Genome-scale metabolic modelling of human gut microbes to inform rational community design. 17(1):2534673–2534673, 2025. [DOI].
Almut Heinken, Timothy Otto Hulshof, Bram Nap, Filippo Martinelli Boneschi, Arianna Basile, Amy O’Brolchain, Neil Francis O’Sullivan, Celine Gallagher, E.L. Magee, Francesca McDonagh, Ian Lalor, Maeve Bergin, Phoebe Evans, Rachel Daly, Ronan Farrell, Robert Delaney, Saoirse Hill, Saoirse Roisin McAuliffe, Trevor Kilgannon, Ronan M. T. Fleming, Cyrille C. Thinnes, and Ines Thiele. A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. 16(2):101196–101196, 2025. [DOI].
Nora Scherer, Daniel Fässler, Oleg Borisov, Yurong Cheng, Pascal Schlosser, Matthias Wuttke, Stefan Haug, Yong Li, Fabian Telkämper, Suraj Patil, Heike Meiselbach, Christina S.F. Wong, Urs Berger, Peggy Sekula, Anselm Hoppmann, Ulla T. Schultheiß, Sahar V. Mozaffari, Yannan Xi, Robert Graham, Miriam Schmidts, Michael Köttgen, Peter J. Oefner, Felix Knauf, Kai‐Uwe Eckardt, Sarah C. Grünert, Karol Estrada, Ines Thiele, Johannes Hertel, and Anna Köttgen. Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits. 57(1):193–205, 2025. [DOI].
Shamsur Rehman, Muhammad Ibtisam Nasar, Cristina Sousa Mesquita, Souhaila Al Khodor, Richard A. Notebaart, Sascha Ott, Sunil Mundra, Ramesh P Arasardanam, Khalid Muhammad, and Mohammad Tauqeer Alam. Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions. 26(4):, 2025. [DOI].
Sungwon Jung. Advances in functional analysis of the microbiome: integrating metabolic modeling, metabolite prediction, and pathway inference with next-generation sequencing data. 63(1):e:2411006–e:2411006, 2025. [DOI].
Alise Žagare, Jānis Kurlovičs, Catarina Serra-Almeida, Daniele Ferrante, Daniela Frangenberg, Armelle Vitali, Gemma Gomez‐Giro, Christian Jäger, Paul Antony, Rashi Halder, Rejko Krueger, Enrico Glaab, Egils Stalidzāns, Giuseppe Arena, and Jens C. Schwamborn. Insulin resistance compromises midbrain organoid neuronal activity and metabolic efficiency predisposing to parkinson’s disease pathology. 16():20417314241295928–20417314241295928, 2025. [DOI].
Chunjun Zhan, Guangxu Lan, Qingyun Dan, Ning Qin, Allie Pearson, Peter Mellinger, Yuzhong Liu, Zilong Wang, Seokjung Cheong, Chang Dou, Chenyi Li, Robert W. Haushalter, and Jay D. Keasling. Hybrid biological-chemical strategy for converting polyethylene into a recyclable plastic monomer using engineered corynebacterium glutamicum. 90():106–116, 2025. [DOI].
Òscar Puiggené, Jaime Muñoz-Triviño, Laura Civil-Ferrer, Line Gille, Helena Schulz-Mirbach, Daniel Bergen, Tobias J. Erb, Birgitta E. Ebert, and Pablo I. Nikel. Systematic engineering of synthetic serine cycles in pseudomonas putida uncovers emergent topologies for methanol assimilation. 43(10):2539–2565, 2025. [DOI].
Lena Peters, Moritz Drechsler, Michael A. Herrera, Jing Liu, Barbara Pees, Johanna Jarstorff, Anna Czerwinski, Francesca Lubbock, Georgia Angelidou, Liesa Salzer, Karlis Arturs Moors, Nicole Paczia, Yi‐Ming Shi, Hinrich Schulenburg, Christoph Kaleta, Michael Witting, Manuel Liebeke, Dominic J. Campopiano, Helge B. Bode, and Katja Dierking. Polyketide synthase-derived sphingolipids mediate microbiota protection against a bacterial pathogen in c. elegans. 16(1):5151–5151, 2025. [DOI].
Dilara Uzuner, Atılay İlgün, Fatma Betül Bozkurt, and Tunahan Çakır. A personalized metabolic modelling approach through integrated analysis of rna-seq-based genomic variants and gene expression levels in alzheimer’s disease. 8(1):502–502, 2025. [DOI].
Drew Alessi, Chloe V. McCreery, and Ali R. Zomorrodi. In silico dietary interventions using whole-body metabolic models reveal sex-specific and differential dietary risk profiles for metabolic syndrome. 16():1586750–1586750, 2025. [DOI].
Amal Saeed Alblooshi, Muhammad Ibtisam Nasar, Shamsur Rehman, and Mohammad Tauqeer Alam. Genomic and metabolic network properties in thermophiles and psychrophiles compared to mesophiles. 15(1):19757–19757, 2025. [DOI].
Tim Hensen and Ines Thiele. Metabolic modeling links gut microbiota to metabolic markers of parkinson’s disease. 17(1):2554195–2554195, 2025. [DOI].
Chloe V. McCreery, Drew Alessi, Katarina Mollo, Alessio Fasano, and Ali R. Zomorrodi. Investigating intestinal epithelium metabolic dysfunction in celiac disease using personalized genome-scale models. 23(1):95–95, 2025. [DOI].
Daniel Fässler, Almut Heinken, and Johannes Hertel. Characterising functional redundancy in microbiome communities via relative entropy. 27():1482–1497, 2025. [DOI].
Zhenqiang Zhao, Rongshuai Zhu, Xuanping Shi, Fengyu Yang, Meijuan Xu, Minglong Shao, Rongzhen Zhang, Youxi Zhao, Jiajia You, and Zhiming Rao. Combining biosensor and metabolic network optimization strategies for enhanced l-threonine production in escherichia coli. 18(1):37–37, 2025. [DOI].
Xiangyan Zhao, Hongwei Guo, Hai Huang, Ming Zheng, Xianping Zhang, Jing Li, Congcong Li, Bo Yuan, Chunmei Pan, and Zhoutong Sun. Contamination and biotransformation of deoxynivalenol (don) in common commercial foods: current status, challenges and future perspectives. ():, 2025. [DOI].
Sultana Mohammed Al Zubaidi, Muhammad Ibtisam Nasar, Richard A. Notebaart, Markus Ralser, and Mohammad Tauqeer Alam. An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways. 21(7):870–888, 2025. [DOI].
David Armitage, Alexandro Alonso-Sánchez, Samantha R Coy, Zhuli Cheng, Arno Hagenbeek, Karla P López-Martínez, Yong Heng Phua, and Alden R Sears. Adaptive pangenomic remodeling in the azolla cyanobiont amid a transient microbiome. 19(1):, 2025. [DOI].
Jonathan Josephs‐Spaulding, Hannah Clara Rettig, Johannes Zimmermann, Mariam Chkonia, Alexander Mischnik, Sören Franzenburg, Simon Graspeuntner, Jan Rupp, and Christoph Kaleta. Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection. 11(1):183–183, 2025. [DOI].
Kashif R. Siddique, Debajyoti Bose, Riya Bhattacharya, Raul V. Rodriguez, and Aritra Ray. Artificial intelligence driven bioinformatics for sustainable bioremediation: integrating computational intelligence with ecological restoration. 4(12):1987–1997, 2025. [DOI].
Zahrasadat Seyyedi, Hamed Haddad Kashani, Atefeh Parchebafi, Romina Ghayoumi, Mohammad Mehdi Haghighat Lari, and Elahe Seyed Hosseini. Integrating probiotics and microbiome-derived metabolites into cancer therapy: mechanistic insights, multi-omics strategies, and clinical potential. 10():100340–100340, 2025. [DOI].
Henry Kurniawan, Sarah Nickels, Alise Žagare, Elisa Zuccoli, Isabel Rosety, Gemma Gomez‐Giro, Enrico Glaab, and Jens C. Schwamborn. The parkinson’s disease-associated lrrk2-g2019s variant restricts serine metabolism, leading to microglial inflammation and dopaminergic neuron degeneration. 22(1):244–244, 2025. [DOI].
Luke N. Yaeger, David Sychantha, Princeton Luong, Shahrokh Shekarriz, Océane Goncalves, Annamaria Dobrin, Michael R. M. Ranieri, Ryan P. Lamers, Hanjeong Harvey, George C. diCenzo, Michael G. Surette, Jean‐Philippe Côté, Jakob Magolan, and Lori L. Burrows. Perturbation of pseudomonas aeruginosa peptidoglycan recycling by anti-folates and design of a dual-action inhibitor. 16(3):e0298424–e0298424, 2025. [DOI].
Mohamed E. Hasan, Mohammed Osman, Alaa A. Hemeida, and Mahmoud ElHefnawi. Bioinformatics and artificial intelligence approaches in metabolic pathways. ():17–32, 2025. [DOI].
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