Citations¶

Publications that cited COBRA Toolbox¶

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. BMC MEDICINE, FEB 21 2025. [DOI].
Silvia avila-Cabre, Joan Albiol, and Pau Ferrer. Metabolic engineering of komagataella phaffii for enhanced 3-hydroxypropionic acid (3-hp) production from methanol. JOURNAL OF BIOLOGICAL ENGINEERING, FEB 20 2025. [DOI].
Sonal Omer, Subasree Sridhar, D. Karunagaran, and G. K. Suraishkumar. Mechanistic insights into hypoxia-induced metabolic reprogramming in colorectal cancer through genome-scale modeling. BIOTECHNOLOGY PROGRESS, 2025 FEB 18 2025. [DOI].
Moses Eterigho Emetere. Progress, limitations, and advances of biohydrogen technologies: bringing the technology close to energy participants in developing countries. BIOFUELS-UK, 2025 FEB 14 2025. [DOI].
Venkat R. Pannala, Archana Hari, Mohamed Diwan M. Abdulhameed, Michele R. Balik-Meisner, Deepak Mav, Dhiral P. Phadke, Elizabeth H. Scholl, Ruchir R. Shah, Scott S. Auerbach, and Anders Wallqvist. Quantifying liver-toxic responses from dose-dependent chemical exposures using a rat genome-scale metabolic model. TOXICOLOGICAL SCIENCES, 2025 JAN 25 2025. [DOI].
Artai R. Moimenta, Diego Troitino-Jordedo, David Henriques, Alba Contreras-Ruiz, 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. MSYSTEMS, FEB 18 2025. [DOI].
Michael Weldon and Christian Euler. Physiology-informed use of cupriavidus necator in biomanufacturing: a review of advances and challenges. MICROBIAL CELL FACTORIES, JAN 22 2025. [DOI].
Eduardo Luis 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. BIOCHEMICAL ENGINEERING JOURNAL, MAR 2025. [DOI].
Deepanwita Banerjee, Javier Menasalvas, Yan Chen, Jennifer W. 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. NPJ SYSTEMS BIOLOGY AND APPLICATIONS, JAN 14 2025. [DOI].
Qiannan Peng, Cheng Zhao, Xiaopeng Wang, Kelin Cheng, Congcong Wang, Xihui Xu, and Lu Lin. Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium. NATURE COMMUNICATIONS, JAN 14 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. COMMUNICATIONS BIOLOGY, JAN 9 2025. [DOI].
Nora Scherer, Daniel Faessler, Oleg Borisov, Yurong Cheng, Pascal Schlosser, Matthias Wuttke, Stefan Haug, Yong Li, Fabian Telkaemper, Suraj Patil, Heike Meiselbach, Casper Wong, Urs Berger, Peggy Sekula, Anselm Hoppmann, Ulla T. Schultheiss, Sahar Mozaffari, Yannan Xi, Robert Graham, Miriam Schmidts, Michael Koettgen, Peter J. Oefner, Felix Knauf, Kai-Uwe Eckardt, Sarah C. Gruenert, Karol Estrada, Ines Thiele, Johannes Hertel, and Anna Koettgen. Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits. NATURE GENETICS, JAN 2025. [DOI].
Qin-Tian Qiu, Cai-Yun Zhang, Zhi-Peng Gao, and Bin-Guang Ma. Spatial chromosome organization and adaptation of the radiation-resistant extremophile deinococcus radiodurans. JOURNAL OF BIOLOGICAL CHEMISTRY, JAN 2025. [DOI].
Sergio Sanchez-Garcia, Adrian Povo-Retana, Silvia Marin, Sergio Madurga, Marco Farinas, Nuria Aleixandre, Antonio Castrillo, Juan V. de la Rosa, Carlota Alvarez-Lucena, Rodrigo Landauro-Vera, Patricia Prieto, Marta Cascante, and Lisardo Bosca. Immunometabolic effect of nitric oxide on human macrophages challenged with the sars-cov2-induced cytokine storm. a fluxomic approach. ADVANCED HEALTHCARE MATERIALS, JAN 2025. [DOI].
Helen Scott and Daniel Segre. Metabolic flux modeling in marine ecosystems. ANNUAL REVIEW OF MARINE SCIENCE, 17:593–620, 2025. [DOI].
Diego Tec-Campos, Juan D. Tibocha-Bonilla, Celina Jiang, Anurag Passi, Deepan Thiruppathy, Cristal Zuniga, 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. PLOS COMPUTATIONAL BIOLOGY, JAN 2025. [DOI].
Xuangao Wu, Hee-Jong Yang, Myeong-Seon Ryu, Su-Jin Jung, Kwangsu Ha, Do-Yeon Jeong, and Sunmin Park. Association of mucin-degrading gut microbiota and dietary patterns with colonic transit time in constipation: a secondary analysis of a randomized clinical trial. NUTRIENTS, JAN 2025. [DOI].
Alise Zagare, Janis Kurlovics, Catarina Almeida, Daniele Ferrante, Daniela Frangenberg, Armelle Vitali, Gemma Gomez-Giro, Christian Jaeger, Paul Antony, Rashi Halder, Rejko Krueger, Enrico Glaab, Egils Stalidzans, Giuseppe Arena, and Jens C. Schwamborn. Insulin resistance compromises midbrain organoid neuronal activity and metabolic efficiency predisposing to parkinson's disease pathology. JOURNAL OF TISSUE ENGINEERING, 2025. [DOI].
Lidan Bai, Jun Sun, Vasile Palade, Chao Li, Hengyang Lu, and Cong Gao. Optimizing metabolite production with neighborhood-based binary quantum-behaved particle swarm optimization and flux balance analysis. JOURNAL OF COMPUTATIONAL BIOLOGY, 32(1):64–88, JAN 1 2025. [DOI].
Hadi Nazem-Bokaee, Erik F. Y. Hom, Sarah Mathews, and Cecile Gueidan. Analyzing sorbitol biosynthesis using a metabolic network flux model of a lichenized strain of the green microalga diplosphaera chodatii. MICROBIOLOGY SPECTRUM, JAN 7 2025. [DOI].
Henry Ehlers, Nicolas Brich, Michael Krone, Martin Noellenburg, Jiacheng Yu, Hiroaki Natsukawa, Xiaoru Yuan, and Hsiang-Yun Wu. An introduction to and survey of biological network visualization. COMPUTERS & GRAPHICS-UK, FEB 2025. [DOI].
Wei-Ze Kong and Morihisa Fujita. Glycomaple: recent updates and applications in visualization and analysis of glycosylation pathways. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 417(5, SI):885–894, FEB 2025. [DOI].

Jinlin Zhu, Jialin Yin, Jing Chen, Mingyi Hu, Wenwei Lu, Hongchao Wang, Hao Zhang, and Wei Chen. Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis. GUT MICROBES, DEC 31 2024. [DOI].
Sandra Correa Cordoba, Asdrubal Burgos, Alvaro Cuadros-Inostroza, Ke Xu, Yariv Brotman, and Zoran Nikoloski. A data-integrative modeling approach accurately characterizes the effects of mutations on arabidopsis lipid metabolism. PLANT PHYSIOLOGY, DEC 19 2024. [DOI].
Chania Clare, Jack W. Rutter, Alex J. H. Fedorec, Stefanie Frank, and Chris P. Barnes. Bacterial microcompartment utilization in the human commensal escherichia coli nissle 1917. JOURNAL OF BACTERIOLOGY, DEC 19 2024. [DOI].
Danlei Chen, Zheping Qu, Shujuan Yang, Yujie Li, Shuxuan Yu, Xin Li, Yutong Lu, Aidong Yang, Chunjiang Liu, Shengbo Wu, and Jianjun Qiao. Quorum sensing regulating the productivity and stability of cross-feeding cocultivation. CHEMICAL ENGINEERING JOURNAL, DEC 15 2024. [DOI].
Sandhya Mishra, Anju Patel, Pankaj Bhatt, Shaohua Chen, and Pankaj Kumar Srivastava. Perspective evaluation of synthetic biology approaches for effective mitigation of heavy metal pollution. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY, DEC 2024. [DOI].
Seo-Young Park, Jinsung Song, Dong-Hyuk Choi, Uiseon Park, Hyeran Cho, Bee Hak Hong, Yaron R. Silberberg, and Dong-Yup Lee. Exploring metabolic effects of dipeptide feed media on cho cell cultures by in silico model-guided flux analysis. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 108(1):16, DEC 2024. [DOI].
Jiahang Li, Wolfram Weckwerth, and Steffen Waldherr. Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse jacobian. NPJ SYSTEMS BIOLOGY AND APPLICATIONS, NOV 23 2024. [DOI].
Shengbo Wu, Yongsheng Zhou, Lei Dai, Aidong Yang, and Jianjun Qiao. Assembly of functional microbial ecosystems: from molecular circuits to communities. FEMS MICROBIOLOGY REVIEWS, NOV 23 2024. [DOI].
Silvia Sabatini, Partho Sen, Fabrizia Carli, Samantha Pezzica, Chiara Rosso, Erminia Lembo, Ornella Verrastro, Ann Daly, Olivier Govaere, Simon Cockell, Tuulia Hyotylainen, Geltrude Mingrone, Elisabetta Bugianesi, Quentin M. Anstee, Matej Oresic, and Amalia Gastaldelli. Hepatic glucose production rises with the histological severity of metabolic dysfunction-associated steatohepatitis. CELL REPORTS MEDICINE, NOV 19 2024. [DOI].
Alexandra Manchel, Michelle Gee, and Rajanikanth Vadigepalli. From sampling to simulating: single-cell multiomics in systems pathophysiological modeling. ISCIENCE, DEC 20 2024. [DOI].
Guangjian Li, Hui Liang, Ruichen Gao, Ling Qin, Pei Xu, Mingtao Huang, Min-Hua Zong, Yufei Cao, and Wen-Yong Lou. Yeast metabolism adaptation for efficient terpenoids synthesis via isopentenol utilization. NATURE COMMUNICATIONS, NOV 13 2024. [DOI].
Boatema Ofori-Anyinam, Meagan Hamblin, Miranda L. Coldren, Barry Li, Gautam Mereddy, Mustafa Shaikh, Avi Shah, Courtney Grady, Navpreet Ranu, Sean Lu, Paul C. Blainey, Shuyi Ma, James J. Collins, and Jason H. Yang. Catalase activity deficiency sensitizes multidrug-resistant mycobacterium tuberculosis to the atp synthase inhibitor bedaquiline. NATURE COMMUNICATIONS, NOV 13 2024. [DOI].
Siqing Fan, Hao Ren, Xueni Fu, Xiangyu Kong, Hao Wu, and Zhenmei Lu. Genome streamlining of pseudomonas putida b6-2 for bioremediation. MSYSTEMS, DEC 17 2024. [DOI].
Sergio Sanchez-Garcia, Adrian Povo-Retana, Silvia Marin, Sergio Madurga, Marco Farinas, Nuria Aleixandre, Antonio Castrillo, Juan V. de la Rosa, Carlota Alvarez-Lucena, Rodrigo Landauro-Vera, Patricia Prieto, Marta Cascante, and Lisardo Bosca. Immunometabolic effect of nitric oxide on human macrophages challenged with the sars-cov2-induced cytokine storm. a fluxomic approach. ADVANCED HEALTHCARE MATERIALS, 2024 NOV 6 2024. [DOI].
Abdulla Abu-Salah, Muberra Fatma Cesur, Aiesha Anchan, Muhammet Ay, Monica R. Langley, Ahmed Shah, Pablo Reina-Gonzalez, Rachel Strazdins, Tunahan Cakir, and Souvarish Sarkar. Comparative proteomics highlights that genx exposure leads to metabolic defects and inflammation in astrocytes. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 58(46):20525–20539, NOV 5 2024. [DOI].
Miha Moskon and Tadeja Rezen. Integration and analysis of omics data using genome-scale metabolic models. METABOLITES, NOV 2024. [DOI].
Thomaz Satuye Prieto-de Lima, Keilor Rojas-Jimenez, and Christopher Vaglio. Strategy for optimizing vitamin b12 production in pseudomonas putida kt2440 using metabolic modeling. METABOLITES, NOV 2024. [DOI].
Jungyeon Kim, Ye-Bin Kim, Ju-Young Kim, Min-Ju Seo, Soo-Jin Yeom, and Bong Hyun Sung. Investigation of bottleneck enzyme through flux balance analysis to improve glycolic acid production in escherichia coli. JOURNAL OF MICROBIOLOGY, 62(11):1023–1033, NOV 2024. [DOI].
Xin Bush, Erica J. Fratz-Berilla, Casey L. Kohnhorst, Roberta King, Cyrus Agarabi, David N. Powers, and Nicholas Trunfio. Defining golden batches in biomanufacturing processes from internal metabolic activity to detect process changes that may affect product quality. BIOTECHNOLOGY AND BIOENGINEERING, 2024 OCT 27 2024. [DOI].
Elena Lucy Carter, Nicholas R. Waterfield, Chrystala Constantinidou, and Mohammad Tauqeer Alam. A temperature-induced metabolic shift in the emerging human pathogen photorhabdus asymbiotica. MSYSTEMS, NOV 19 2024. [DOI].
Hatice Busra Luleci, Dilara Uzuner, Muberra Fatma Cesur, Atilay Ilgun, Elif Duz, Ecehan Abdik, Regan Odongo, and Tunahan Cakir. A benchmark of rna-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks. NPJ SYSTEMS BIOLOGY AND APPLICATIONS, OCT 24 2024. [DOI].
Daniella M. Hernandez, Melissa Marzouk, Madeline Cole, Marla C. Fortoul, Saipranavi Reddy Kethireddy, Rehan Contractor, Habibul Islam, Trent Moulder, Ariane R. Kalifa, Estefania Marin Meneses, Maximiliano Barbosa Mendoza, Ruth Thomas, Saad Masud, Sheena Pubien, Patricia Milanes, Gabriela Diaz-Tang, Allison J. Lopatkin, and Robert P. Smith. Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics. MICROBIOLOGY SPECTRUM, DEC 5 2024. [DOI].
Yonggang Gao and Cheng Zhao. Development and applications of metabolic models in plant multi-omics research. FRONTIERS IN PLANT SCIENCE, OCT 17 2024. [DOI].
Ye Li, Jingzhen Sun, Zhenhao Fu, Yubing He, Xiaorui Chen, Shijie Wang, Lele Zhang, Jiansheng Jian, Weihua Yang, Chunli Liu, Xiuxia Liu, Yankun Yang, and Zhonghu Bai. Engineering the l-tryptophan metabolism for efficient de novo biosynthesis of tryptophol in saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS, OCT 16 2024. [DOI].
Matthew Lima, Charandatta Muddana, Zhengyang Xiao, Anindita Bandyopadhyay, Pramod P. Wangikar, Himadri B. Pakrasi, and Yinjie J. Tang. The new chassis in the flask: advances in vibrio natriegens biotechnology research. BIOTECHNOLOGY ADVANCES, DEC 2024. [DOI].
Arturo Vera-Ponce de Leon, Tim Hensen, Matthias Hoetzinger, Shashank Gupta, Bronson Weston, Sander M. Johnsen, Jacob A. Rasmussen, Cecilie Gronlund Clausen, Louisa Pless, Ana Raquel Andrade Verissimo, Knut Rudi, Lars Snipen, Christian Rene Karlsen, Morten T. Limborg, Stefan Bertilsson, Ines Thiele, Torgeir R. Hvidsten, Simen R. Sandve, Phillip B. Pope, and Sabina Leanti La Rosa. Genomic and functional characterization of the atlantic salmon gut microbiome in relation to nutrition and health. NATURE MICROBIOLOGY, NOV 2024. [DOI].
Maxwell Neal, William Brakewood, Michael Betenbaugh, and Karsten Zengler. Pan-genome-scale metabolic modeling of bacillus subtilis reveals functionally distinct groups. MSYSTEMS, NOV 19 2024. [DOI].
Jorge E. Arellano-Villavicencio, Aaron Vazquez-Jimenez, Juan Jose Oropeza-Valdez, Cristian Padron-Manrique, Heriberto Prado-Garcia, Armando R. Tovar, and Osbaldo Resendis-Antonio. Intratumoral heterogeneity and metabolic cross-feeding in a three-dimensional breast cancer culture: an in silico perspective. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, OCT 2024. [DOI].
Jasmeet Kaur Khanijou, Yan Ting Hee, Clement P. M. Scipion, Xixian Chen, and Kumar Selvarajoo. Systems biology approach for enhancing limonene yield by re-engineering escherichia coli. NPJ SYSTEMS BIOLOGY AND APPLICATIONS, OCT 1 2024. [DOI].
Karel Olavarria and Diana Z. Sousa. Thermodynamic tools for more efficient biotechnological processes: an example in poly-(3-hydroxybutyrate) production from carbon monoxide. CURRENT OPINION IN BIOTECHNOLOGY, DEC 2024. [DOI].
Natchapon Srinak, Porntip Chiewchankaset, Saowalak Kalapanulak, Pornpan Panichnumsin, and Treenut Saithong. Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters. PLOS COMPUTATIONAL BIOLOGY, OCT 2024. [DOI].
Farid Zare and Ronan M. T. Fleming. Integration of proteomic data with genome-scale metabolic models: a methodological overview. PROTEIN SCIENCE, OCT 2024. [DOI].
Jianhang Zhou, Xiaogang Wu, Yiming Feng, Tangran Huo, Yunpeng Zhao, Juejun Pan, and Sitong Liu. Bacterial communication intelligently regulates their interactions in anammox consortia under decreasing temperatures. SCIENCE OF THE TOTAL ENVIRONMENT, DEC 1 2024. [DOI].
Somdutt Ravindran, Nima Hajinajaf, Pritam Kundu, Jackson Comes, David R. Nielsen, Arul M. Varman, and Amit Ghosh. Genome-scale metabolic model reconstruction and investigation into the fluxome of the fast-growing cyanobacterium synechococcus sp. pcc 11901. ACS SYNTHETIC BIOLOGY, 13(10):3281–3294, SEP 19 2024. [DOI].
Carolina A. Contador, Ailin Liu, Ming-Sin Ng, Yee-Shan Ku, Siu H. J. Chan, and Hon-Ming Lam. Contextualized metabolic modelling revealed factors affecting isoflavone accumulation in soybean seeds. PLANT CELL AND ENVIRONMENT, 2024 SEP 18 2024. [DOI].
Sowmya Manojna Narasimha, Tanisha Malpani, Omkar S. Mohite, J. Saketha Nath, and Karthik Raman. Understanding flux switching in metabolic networks through an analysis of synthetic lethals. NPJ SYSTEMS BIOLOGY AND APPLICATIONS, SEP 17 2024. [DOI].
Zhepu Ruan, Mengjun Xu, Youwen Xing, Kaiqing Yang, Xihui Xu, Jiandong Jiang, and Rongliang Qiu. Enhanced growth of wheat in contaminated fields via synthetic microbiome as revealed by genome-scale metabolic modeling. SCIENCE OF THE TOTAL ENVIRONMENT, NOV 25 2024. [DOI].
Olivia Gallup, Kirill Sechkar, Sebastian Towers, and Harrison Steel. Computational synthetic biology enabled through jax: a showcase. ACS SYNTHETIC BIOLOGY, 13(9):3046–3050, SEP 4 2024. [DOI].
Nicola Cortese, Anna Procopio, Alessio Merola, Paolo Zaffino, and Carlo Cosentino. Applications of genome-scale metabolic models to the study of human diseases: a systematic review. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, NOV 2024. [DOI].
Alexander A. Aksenov, Alex Blacutt, Nichole Ginnan, Philippe E. Rolshausen, Alexey V. Melnik, Ali Lotfi, Emily C. Gentry, Manikandan Ramasamy, Cristal Zuniga, Karsten Zengler, Kranthi K. Mandadi, Pieter C. Dorrestein, and M. Caroline Roper. Spatial chemistry of citrus reveals molecules bactericidal to candidatus liberibacter asiaticus. SCIENTIFIC REPORTS, SEP 2 2024. [DOI].
Sara Bertorello, Francesco Cei, Dorian Fink, Elena Niccolai, and Amedeo Amedei. The future exploring of gut microbiome-immunity interactions: from in vivo/vitro models to in silico innovations. MICROORGANISMS, SEP 2024. [DOI].
Fatma Zehra Sari and Tunahan Cakir. Deciphering antibiotic-targeted metabolic pathways in acinetobacter baumannii: insights from transcriptomics and genome-scale metabolic modeling. LIFE-BASEL, SEP 2024. [DOI].
Nan Xu, Jiaojiao Zuo, Chenghao Li, Cong Gao, and Minliang Guo. Reconstruction and analysis of a genome-scale metabolic model of acinetobacter lwoffii. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, SEP 2024. [DOI].
Xia Yang, Huiying Wang, Dongqin Ding, Huan Fang, Huina Dong, and Dawei Zhang. A hybrid rna-protein biosensor for high-throughput screening of adenosylcobalamin biosynthesis. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY, 9(3):513–521, SEP 2024. [DOI].
Mauricio Alexander de Moura Ferreira and Wendel Batista da Silveira. Multi-omics data and model integration reveal the main mechanisms associated with respiro-fermentative metabolism and ethanol stress responses in kluyveromyces marxianus. BIOCHEMICAL ENGINEERING JOURNAL, NOV 2024. [DOI].
Muhammed E. Karabekmez. Insights into yeast response to chemotherapeutic agent through time series genome-scale metabolic models. BIOTECHNOLOGY AND BIOENGINEERING, 121(10):3351–3359, OCT 2024. [DOI].
Jacob J. Valenzuela, Selva Rupa Christinal Immanuel, James Wilson, Serdar Turkarslan, Maryann Ruiz, Sean M. Gibbons, Kristopher A. Hunt, Nejc Stopnisek, Manfred Auer, Marcin Zemla, David A. Stahl, and Nitin S. Baliga. Origin of biogeographically distinct ecotypes during laboratory evolution. NATURE COMMUNICATIONS, AUG 28 2024. [DOI].
Lvjing Wang, Xiaoyu Wang, Hao Wu, Haixia Wang, and Zhenmei Lu. Interspecies synergistic interactions mediated by cofactor exchange enhance stress tolerance by inducing biofilm formation. MSYSTEMS, SEP 17 2024. [DOI].
Yuchao Zhao, Jian Tan, Luoyun Fang, and Linshu Jiang. Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: integrative approaches and future directions. SCIENCE OF THE TOTAL ENVIRONMENT, NOV 15 2024. [DOI].
Carlos Alberto Garcia-Mogollon, Diego F. Mendoza, and Juan Carlos Quintero-Diaz. Electrostatic ethanol fermentation: experimental study and kinetic-based metabolic modeling. HELIYON, SEP 15 2024. [DOI].
Xihui Xu, Can Li, Weimiao Cao, Lulu Yan, Lulu Cao, Qi Han, Minling Gao, Yahua Chen, Zhenguo Shen, Jiandong Jiang, and Chen Chen. Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions. ISME JOURNAL, AUG 23 2024. [DOI].
Aparajitha Srinivasan, Kevin Chen-Xiao, Deepanwita Banerjee, Asun Oka, Venkataramana R. Pidatala, Aymerick Eudes, Blake A. Simmons, Thomas Eng, and Aindrila Mukhopadhyay. Sustainable production of 2,3,5,6-tetramethylpyrazine at high titer in engineered corynebacterium glutamicum. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, AUG 6 2024. [DOI].
Elaine Zaunseder, Ulrike Muetze, Jueurorgen G. Okun, Georg F. Hoffmann, Stefan Koelker, Vincent Heuveline, and Ines Thiele. Personalized metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases. CELL METABOLISM, AUG 6 2024. [DOI].
Anna Kattel, Valter Aro, Petri-Jaan Lahtvee, Jekaterina Kazantseva, Arvi Joers, Ranno Nahku, and Isma Belouah. Exploring the resilience and stability of a defined human gut microbiota consortium: an isothermal microcalorimetric study. MICROBIOLOGYOPEN, AUG 2024. [DOI].
Jungyeon Kim, Gun-Hwi Yeon, Mi-Jin Kim, Jung-Hoon Bae, Jung-Hoon Sohn, and Bong Hyun Sung. Systems metabolic engineering to elucidate and enhance intestinal metabolic activities of escherichia coli nissle 1917. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 72(32):18234–18246, AUG 1 2024. [DOI].
Renan Tosin, Igor Portis, Leandro Rodrigues, Igor Goncalves, Catarina Barbosa, Jorge Teixeira, Rafael J. Mendes, Filipe Santos, Conceicao Santos, Rui Martins, and Mario Cunha. Integrating spectral sensing and systems biology for precision viticulture: effects of shade nets on grapevine leaves. HORTICULTURAE, AUG 2024. [DOI].
Hatice Busra Luleci, Attila Jones, and Tunahan Cakir. Multi-omics analyses highlight molecular differences between clinical and neuropathological diagnoses in alzheimer's disease. EUROPEAN JOURNAL OF NEUROSCIENCE, 60(5):4922–4936, SEP 2024. [DOI].
Hongzhong Lu, Luchi Xiao, Wenbin Liao, Xuefeng Yan, and Jens Nielsen. Cell factory design with advanced metabolic modelling empowered by artificial intelligence. METABOLIC ENGINEERING, 85:61–72, SEP 2024. [DOI].
N. Suhas Jagannathan, Javier Yu Peng Koh, Younghwan Lee, Radoslaw Mikolaj Sobota, Aaron T. Irving, Lin-fa Wang, Yoko Itahana, Koji Itahana, and Lisa Tucker-Kellogg. Multi-omic analysis of bat versus human fibroblasts reveals altered central metabolism. ELIFE, JUL 22 2024. [DOI].
Marina Maurizio, Maria Masid, Kerry Woods, Reto Caldelari, John G. Doench, Arunasalam Naguleswaran, Denis Joly, Martin Gonzalez-Fernandez, Jonas Zemp, Melanie Borteele, Vassily Hatzimanikatis, Volker Heussler, Sven Rottenberg, and Philipp Olias. Host cell crispr genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of plasmodium falciparum and related hemoparasites. NATURE COMMUNICATIONS, JUL 21 2024. [DOI].
Manish Kumar, Juan D. Tibocha-Bonilla, Zoltan Fussy, Chloe Lieng, Sarah M. Schwenck, Alice V. Levesque, Mahmoud M. Al-Bassam, Anurag Passi, Maxwell Neal, Cristal Zuniga, Farrah Kaiyom, Josh L. Espinoza, Hyungyu Lim, Shawn W. Polson, Lisa Zeigler Allen, and Karsten Zengler. Mixotrophic growth of a ubiquitous marine diatom. SCIENCE ADVANCES, JUL 17 2024. [DOI].
Richard D. Paul, Johann F. Jadebeck, Anton Stratmann, Wolfgang Wiechert, and Katharina Noeh. Hopsy - a methods marketplace for convex polytope sampling in python. BIOINFORMATICS, JUL 12 2024. [DOI].
Indumathi Palanikumar, Himanshu Sinha, and Karthik Raman. Panera: an innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models. ISCIENCE, JUL 19 2024. [DOI].
Pritam Kundu, Satyajit Beura, Suman Mondal, Amit Kumar Das, and Amit Ghosh. Machine learning for the advancement of genome-scale metabolic modeling. BIOTECHNOLOGY ADVANCES, SEP 2024. [DOI].
Cecilia Noecker and Peter J. Turnbaugh. Emerging tools and best practices for studying gut microbial community metabolism. NATURE METABOLISM, 6(7):1225–1236, JUL 2024. [DOI].
Jesse Bucksot, Katherine Ritchie, Matthew Biancalana, John A. Cole, and Daniel Cook. Pan-cancer, genome-scale metabolic network analysis of over 10,000 patients elucidates relationship between metabolism and survival. CANCERS, JUL 2024. [DOI].
Nayeon Kim, Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky, and Insuk Lee. Genome-resolved metagenomics: a game changer for microbiome medicine. EXPERIMENTAL AND MOLECULAR MEDICINE, 56(7):1501–1512, JUL 2024. [DOI].
Wheaton L. Schroeder, Patrick F. Suthers, Thomas C. Willis, Eric J. Mooney, and Costas D. Maranas. Current state, challenges, and opportunities in genome-scale resource allocation models: a mathematical perspective. METABOLITES, JUL 2024. [DOI].
Xi Luo, Yanjun Liu, Alexander Balck, Christine Klein, and Ronan M. T. Fleming. Identification of metabolites reproducibly associated with parkinson's disease via meta-analysis and computational modelling. NPJ PARKINSONS DISEASE, JUN 29 2024. [DOI].
Ehsan Motamedian, Matiss Ricards Baumanis, Janis Edmunds Daugavietis, Ieva Berzina, Karlis Shvirksts, Elina Dace, Janis Liepins, and Egils Stalidzans. A hybrid strategy for growth-associated production of sophorolipid using a reconstructed genome-scale metabolic model for the fructophilic yeast starmerella bombicola. PROCESS SAFETY AND ENVIRONMENTAL PROTECTION, 189:541–548, SEP 2024. [DOI].
Lu Liu, Weihe Rong, Xiang Du, Qianqian Yuan, Zhaoyu Xu, Chang Yu, Hongzhong Lu, Yanfei Wang, Yan Zhu, Zhijia Liu, and Guokun Wang. Integrating experimental and computational analyses of yeast protein profiles for optimizing the production of high-quality microbial proteins. APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY, 196(12):8741–8762, DEC 2024. [DOI].
Carlos J. Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal, Idoia Ochoa, Luis V. Valcarcel, and Francisco J. Planes. Gmcspy: efficient and accurate computation of genetic minimal cut sets in python. BIOINFORMATICS, JUN 25 2024. [DOI].
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