Citations — The COBRA Toolbox (2024)


Publications that cited COBRA Toolbox

  1. 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].

  2. Seo-Young Park, Jinsung Song, Dong-Hyuk Choi, Uiseon Park, Hyeran Cho, BeeHak Hong, YaronR. 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].

  3. Ehsan Motamedian, MatissRicards Baumanis, JanisEdmunds 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].

  4. 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].

  5. Aparajitha Srinivasan, Kevin Chen-Xiao, Deepanwita Banerjee, Asun Oka, VenkataramanaR. Pidatala, Aymerick Eudes, BlakeA. 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].

  6. Elaine Zaunseder, Ulrike Muetze, JueurorgenG. Okun, GeorgF. 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].

  7. 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].

  8. Jungyeon Kim, Gun-Hwi Yeon, Mi-Jin Kim, Jung-Hoon Bae, Jung-Hoon Sohn, and BongHyun Sung. Systems metabolic engineering to elucidate and enhance intestinal metabolic activities of <i>escherichia coli </i>nissle 1917. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 72(32):18234–18246, AUG 1 2024. [DOI].

  9. HaticeBusra 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, 2024 JUL 28 2024. [DOI].

  10. 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].

  11. N.Suhas Jagannathan, Javier YuPeng Koh, Younghwan Lee, RadoslawMikolaj Sobota, AaronT. 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].

  12. Marina Maurizio, Maria Masid, Kerry Woods, Reto Caldelari, JohnG. 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 <i>plasmodium falciparum</i> and related hemoparasites. NATURE COMMUNICATIONS, JUL 21 2024. [DOI].

  13. 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].

  14. Manish Kumar, JuanD. Tibocha-Bonilla, Zoltan Fussy, Chloe Lieng, SarahM. Schwenck, AliceV. Levesque, MahmoudM. Al-Bassam, Anurag Passi, Maxwell Neal, Cristal Zuniga, Farrah Kaiyom, JoshL. Espinoza, Hyungyu Lim, ShawnW. Polson, LisaZeigler Allen, and Karsten Zengler. Mixotrophic growth of a ubiquitous marine diatom. SCIENCE ADVANCES, JUL 17 2024. [DOI].

  15. RichardD. Paul, JohannF. Jadebeck, Anton Stratmann, Wolfgang Wiechert, and Katharina Noeh. Hopsy - a methods marketplace for convex polytope sampling in python. BIOINFORMATICS, JUL 12 2024. [DOI].

  16. Pritam Kundu, Satyajit Beura, Suman Mondal, AmitKumar Das, and Amit Ghosh. Machine learning for the advancement of genome-scale metabolic modeling. BIOTECHNOLOGY ADVANCES, SEP 2024. [DOI].

  17. Cecilia Noecker and PeterJ. Turnbaugh. Emerging tools and best practices for studying gut microbial community metabolism. NATURE METABOLISM, 6(7):1225–1236, JUL 2024. [DOI].

  18. Jesse Bucksot, Katherine Ritchie, Matthew Biancalana, JohnA. 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].

  19. 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].

  20. WheatonL. Schroeder, PatrickF. Suthers, ThomasC. Willis, EricJ. Mooney, and CostasD. Maranas. Current state, challenges, and opportunities in genome-scale resource allocation models: a mathematical perspective. METABOLITES, JUL 2024. [DOI].

  21. XiLuo, 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].

  22. LuLiu, 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, 2024 JUN 26 2024. [DOI].

  23. CarlosJ. Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal, Idoia Ochoa, LuisV. Valcarcel, and FranciscoJ. Planes. Gmcspy: efficient and accurate computation of genetic minimal cut sets in python. BIOINFORMATICS, JUN 25 2024. [DOI].

  24. Magdalena Wutkowska, Vojtech Tlaskal, Sergio Bordel, LisaY. Stein, JustusAmuche Nweze, and Anne Daebeler. Leveraging genome-scale metabolic models to understand aerobic methanotrophs. ISME JOURNAL, JUN 24 2024. [DOI].

  25. Lizhan Zhang, Jian-Wen Ye, Gang Li, Helen Park, Hao Luo, Yina Lin, Shaowei Li, Weinan Yang, Yuying Guan, Fuqing Wu, Wuzhe Huang, Qiong Wu, NigelS. Scrutton, Jens Nielsen, and Guo-Qiang Chen. A long-term growth stable halomonas sp. deleted with multiple transposases guided by its metabolic network model halo-ecgem. METABOLIC ENGINEERING, 84:95–108, JUL 2024. [DOI].

  26. Fatima Zulqarnain, Xueheng Zhao, Kenneth D.R. Setchell, Yash Sharma, Phillip Fernandes, Sanjana Srivastava, Aman Shrivastava, Lubaina Ehsan, Varun Jain, Shyam Raghavan, Christopher Moskaluk, Yael Haberman, LeeA. Denson, Khyati Mehta, NajeehaT. Iqbal, Najeeb Rahman, Kamran Sadiq, Zubair Ahmad, Romana Idress, Junaid Iqbal, Sheraz Ahmed, Aneeta Hotwani, Fayyaz Umrani, Beatrice Amadi, Paul Kelly, DonaldE. Brown, SeanR. Moore, SyedAsad Ali, and Sana Syed. Machine-learning-based integrative -'omics analyses reveal immunologic and metabolic dysregulation in environmental enteric dysfunction. ISCIENCE, JUN 21 2024. [DOI].

  27. Emanuel Lange, Lena Kranert, Jacob Kruger, Dirk Benndorf, and Robert Heyer. Microbiome modeling: a beginner's guide. FRONTIERS IN MICROBIOLOGY, JUN 19 2024. [DOI].

  28. Zixin Yang, Jinlin Zhu, Wenwei Lu, Fengwei Tian, Hao Zhang, and Wei Chen. Integrating artificial intelligence in exploring multiscale gut microbiota and diet relations for health promotion: a comprehensive review. FOOD BIOSCIENCE, OCT 2024. [DOI].

  29. Chaimaa Tarzi, Guido Zampieri, Neil Sullivan, and Claudio Angione. Emerging methods for genome-scale metabolic modeling of microbial communities. TRENDS IN ENDOCRINOLOGY AND METABOLISM, 35(6):533–548, JUN 2024. [DOI].

  30. Soraya Mirzaei and Mojtaba Tefagh. Gem-based computational modeling for exploring metabolic interactions in a microbial community. PLOS COMPUTATIONAL BIOLOGY, JUN 2024. [DOI].

  31. Lorenzo Pasotti, Ilaria Massaiu, Paolo Magni, and Cinzia Calvio. Metabolic engineering of <i>bacillus subtilis</i> for the production of poly-γ-glutamic acid from glycerol feedstock. FERMENTATION-BASEL, JUN 2024. [DOI].

  32. Zhepu Ruan, Kai Chen, Weimiao Cao, Lei Meng, Bingang Yang, Mengjun Xu, Youwen Xing, Pengfa Li, Shiri Freilich, Chen Chen, Yanzheng Gao, Jiandong Jiang, and Xihui Xu. Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling. NATURE COMMUNICATIONS, JUN 1 2024. [DOI].

  33. JoshA. Taylor, Alain Rapaport, and Denis Dochain. Convex representation of metabolic networks with michaelis-menten kinetics. BULLETIN OF MATHEMATICAL BIOLOGY, JUN 2024. [DOI].

  34. Priyanka Choudhury, Sanjukta Dasgupta, Parthasarathi Bhattacharyya, Sushmita Roychowdhury, and Koel Chaudhury. Understanding pulmonary hypertension: the need for an integrative metabolomics and transcriptomics approach. MOLECULAR OMICS, 20(6):366–389, JUL 8 2024. [DOI].

  35. Shengbo Wu, Zheping Qu, Danlei Chen, Hao Wu, Qinggele Caiyin, and Jianjun Qiao. Deciphering and designing microbial communities by genome-scale metabolic modelling. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 23:1990–2000, DEC 2024. [DOI].

  36. AswathyK. Raghu, Indumathi Palanikumar, and Karthik Raman. Designing function-specific minimal microbiomes from large microbial communities. NPJ SYSTEMS BIOLOGY AND APPLICATIONS, MAY 3 2024. [DOI].

  37. Telmo Blasco, Francesco Balzerani, LuisV. Valcarcel, Pedro Larranaga, Concha Bielza, MariaPilar Francino, JoseAngel Rufian-Henares, FranciscoJ. Planes, and Sergio Perez-Burillo. Bn-bacarena: bayesian network extension of bacarena for the dynamic simulation of microbial communities. BIOINFORMATICS, MAY 2 2024. [DOI].

  38. Ali Kishk, MariaPires Pacheco, Tony Heurtaux, and Thomas Sauter. Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas. BRIEFINGS IN BIOINFORMATICS, MAY 2 2024. [DOI].

  39. Fernando Silva-Lance, Isabel Montejano-Montelongo, Eric Bautista, LarsK. Nielsen, ParI. Johansson, and IgorMarin deMas. Integrating genome-scale metabolic models with patient plasma metabolome to study endothelial metabolism in situ. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, MAY 2024. [DOI].

  40. Merve Atasoy, WilliamT. ScottJr, Alberte Regueira, Miguel Mauricio-Iglesias, PeterJ. Schaap, and Hauke Smidt. Biobased short chain fatty acid production - exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches. BIOTECHNOLOGY ADVANCES, JUL-AUG 2024. [DOI].

  41. Tong Hao, Zhentao Song, Mingzhi Zhang, Lingrui Zhang, Jiarui Yang, Jingjing Li, and Jinsheng Sun. Reconstruction of metabolic-protein interaction integrated network of <i>eriocheir sinensis</i> and analysis of ecdysone synthesis. GENES, APR 2024. [DOI].

  42. Danel Olaverri-Mendizabal, LuisV. Valcarcel, Naroa Barrena, CarlosJ. Rodriguez, and FranciscoJ. Planes. Review and meta-analysis of the genetic minimal cut set approach for gene essentiality prediction in cancer metabolism. BRIEFINGS IN BIOINFORMATICS, MAR 27 2024. [DOI].

  43. Pavel Dvorak, Barbora Buryskova, Barbora Popelarova, BirgittaE. Ebert, Tibor Botka, Dalimil Bujdos, Alberto Sanchez-Pascuala, Hannah Schoettler, Heiko Hayen, Victor deLorenzo, LarsM. Blank, and Martin Benesik. Synthetically-primed adaptation of <i>pseudomonas putida</i> to a non-native substrate d-xylose. NATURE COMMUNICATIONS, MAR 26 2024. [DOI].

  44. Zhijin Gong, Jiayao Chen, Xinyu Jiao, Hao Gong, Danzi Pan, Lingli Liu, Yang Zhang, and Tianwei Tan. Genome-scale metabolic network models for industrial microorganisms metabolic engineering: current advances and future prospects. BIOTECHNOLOGY ADVANCES, MAY-JUN 2024. [DOI].

  45. Anqiang Ye, Jian-Ning Shen, Yong Li, Xiang Lian, Bin-Guang Ma, and Feng-Biao Guo. Reconstruction of the genome-scale metabolic network model of <i>sinorhizobium fredii</i> ccbau45436 for free-living and symbiotic states. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, MAR 25 2024. [DOI].

  46. Maria-Tsampika Manoli, Alvaro Gargantilla-Becerra, Carlos delCerro Sanchez, Virginia Rivero-Buceta, M.Auxiliadora Prieto, and Juan Nogales. A model-driven approach to upcycling recalcitrant feedstocks in pseudomonas putida by decoupling pha production from nutrient limitation. CELL REPORTS, APR 23 2024. [DOI].

  47. Amandine Paulay, GhjuvanM. Grimaud, Raphael Caballero, Beatrice Laroche, Marion Leclerc, Simon Labarthe, and Emmanuelle Maguin. Design of a proteolytic module for improved metabolic modeling of <i>bacteroides caccae</i>. MSYSTEMS, 2024 MAR 22 2024. [DOI].

  48. Mustafa Sertbas and KutluO. Ulgen. Uncovering the effect of sars-cov-2 on liver metabolism via genome-scale metabolic modeling for reprogramming and therapeutic strategies. ACS OMEGA, 9(13):15535–15546, MAR 22 2024. [DOI].

  49. Abhirami Thumsi, Diego Martinez, SrivatsanJ. Swaminathan, Arezoo Esrafili, AbhiramiP. Suresh, Madhan MohanChandrasekhar Jaggarapu, Kelly Lintecum, Michelle Halim, ShivaniV. Mantri, Yasmine Sleiman, Nicole Appel, Haiwei Gu, Marion Curtis, Cristal Zuniga, and AbhinavP. Acharya. Inverse-vaccines for rheumatoid arthritis re-establish metabolic and immunological homeostasis in joint tissues. ADVANCED HEALTHCARE MATERIALS, 2024 MAR 19 2024. [DOI].

  50. Carolina Shene, Allison Leyton, Liset Flores, Daniela Chavez, JuanA. Asenjo, and Yusuf Chisti. Genome-scale metabolic modeling of <i>thraustochytrium</i> sp. rt2316-16: effects of nutrients on metabolism. BIOTECHNOLOGY AND BIOENGINEERING, 121(6):1986–2001, JUN 2024. [DOI].

  51. AnitaL. Ziegler, Lena Ullmann, Manuel Bossmann, KarlaL. Stein, UlfW. Liebal, Alexander Mitsos, and LarsM. Blank. Itaconic acid production by co-feeding of <i>ustilago maydis</i>: a combined approach of experimental data, design of experiments, and metabolic modeling. BIOTECHNOLOGY AND BIOENGINEERING, 121(6):1846–1858, JUN 2024. [DOI].

  52. MarciaR. Couto, JoanaL. Rodrigues, Adelaide Braga, Oscar Dias, and LigiaR. Rodrigues. Optimization of chondroitin production in <i>e. coli</i> using genome scale models. MOLECULAR SYSTEMS DESIGN & ENGINEERING, 9(6):597–611, JUN 4 2024. [DOI].

  53. Filippo Martinelli, Almut Heinken, Ann-Kristin Henning, MariaA. Ulmer, Tim Hensen, Antonio Gonzalez, Matthias Arnold, Sanjay Asthana, Kathrin Budde, CorinneD. Engelman, Mehrbod Estaki, Hans-Joergen Grabe, MargoB. Heston, Sterling Johnson, Gabi Kastenmueller, Cameron Martino, Daniel Mcdonald, FedericoE. Rey, Ingo Kilimann, Olive Peters, Xiao Wang, EikeJakob Spruth, Anja Schneider, Klaus Fliessbach, Jens Wiltfang, Niels Hansen, Wenzel Glanz, Katharina Buerger, Daniel Janowitz, Christoph Laske, MatthiasH. Munk, Annika Spottke, Nina Roy, Matthias Nauck, Stefan Teipel, Rob Knight, RimaF. Kaddurah-Daouk, BarbaraB. Bendlin, Johannes Hertel, and Ines Thiele. Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in alzheimer's disease. SCIENTIFIC REPORTS, MAR 13 2024. [DOI].

  54. AlvaroR. Lara, Flavio Kunert, Vincent Vandenbroucke, Hilal Taymaz-Nikerel, LuzMaria Martinez, Juan-Carlos Sigala, Frank Delvigne, Guillermo Gosset, and Jochen Buechs. Transport-controlled growth decoupling for self-induced protein expression with a glycerol-repressible genetic circuit. BIOTECHNOLOGY AND BIOENGINEERING, 121(6):1789–1802, JUN 2024. [DOI].

  55. Fernando Cruz, Joao Capela, EugenioCampos Ferreira, Miguel Rocha, and Oscar Dias. Bioiso: an objective-oriented application for assisting the curation of genome-scale metabolic models. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 21(2):215–226, MAR-APR 2024. [DOI].

  56. QuinnS. Solfisburg, Federico Baldini, Brittany Baldwin-Hunter, GeorgeI. Austin, HarryH. Lee, Heekuk Park, DanielE. Freedberg, CharlesJ. Lightdale, Tal Korem, and JulianA. Abrams. The salivary microbiome and predicted metabolite production are associated with barrett's esophagus and high-grade dysplasia or adenocarcinoma. CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION, 33(3):371–380, MAR 1 2024. [DOI].

  57. Panyawarin Soommat, Nachon Raethong, Ratchaprapa Ruengsang, Roypim Thananusak, Teeraphan Laomettachit, Kobkul Laoteng, Treenut Saithong, and Wanwipa Vongsangnak. Light-exposed metabolic responses of <i>cordyceps militaris</i> through transcriptome-integrated genome-scale modeling. BIOLOGY-BASEL, MAR 2024. [DOI].

  58. Debiao Wu, Feng Xu, Yaying Xu, Mingzhi Huang, Zhimin Li, and JuChu. Towards a hybrid model-driven platform based on flux balance analysis and a machine learning pipeline for biosystem design. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY, 9(1):33–42, MAR 2024. [DOI].

  59. Meng Luo, Jinlin Zhu, Jiajia Jia, Hao Zhang, and Jianxin Zhao. Progress on network modeling and analysis of gut microecology: a review. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, MAR 20 2024. [DOI].

  60. Deepanwita Banerjee, IanS. Yunus, XiWang, Jinho Kim, Aparajitha Srinivasan, Russel Menchavez, Yan Chen, JenniferW. Gin, ChristopherJ. Petzold, HectorGarcia Martin, JonK. Magnuson, PaulD. Adams, BlakeA. Simmons, Aindrila Mukhopadhyay, Joonhoon Kim, and TaekSoon Lee. Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in<i> pseudomonas</i><i> putida</i>. METABOLIC ENGINEERING, 82:157–170, MAR 2024. [DOI].

  61. Xavier Marbehan, Magali Roger, Frantz Fournier, Pascale Infossi, Emmanuel Guedon, Louis Delecourt, Regine Lebrun, Marie-Therese Giudici-Orticoni, and Stephane Delaunay. Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of <i>desulfovibrio vulgaris</i> hildenborough. FRONTIERS IN MICROBIOLOGY, FEB 23 2024. [DOI].

  62. Ning Qin, Lingyun Li, Xiaozhen Wan, XuJi, YuChen, Chaokun Li, Ping Liu, Yijie Zhang, Weijie Yang, Junfeng Jiang, Jianye Xia, Shuobo Shi, Tianwei Tan, Jens Nielsen, Yun Chen, and Zihe Liu. Increased co<sub>2</sub> fixation enables high carbon-yield production of 3-hydroxypropionic acid in yeast. NATURE COMMUNICATIONS, FEB 21 2024. [DOI].

  63. Loreto Roman, Felipe Melis-Arcos, Tomas Proschle, PedroA. Saa, and Daniel Garrido. Genome-scale metabolic modeling of the human milk oligosaccharide utilization by <i>bifidobacterium longum</i> subsp. <i>infantis</i>. MSYSTEMS, MAR 19 2024. [DOI].

  64. YuChen, Johan Gustafsson, Jingyu Yang, Jens Nielsen, and EduardJ. Kerkhoven. Single-cell omics analysis with genome-scale metabolic modeling. CURRENT OPINION IN BIOTECHNOLOGY, APR 2024. [DOI].

  65. DavidM. Versluis, Ruud Schoemaker, Ellen Looijesteijn, Jan M.W. Geurts, and Roeland M.H. Merks. 2'-fucosyllactose helps butyrate producers outgrow competitors in infant gut microbiota simulations. ISCIENCE, MAR 15 2024. [DOI].

  66. Eduardo LuisMenezes deAlmeida, EduardJ. Kerkhoven, and WendelBatista daSilveira. Reconstruction of genome-scale metabolic models of non-conventional yeasts: current state, challenges, and perspectives. BIOTECHNOLOGY AND BIOPROCESS ENGINEERING, 29(1):177–183, FEB 2024. [DOI].

  67. Chenguang Liang, Sue Murray, Yang Li, Richard Lee, Audrey Low, Shruti Sasaki, Austin W.T. Chiang, Wen-Jen Lin, Joel Mathews, Will Barnes, and NathanE. Lewis. Lipidsim: inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, markov modeling framework. METABOLIC ENGINEERING, 82:110–122, MAR 2024. [DOI].

  68. ZacharyM. Burcham, AerielD. Belk, BridgetB. Mcgivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, AnruR. Zhang, Pixu Shi, Alexandra Emmons, HeatherL. Deel, ZhenjiangZech Xu, Victoria Nieciecki, Qiyun Zhu, Michael Shaffer, Morgan Panitchpakdi, KellyC. Weldon, Kalen Cantrell, Asa Ben-Hur, SashaC. Reed, GregC. Humphry, Gail Ackermann, Daniel Mcdonald, Siu HungJoshua Chan, Melissa Connor, Derek Boyd, Jake Smith, Jenna M.S. Watson, Giovanna Vidoli, Dawnie Steadman, AaronM. Lynne, Sibyl Bucheli, PieterC. Dorrestein, KellyC. Wrighton, DavidO. Carter, Rob Knight, and JessicaL. Metcalf. A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. NATURE MICROBIOLOGY, MAR 2024. [DOI].

  69. Aruldoss Immanuel, RagothamanM. Yennamalli, and Venkatasubramanian Ulaganathan. Targeting the bottlenecks in levan biosynthesis pathway in <i>bacillus subtilis</i> and strain optimization by computational modeling and omics integration. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 28(2):49–58, FEB 1 2024. [DOI].

  70. Gustav Sjoberg, Alina Rekena, Matilda Fornstad, Petri-Jaan Lahtvee, and Antonius J.A. van Maris. Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2,3-butanediol and glycerol by <i>saccharomyces cerevisiae</i>. METABOLIC ENGINEERING, 82:49–59, MAR 2024. [DOI].

  71. Egeria Scoditti, Silvia Sabatini, Fabrizia Carli, and Amalia Gastaldelli. Hepatic glucose metabolism in the steatotic liver. NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY, 21(5):319–334, MAY 2024. [DOI].

  72. Naveed Ziari and MarcK. Hellerstein. Pymida: a graphical user interface for mass isotopomer distribution analysis. ANALYTICAL CHEMISTRY, 96(6):2303–2308, FEB 2 2024. [DOI].

  73. Freyr Johannsson, JamesT. Yurkovich, Steinn Guomundsson, OlafurE. Sigurjonsson, and Ottar Rolfsson. Temperature dependence of platelet metabolism. METABOLITES, FEB 2024. [DOI].

  74. BrunoG. Galuzzi, Luca Milazzo, and Chiara Damiani. Adjusting for false discoveries in constraint-based differential metabolic flux analysis. JOURNAL OF BIOMEDICAL INFORMATICS, FEB 2024. [DOI].

  75. Leila Hassani, MohammadR. Moosavi, Payam Setoodeh, and Habil Zare. Fastknock: an efficient next-generation approach to identify all knockout strategies for strain optimization. MICROBIAL CELL FACTORIES, JAN 29 2024. [DOI].

  76. Sonia Alcala, Lara Villarino, Laura Ruiz-Canas, JoseR. Couceiro, Miguel Martinez-Calvo, Adrian Palencia-Campos, Diego Navarro, Pablo Cabezas-Sainz, Iker Rodriguez-Arabaolaza, Alfonso Cordero-Barreal, Lucia Trilla-Fuertes, JuanA. Rubiolo, Sandra Batres-Ramos, Mireia Vallespinos, Cristina Gonzalez-Paramos, Jessica Rodriguez, Angelo Gamez-Pozo, Juan angelFresno Vara, SaraFra Fernandez, AmparoBenito Berlinches, Nicolas Moreno-Mata, Ana MariaTorres Redondo, Alfredo Carrato, PatrickC. Hermann, Laura Sanchez, Susana Torrente, MiguelAngel Fernandez-Moreno, JoseL. Mascarenas, and Bruno SainzJr. Targeting cancer stem cell oxphos with tailored ruthenium complexes as a new anti-cancer strategy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH, JAN 27 2024. [DOI].

  77. Eliott Jacopin, Yuki Sakamoto, Kozo Nishida, Kazunari Kaizu, and Koichi Takahashi. An architecture for collaboration in systems biology at the age of the metaverse. NPJ SYSTEMS BIOLOGY AND APPLICATIONS, JAN 27 2024. [DOI].

  78. Mahnoor Zulfiqar, Vinay Singh, Christoph Steinbeck, and Maria Sorokina. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. CRITICAL REVIEWS IN MICROBIOLOGY, 2024 JAN 24 2024. [DOI].

  79. Clemence Joseph, Haris Zafeiropoulos, Kristel Bernaerts, and Karoline Faust. Predicting microbial interactions with approaches based on flux balance analysis: an evaluation. BMC BIOINFORMATICS, JAN 23 2024. [DOI].

  80. Klara Cerk, Pablo Ugalde-Salas, ChabnameGhassemi Nedjad, Maxime Lecomte, Coralie Muller, DavidJ. Sherman, Falk Hildebrand, Simon Labarthe, and Clemence Frioux. Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing. MICROBIAL BIOTECHNOLOGY, 2024. [DOI].

  81. YuChen, Johan Gustafsson, Albert TafurRangel, Mihail Anton, Ivan Domenzain, Cheewin Kittikunapong, Feiran Li, LeYuan, Jens Nielsen, and EduardJ. Kerkhoven. Reconstruction, simulation and analysis of enzyme-constrained metabolic models using gecko toolbox 3.0. NATURE PROTOCOLS, 19(3):629–667, MAR 2024. [DOI].

  82. HimelNahreen Khaleque, Hadi Nazem-Bokaee, Yosephine Gumulya, RossP. Carlson, and AnnaH. Kaksonen. Simulating compatible solute biosynthesis using a metabolic flux model of the biomining acidophile,<i> acidithiobacillus</i><i> ferrooxidans</i> atcc 23270. RESEARCH IN MICROBIOLOGY, JAN-FEB 2024. [DOI].

  83. Sol Han, Dohyeon Kim, Youngshin Kim, and SungHo Yoon. Genome-scale metabolic network model and phenome of solvent-tolerant <i>pseudomonas putida</i> s12. BMC GENOMICS, JAN 16 2024. [DOI].

  84. PedroA. Saa, Sebastian Zapararte, ChristopherC. Drovandi, and LarsK. Nielsen. Looplessfluxsampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models. BMC BIOINFORMATICS, JAN 2 2024. [DOI].

  85. Andrea Angarita-Rodriguez, Yeimy Gonzalez-Giraldo, JuanJ. Rubio-Mesa, AndresFelipe Aristizabal, Andres Pinzon, Janneth Gonzalez, and King-Ho Cheung. Control theory and systems biology: potential applications in neurodegeneration and search for therapeutic targets. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, JAN 2024. [DOI].

  86. ElenaLucy Carter, Chrystala Constantinidou, and MohammadTauqeer Alam. Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations. BRIEFINGS IN BIOINFORMATICS, JAN 2024. [DOI].

  87. Mitzi dela Cruz, Flavio Kunert, Hilal Taymaz-Nikerel, Juan-Carlos Sigala, Guillermo Gosset, Jochen Buchs, and AlvaroR. Lara. Increasing the pentose phosphate pathway flux to improve plasmid dna production in engineered <i>e. coli</i>. MICROORGANISMS, JAN 2024. [DOI].

  88. Isaac Klapper, DanielB. Szyld, Xinli Yu, Karsten Zengler, Tianyu Zhang, and Cristal Zuniga. A domain decomposition method for solution of a pde-constrained generalized nash equilibrium model of biofilm community metabolism. SIAM JOURNAL ON APPLIED MATHEMATICS, 84(1):97–113, 2024. [DOI].

  89. Weiren Liu, Huqiang Wang, Qianfu Zhao, Chenyang Tao, Weifeng Qu, Yushan Hou, Run Huang, Zimei Sun, Guiqi Zhu, Xifei Jiang, Yuan Fang, Jun Gao, Xiaoling Wu, Zhixiang Yang, Rongyu Ping, Jiafeng Chen, Rui Yang, Tianhao Chu, Jian Zhou, Jia Fan, Zheng Tang, Dong Yang, and Yinghong Shi. Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (dgka) as a potential therapeutic target for intrahepatic cholangiocarcinoma. CANCER COMMUNICATIONS, 44(2):226–250, FEB 2024. [DOI].

  90. Maximilian Luginsland, Cleo Kontoravdi, Andy Racher, Colin Jaques, and Alexandros Kiparissides. Elucidating lactate metabolism in industrial cho cultures through the combined use of flux balance and principal component analyses. BIOCHEMICAL ENGINEERING JOURNAL, FEB 2024. [DOI].

  91. Joshua A.M. Kaste and Yair Shachar-Hill. Model validation and selection in metabolic flux analysis and flux balance analysis. BIOTECHNOLOGY PROGRESS, JAN 2024. [DOI].

  92. MariaTeresita Castaneda, Sebastian Nunez, Martin Jamilis, and Hernan DeBattista. Computational assessment of lipid production in <i>rhodosporidium toruloides</i> in two-stage and one-stage batch bioprocesses. BIOTECHNOLOGY AND BIOENGINEERING, 121(1):238–249, JAN 2024. [DOI].

  93. Chengjie Hou, Xin Song, Zhiqiang Xiong, Guangqiang Wang, Yongjun Xia, and Lianzhong Ai. Genome-scale reconstruction of the metabolic network in <i>streptococcus thermophilus</i> s-3 and assess urea metabolism. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, 104(3):1458–1469, FEB 2024. [DOI].

  94. Dario Neves, Daniel Meinen, Tobias B.B. Alter, Lars M.M. Blank, and Birgitta E.E. Ebert. Expanding <i>pseudomonas taiwanensis</i> vlb120's acyl-coa portfolio: propionate production in mineral salt medium. MICROBIAL BIOTECHNOLOGY, 2024. [DOI].

Citations — The COBRA Toolbox (2024)
Top Articles
Latest Posts
Recommended Articles
Article information

Author: Duncan Muller

Last Updated:

Views: 5983

Rating: 4.9 / 5 (59 voted)

Reviews: 90% of readers found this page helpful

Author information

Name: Duncan Muller

Birthday: 1997-01-13

Address: Apt. 505 914 Phillip Crossroad, O'Konborough, NV 62411

Phone: +8555305800947

Job: Construction Agent

Hobby: Shopping, Table tennis, Snowboarding, Rafting, Motor sports, Homebrewing, Taxidermy

Introduction: My name is Duncan Muller, I am a enchanting, good, gentle, modern, tasty, nice, elegant person who loves writing and wants to share my knowledge and understanding with you.