Citations¶

Publications that cited COBRA Toolbox¶

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].
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].
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].
Iqra Mariam, Ulrika Rova, Paul Christakopoulos, Λεωνίδας Μάτσακας, and Alok Patel. Data-driven synthetic microbes for sustainable future. 11(1):74–74, 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].
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].
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].
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. Systematic sensitivity analyses of growth modelling to evaluate the robustness of genome scale metabolic network models — case study with the filamentous fungus penicillium rubens. ():, 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].
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].
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].
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].
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].
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].
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].
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].
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].
Maria Masid, Ioanna A. Rota, David Barras, Flavia De Carlo, Pierpaolo Ginefra, Mathieu Desbuisson, Yaquelin Ortiz-Miranda, Dmitriy Zamarin, Sohrab P Shah, Nicola Vannini, George Coukos, Denarda Dangaj Laniti, Vassily Hatzimanikatis, and Matthieu Desbuisson. Computational inference of metabolic programs: a case study analyzing the effect of brca1 loss. ():, 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. ():, 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].
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].
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].
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].
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].
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].
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].
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].
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].
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].
Steffen Klamt, Jürgen Zanghellini, and Axel von Kamp. Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine. 26(2):, 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].
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].
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].
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].
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].
Tim Hensen and Ines Thiele. Metabolic modeling links gut microbiota to metabolic markers of parkinson’s disease. 17(1):2554195–2554195, 2025. [DOI].
Almut Heinken, John M. Asara, Gopalan Gnanaguru, and Charandeep Singh. Systemic regulation of retinal medium-chain fatty acid oxidation repletes tca cycle flux in oxygen-induced retinopathy. 8(1):25–25, 2025. [DOI].
Venkat R. Pannala, Archana Hari, Mohamed AbdulHameed, Michele R. Balik-Meisner, Deepak Mav, Dhiral Phadke, Elizabeth H. Scholl, Ruchir Shah, Scott S. Auerbach, and Anders Wallqvist. Quantifying liver-toxic responses from dose-dependent chemical exposures using a rat genome-scale metabolic model. 204(2):154–168, 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. ():, 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].
Vikash Pandey. Mineapy: enhancing enrichment network analysis in metabolic networks. 41(3):, 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].
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].
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].
Devlin C. Moyer, Justin Reimertz, Daniel Segrè, and Juan I. Fuxman Bass. Macaw: a method for semi-automatic detection of errors in genome-scale metabolic models. 26(1):79–79, 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].
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].
Eduardo Luís Menezes de Almeida and Wendel Batista da Silveira. Insights into the response and tolerance mechanisms of papiliotrema laurentii to acetic acid stress by rna-seq and genome-scale metabolic modeling analysis. 215():109634–109634, 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].
Sonal Omer, Subasree Sridhar, Devarajan Karunagaran, and G. K. Suraishkumar. Mechanistic insights into hypoxia‐induced metabolic reprogramming in colorectal cancer through genome‐scale modeling. 41(3):e70002–e70002, 2025. [DOI].
M.E. Emetere. Progress, limitations, and advances of biohydrogen technologies: bringing the technology close to energy participants in developing countries. 16(8):912–928, 2025. [DOI].
Maurício Alexander de Moura Ferreira, Eduardo Luís Menezes de Almeida, Wendel Batista da Silveira, and Zoran Nikoloski. Protein-constrained models pinpoints the role of underground metabolism in robustness of metabolic phenotypes. 28(3):112126–112126, 2025. [DOI].
Jyoti Jyoti and Marc-Thorsten Hütt. Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns. 41(4):, 2025. [DOI].
Mustafa Sertbaş and Kutlu Ö. Ülgen. Exploring human brain metabolism via genome-scale metabolic modeling with highlights on multiple sclerosis. 16(7):1346–1360, 2025. [DOI].
Pengyang Liu, Yingwei Ai, Muzi Li, Jiacheng Shi, Ning Xiao, Xiaoyu Zhang, Hongbo Yu, Fuying Ma, Su Sun, and Shangxian Xie. Discovery of mannose as an alternative non-nutrient-deficient regulator of lipid accumulation in microalgae. ():, 2025. [DOI].
Ziwei Yang and Takeyuki Tamura. Dbgdel: database-enhanced gene deletion framework for growth-coupled production in genome-scale metabolic models. 22(4):1415–1427, 2025. [DOI].
Rami Balasubramanian, Debajit Saha, A. Arun, and P. K. Vinod. Hypometabolism in autism spectrum disorder: insights from brain and blood transcriptomics. 62(8):10765–10778, 2025. [DOI].
Pablo Di Giusto, Dong‐Hyuk Choi, Athanasios Antonakoudis, Vikash Gokul Duraikannan, Pierrick Craveur, Nicholas Luke Cowie, Tejaswini Ganapathy, K Ramesh, Santiago Benavides-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, Juchen 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-consensus reconstruction of chinese hamster metabolism enables structural systems biology analyses to decipher metabolic rewiring in lactate-free cho cells. ():, 2025. [DOI].
Ian Sofian Yunus, David Carruthers, Yan Chen, Jennife W Gin, Edward E. K. Baidoo, Christopher J. Petzold, Héctor García Martín, Paul D. Adams, Aindrila Mukhopadhyay, and Taek Soon Lee. Predictive genome-wide crispr-mediated gene downregulation for enhanced bioproduction. ():, 2025. [DOI].
Min Chen, Junfeng Jiang, Tingting Xie, Yingping Zhuang, and Jianye Xia. Allosteric effectors outcompete transcript levels and substrate concentration in regulating central carbon flux during the crabtree effect transition. 20(4):e70024–e70024, 2025. [DOI].
Merve Yarıcı, Furkan Cantürk, Serdar Dursun, Hatice Nur Aydın, and Muhammed Erkan Karabekmez. Rsea: a web server for pathway enrichment analysis of metabolic reaction sets. 122(8):2251–2258, 2025. [DOI].
Srijith Sasikumar, S Pavan Kumar, Nirav Bhatt, and Himanshu Sinha. Genome-scale metabolic modelling identifies reactions mediated by snp-snp interactions associated with yeast sporulation. 11(1):50–50, 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].
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, Angelika 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, and Wenhan Zhu. An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut. ():, 2025. [DOI].
Y. Zhang, Guannan Mao, Wei Hu, Zhineng Wu, Zhao Yang, Yanan Wang, Mark Bartlam, and Yingying Wang. Enhanced bde-47 biotransformation via cross-feeding in an aerobic-facultative anaerobic bacterial synthetic community. 282():122047–122047, 2025. [DOI].
Xi Luo, Diana C. El Assal, Yanjun Liu, Samira Ranjbar, and Ronan M. T. Fleming. Constraint-based modeling of bioenergetic differences between synaptic and non-synaptic components of dopaminergic neurons in parkinson’s disease. 19():1594330–1594330, 2025. [DOI].
Gong‐Hua Li, Feifei Han, Efthymios Kalafatis, Qing‐Peng Kong, and Wenzhong Xiao. Systems modeling reveals shared metabolic dysregulation and potential treatments in me/cfs and long covid. 26(13):6082–6082, 2025. [DOI].
Boyu Jiang, Nick Quinn-Bohmann, Christian Diener, Vignesh Bose Nathan, Yu Han-Hallett, Lavanya Reddivari, Sean M. Gibbons, and Priyanka Baloni. Understanding disease-associated metabolic changes in human colonic epithelial cells using the icolonepithelium metabolic reconstruction. 21(7):e1013253–e1013253, 2025. [DOI].
Anurag Passi, Diego Tec-Campos, Manish Kumar, Juan D. Tibocha‐Bonilla, Cristal Zúñiga, Beth B. Peacock, Amanda R. Hale, Rodrigo Santibáñez, James Borneman, and Karsten Zengler. Unveiling organ-specific metabolism of citrus clementina. 122(29):e2503406122–e2503406122, 2025. [DOI].
Míriam Tarrado‐Castellarnau, Carles Foguet, Josep Tarragó‐Celada, Marc Palobart, Claudia Hernández-Carro, Jordi Perarnau, Erika Zodda, Ibrahim H. Polat, Silvia Marín, Alejandro Suárez‐Bonnet, Juan José Lozano, Mariia Yuneva, Timothy M. Thomson, and Marta Cascante. Glutaminase as a metabolic target of choice to counter acquired resistance to palbociclib by colorectal cancer cells. 44(36):3386–3406, 2025. [DOI].
Massimo Bilancioni and Massimiliano Esposito. Energy transduction in complex networks with multiple resources: the chemistry paradigm. 163(4):, 2025. [DOI].
Walter Vieri, Veronica Ghini, Paola Turano, Lara Massai, Luigi Messori, and Marco Fondi. Modeling the metabolic response of a2780 ovarian cancer cells to gold-based cytotoxic drugs. 11(1):83–83, 2025. [DOI].
Wenbo Han, Luchi Xiao, Haocheng Sun, G. M. Xiang, Qiyue Jia, Haoyu Wang, Boyang Ji, Cheng Zhang, Eduard J. Kerkhoven, Jens Nielsen, and Hongzhong Lu. Alphagem enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining. ():, 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].
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].
Devlin C. Moyer, Justin Reimertz, Juan I. Fuxman Bass, and Daniel Segrè. Flux sampling and context-specific genome-scale metabolic models for biotechnological applications. ():, 2025. [DOI].
Almut Heinken, Hussein Awada, Vito Riccardo Tomaso Zanotelli, D. Sean Froese, Rosa‐Maria Guéant‐Rodriguez, and Jean‐Louis Guéant. Personalized genome‐scale modeling reveals metabolic perturbations in fibroblasts of methylmalonic aciduria patients. 48(5):e70077–e70077, 2025. [DOI].
B.B. BAIMAKHANOVA, А.К. САДАНОВ, И.А. Ратникова, Gul Baimakhanova, Saltanat Orasymbet, Aigul Amitova, Gulzat Aitkaliyeva, and Ardak B. Kakimova. In silico modeling of metabolic pathways in probiotic microorganisms for functional food biotechnology. 11(8):458–458, 2025. [DOI].
Andreas Kremling. From flux analysis to self contained cellular models. 5():1546072–1546072, 2025. [DOI].
Jeffrey J. Czajka, Joonhoon Kim, Yinjie Tang, Kyle Pomraning, Aindrila Mukhopadhyay, and Héctor García Martín. Fluxretap: a reaction target prioritization genome-scale modeling technique for selecting genetic targets. 41(9):, 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].
Aline Ovalle, Estefanía López, Jimena Sierralta, Nuria Paricio, and Daniel Garrido. A rationally designed microbial consortium modulates neurodegeneration in a drosophila melanogaster model of parkinson’s disease. 11(1):185–185, 2025. [DOI].
Pınar Kocabaş. Modeling meets metabolic engineering: the ipichia consensus model as basis for metabolic studies in komagataella phaffii. 225():109940–109940, 2025. [DOI].
Jinhui Zhao, Yanyan Zhou, Han Bao, Xinjie Zhao, Xinxin Wang, Chunxia Zhao, Wangshu Qin, Xin Lu, and Guowang Xu. Moda: a graph convolutional network-based multi-omics integration framework for unraveling hub molecules and disease mechanisms. 26(5):, 2025. [DOI].
Andrea Angarita-Rodríguez, Nicolás Mendoza-Mejía, Janneth González, Jason A. Papin, Andrés Felipe Aristizábal-Pachón, and Andrés Pinzón. Improvement in the prediction power of an astrocyte genome-scale metabolic model using multi-omic data. 4():1500710–1500710, 2025. [DOI].
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Cristiana Gomes de Oliveira Dal’Molin, Lake‐Ee Quek, Robin Palfreyman, and Lars K. Nielsen. Algagem – a genome-scale metabolic reconstruction of algae based on the chlamydomonas reinhardtii genome. 12(Suppl 4):S5–S5, 2011. [DOI].
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Paul A. Jensen, Kyla Lutz, and Jason A. Papin. Tiger: toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. 5(1):147–147, 2011. [DOI].
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Caroline B. Milne, James A. Eddy, Ravali Raju, Soroush Ardekani, Pan‐Jun Kim, Ryan S. Senger, Yong‐Su Jin, Hans P. Blaschek, and Nathan D. Price. Metabolic network reconstruction and genome-scale model of butanol-producing strain clostridium beijerinckii ncimb 8052. 5(1):130–130, 2011. [DOI].
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