Works matching DE "METABOLIC models"

Results: 1146

Gut microbiota composition and phylogenetic analysis in autism spectrum disorder: a comparative study.

Published in:

Frontiers in Psychiatry, 2025, p. 1, doi. 10.3389/fpsyt.2025.1609638

By:

Xiang, Fangtao;
Zhang, Mei;
Wei, Xin;
Chang, Jiali

Publication type:

Article

Ripening‐related metabolic changes in different chili pepper cultivars revealed by nuclear magnetic resonance spectroscopy.

Published in:

Journal of the Science of Food & Agriculture, 2025, v. 105, n. 11, p. 6084, doi. 10.1002/jsfa.14313

By:

Seong, Gi‐Un;
Yun, Dae‐Yong;
Cho, Jeong‐Seok;
Park, Seul‐Ki;
Lee, Gyu Seok;
Choi, Jeong Hee;
Park, Kee‐Jai;
Lim, Jeong‐Ho

Publication type:

Article

A country-wide survey into the composition and transformation of short-chain organic acids in anaerobic sludge digesters at wastewater treatment plants in Denmark.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-08493-2

By:

Li, Zijun;
Dueholm, Morten Kam Dahl;
Jiang, Chenjing;
Zhu, Bihe;
Liu, Lei;
Nielsen, Per Halkjær;
Hao, Liping

Publication type:

Article

A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information.

Published in:

PeerJ, 2025, p. 1, doi. 10.7717/peerj.19296

By:

Silva-Andrade, Claudia;
Hernández, Sergio;
Saa, Pedro;
Perez-Rueda, Ernesto;
Garrido, Daniel;
Martin, Alberto J.

Publication type:

Article

Systems metabolic engineering of Corynebacterium glutamicum for efficient L-tryptophan production.

Published in:

Synthetic & Systems Biotechnology, 2025, v. 10, n. 2, p. 511, doi. 10.1016/j.synbio.2025.02.002

By:

Yufei Dong;
Zhen Chen

Publication type:

Article

System-level characterization of engineered and evolved formatotrophic E. coli strains.

Published in:

Synthetic & Systems Biotechnology, 2025, v. 10, n. 2, p. 650, doi. 10.1016/j.synbio.2025.03.001

By:

Yilmaz, Suzan;
Kanis, Boas;
Hogers, Rensco A. H.;
Benito-Vaquerizo, Sara;
Kahnt, Jörg;
Glatter, Timo;
Dronsella, Beau;
Erb, Tobias J.;
Suarez-Diez, Maria;
Claassens, Nico J.

Publication type:

Article

PYF: a multi-functional algorithm for predicting production and optimizing metabolic engineering strategy in Escherichia coli microbial consortia Open Access.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 3, p. 1, doi. 10.1093/bib/bbaf295

By:

Yang, Chen;
Zhao, Yingqi;
Xue, Boyuan;
Wang, Shaojie;
Su, Haijia

Publication type:

Article

Metabolism-associated protein network constructing and host-directed anti-influenza drug repurposing Open Access.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 3, p. 1, doi. 10.1093/bib/bbaf163

By:

Tang, Hao;
Jiang, Feng;
Zhang, Zhi;
Yang, Jiaojiao;
Li, Lu;
Zhang, Qingye

Publication type:

Article

Jaxkineticmodel: Neural ordinary differential equations inspired parameterization of kinetic models.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012733

By:

van Lent, Paul;
Bunkova, Olga;
Magyar, Bálint;
Planken, Léon;
Schmitz, Joep;
Abeel, Thomas

Publication type:

Article

ADME analysis, metabolic prediction, and molecular docking of lipoic acid with SARS-CoV-2 Omicron spike protein.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-93121-2

By:

dos Santos, Carlos Alonso Leite;
de Araújo Monteiro, Antonia Adeublena;
Costa, Adrielle Rodrigues;
Barros, Luiz Marivando;
Aloufi, Abdulaziz;
Almutairi, Mashal M.;
Hassan, Waseem;
Kamdem, Jean Paul;
Duarte, Antonia Eliene;
Ali, Abid;
Ibrahim, Mohammad

Publication type:

Article

Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00555-5

By:

Lee, Yi Qing;
Choi, Yoon-Mi;
Park, Seo-Young;
Kim, Su-Kyung;
Lee, Minouk;
Kim, Dongseok;
Koduru, Lokanand;
Lakshmanan, Meiyappan;
Jung, Sangyong;
Kim, Mi Jin;
Choe, Yon Ho;
Lee, Dong-Yup

Publication type:

Article

Algebraic differentiation for fast sensitivity analysis of optimal flux modes in metabolic models Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 6, p. 1, doi. 10.1093/bioinformatics/btaf287

By:

Chapman, Hester;
Kratochvíl, Miroslav;
Ebenhöh, Oliver;
Wilken, St Elmo

Publication type:

Article

An enzyme activation network reveals extensive regulatory crosstalk between metabolic pathways.

Published in:

Molecular Systems Biology, 2025, v. 21, n. 7, p. 870, doi. 10.1038/s44320-025-00111-7

By:

Al Zubaidi, Sultana Mohammed;
Nasar, Muhammad Ibtisam;
Notebaart, Richard A;
Ralser, Markus;
Alam, Mohammad Tauqeer

Publication type:

Article

Reply to Vaz et al., Editorial Commentary: Should "Heterogeneous response" be considered as new category for assessing treatment response in patients with breast cancer?

Published in:

2025

By:

Altena, Renske;
Tran, Thuy A.;
Tzortzakakis, Antonios

Publication type:

Letter

Charting the state of GEMs in microalgae: progress, challenges, and innovations.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1614397

By:

Tamburro, Jacob;
Boyle, Nanette R.

Publication type:

Article

Diazotrophic growth of free-living Rhizobium etli: Community-like metabolic modeling of growing and non-growing nitrogen-fixing cells.

Published in:

PLoS ONE, 2025, v. 20, n. 6, p. 1, doi. 10.1371/journal.pone.0325888

By:

Afarin, Maryam;
Naeimpoor, Fereshteh

Publication type:

Article

From empirical to theoretical models of light response curves - linking photosynthetic and metabolic acclimation.

Published in:

Photosynthesis Research, 2020, v. 145, n. 1, p. 5, doi. 10.1007/s11120-019-00681-2

By:

Herrmann, Helena A.;
Schwartz, Jean-Marc;
Johnson, Giles N.

Publication type:

Article

Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides.

Published in:

Photosynthesis Research, 2015, v. 123, n. 2, p. 167, doi. 10.1007/s11120-014-0061-1

By:

Imam, Saheed;
Fitzgerald, Colin;
Cook, Emily;
Donohue, Timothy;
Noguera, Daniel

Publication type:

Article

Substrate type and CO<sub>2</sub> addition significantly influence succinic acid production of Basfia succiniciproducens.

Published in:

Biotechnology Letters, 2023, v. 45, n. 9, p. 1133, doi. 10.1007/s10529-023-03406-7

By:

Balázs, Márta;
Bartos, Hunor;
Lányi, Szabolcs;
Bodor, Zsolt;
Miklóssy, Ildikó

Publication type:

Article

Systematically gap-filling the genome-scale metabolic model of CHO cells.

Published in:

Biotechnology Letters, 2021, v. 43, n. 1, p. 73, doi. 10.1007/s10529-020-03021-w

By:

Fouladiha, Hamideh;
Marashi, Sayed-Amir;
Li, Shangzhong;
Li, Zerong;
Masson, Helen O.;
Vaziri, Behrouz;
Lewis, Nathan E.

Publication type:

Article

Additional effects of duodenojejunal bypass on glucose metabolism in a rat model of sleeve gastrectomy.

Published in:

Surgery Today, 2019, v. 49, n. 7, p. 637, doi. 10.1007/s00595-019-1772-x

By:

Takayama, Hiroomi;
Ohta, Masayuki;
Tada, Kazuhiro;
Watanabe, Kiminori;
Kawasaki, Takahide;
Endo, Yuichi;
Iwashita, Yukio;
Inomata, Masafumi

Publication type:

Article

A thermodynamic-based approach to model the entry into metabolic depression by mammals and birds.

Published in:

Journal of Comparative Physiology B: Biochemical, Systemic & Environmental Physiology, 2022, v. 192, n. 5, p. 593, doi. 10.1007/s00360-022-01442-9

By:

Nogueira de Sá, P. G.;
Chaui-Berlinck, José Guilherme

Publication type:

Article

Enhancing endurance performance predictions: the role of movement velocity in metabolic simulations demonstrated by cycling cadence.

Published in:

European Journal of Applied Physiology, 2025, v. 125, n. 4, p. 895, doi. 10.1007/s00421-024-05663-4

By:

Dunst, Anna Katharina;
Hesse, Clemens;
Ueberschär, Olaf

Publication type:

Article

The scaling of human basal and resting metabolic rates.

Published in:

European Journal of Applied Physiology, 2021, v. 121, n. 1, p. 193, doi. 10.1007/s00421-020-04515-1

By:

Bowes, Heather M.;
Burdon, Catriona A.;
Taylor, Nigel A. S.

Publication type:

Article

Systematic optimization of fed-batch simultaneous saccharification and fermentation at high-solid loading based on enzymatic hydrolysis and dynamic metabolic modeling of Saccharomyces cerevisiae.

Published in:

Applied Microbiology & Biotechnology, 2016, v. 100, n. 5, p. 2459, doi. 10.1007/s00253-015-7173-1

By:

Unrean, Pornkamol;
Khajeeram, Sutamat;
Laoteng, Kobkul

Publication type:

Article

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects.

Published in:

Applied Microbiology & Biotechnology, 2015, v. 99, n. 3, p. 1109, doi. 10.1007/s00253-014-6298-y

By:

Liu, Yanfeng;
Shin, Hyun-dong;
Li, Jianghua;
Liu, Long

Publication type:

Article

Cardioprotective effect of green tea and green coffee extract as metformin’s add-on to prevent cardiac fibrosis in a rat model of metabolic syndrome.

Published in:

Journal of Research in Pharmacy, 2024, v. 28, n. 1, p. 16, doi. 10.29228/jrp.668

By:

CHOMSY, Indah Nur;
ROHMAN, Mohammad Saifur;
KHOTIMAH, Husnul;
WIDODO, Nashi;
Panca NUGRAHINI, Nur Ida

Publication type:

Article

Brain in metabolic syndrome model: The effect of exercises and caloric restriction.

Published in:

Journal of Research in Pharmacy, 2022, v. 26, n. 5, p. 1352, doi. 10.29228/jrp.227

By:

ALEV-TUZUNER, Burcin;
GENC-KAHRAMAN, Nevin;
IPEKCI, Hazal;
USTUNDAG, Unsal Veli;
TUNALI-AKBAY, Tugba;
EMEKLI-ALTURFAN, Ebru;
SENER, Goksel;
YARAT, Aysen

Publication type:

Article

Oxidative stress and urinary system damage in fructoseinduced rat model of metabolic syndrome: Effect of calorie restriction and exercise.

Published in:

Journal of Research in Pharmacy, 2020, v. 24, n. 3, p. 318, doi. 10.35333/jrp.2020.153

By:

ŞENER, Tarık Emre;
ÇEVİK, Özge;
ÇETİNEL, Şule;
ŞENER, Göksel

Publication type:

Article

Designing a synthetic microbial community through genome metabolic modeling to enhance plant–microbe interaction.

Published in:

Environmental Microbiome, 2023, v. 18, n. 1, p. 1, doi. 10.1186/s40793-023-00536-3

By:

Gonçalves, Osiel S.;
Creevey, Christopher J.;
Santana, Mateus F.

Publication type:

Article

In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling.

Published in:

Environmental Microbiome, 2023, v. 18, n. 1, p. 1, doi. 10.1186/s40793-022-00458-6

By:

Devika, Neelakantan Thulasi;
Katneni, Vinaya Kumar;
Jangam, Ashok Kumar;
Suganya, Panjan Nathamuni;
Shekhar, Mudagandur Shashi;
Jithendran, Karingalakkandy Poochirian

Publication type:

Article

Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments.

Published in:

Environmental Microbiome, 2022, v. 17, n. 1, p. 1, doi. 10.1186/s40793-022-00438-w

By:

Chiciudean, Iulia;
Russo, Giancarlo;
Bogdan, Diana Felicia;
Levei, Erika Andrea;
Faur, Luchiana;
Hillebrand-Voiculescu, Alexandra;
Moldovan, Oana Teodora;
Banciu, Horia Leonard

Publication type:

Article

A personalized metabolic modelling approach through integrated analysis of RNA-Seq-based genomic variants and gene expression levels in Alzheimer's disease.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-07941-z

By:

Uzuner Odongo, Dilara;
İlgün, Atılay;
Bozkurt, Fatma Betül;
Çakır, Tunahan

Publication type:

Article

A personalized metabolic modelling approach through integrated analysis of RNA-Seq-based genomic variants and gene expression levels in Alzheimer's disease.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-07941-z

By:

Uzuner Odongo, Dilara;
İlgün, Atılay;
Bozkurt, Fatma Betül;
Çakır, Tunahan

Publication type:

Article

The evolutionary landscape of prokaryotic chromosome/plasmid balance.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-07167-5

By:

Xue, Wenzhi;
Hong, Juken;
Wang, Teng

Publication type:

Article

Enhancement of rapamycin production by metabolic engineering in Streptomyces hygroscopicus based on genome-scale metabolic model.

Published in:

Journal of Industrial Microbiology & Biotechnology, 2017, v. 44, n. 2, p. 259, doi. 10.1007/s10295-016-1880-1

By:

Dang, Lanqing;
Liu, Jiao;
Wang, Cheng;
Liu, Huanhuan;
Wen, Jianping

Publication type:

Article

Uricemia in juvenile pigs model: effect of nephrectomy and potassium oxonate.

Published in:

Journal of Animal & Feed Sciences, 2019, v. 28, n. 3, p. 254, doi. 10.22358/jafs/110436/2019

By:

Mosiichuk, N.;
Grujic, D.;
Woliński, J.;
Podpryatov, S. E.;
Podpriatov, S. S.;
Szczurek, P.;
Yatsenko, T.;
Shmihel, H.;
Drahanchuk, O.;
Pierzynowski, S. G.;
Pierzynowska, K. Goncharova

Publication type:

Article

Real-time toxicity and metabolic activity tracking of human cells exposed to Escherichia coli O157:H7 in a mixed consortia.

Published in:

Ecotoxicology, 2015, v. 24, n. 10, p. 2133, doi. 10.1007/s10646-015-1552-3

By:

Xu, Tingting;
Marr, Enolia;
Lam, Haylie;
Ripp, Steven;
Sayler, Gary;
Close, Dan

Publication type:

Article

Comparison of Different Ex-Vivo Preservation Strategies on Cardiac Metabolism in an Animal Model of Donation after Circulatory Death.

Published in:

Journal of Clinical Medicine, 2023, v. 12, n. 10, p. 3569, doi. 10.3390/jcm12103569

By:

Mastrobuoni, Stefano;
Johanns, Manuel;
Vergauwen, Martial;
Beaurin, Gwen;
Rider, Mark;
Gianello, Pierre;
Poncelet, Alain;
Van Caenegem, Olivier

Publication type:

Article

An Interactive Model for Managing Metabolic Resistance.

Published in:

Julius-Kühn-Archiv, 2024, n. 478, p. 92, doi. 10.5073/20240109-072136-0

By:

Richter, Otto;
Beffa, Roland;
Lepke, Janin

Publication type:

Article

Punica granatum L. Extract Shows Cardioprotective Effects Measured by Oxidative Stress Markers and Biomarkers of Heart Failure in an Animal Model of Metabolic Syndrome.

Published in:

Antioxidants, 2023, v. 12, n. 6, p. 1152, doi. 10.3390/antiox12061152

By:

Niewiadomska, Joanna;
Kasztura, Monika;
Janus, Izabela;
Chełmecka, Elżbieta;
Stygar, Dominika Marta;
Frydrychowski, Piotr;
Wojdyło, Aneta;
Noszczyk-Nowak, Agnieszka

Publication type:

Article

Antioxidative Effects of Black Currant and Cornelian Cherry Juices in Different Tissues of an Experimental Model of Metabolic Syndrome in Rats.

Published in:

Antioxidants, 2023, v. 12, n. 6, p. 1148, doi. 10.3390/antiox12061148

By:

Paunovic, Marija;
Kotur-Stevuljevic, Jelena;
Arsic, Aleksandra;
Milosevic, Maja;
Todorovic, Vanja;
Guzonjic, Azra;
Vucic, Vesna;
Petrovic, Snjezana

Publication type:

Article

Effects of Deacetylase Inhibition on the Activation of the Antioxidant Response and Aerobic Metabolism in Cellular Models of Fanconi Anemia.

Published in:

Antioxidants, 2023, v. 12, n. 5, p. 1100, doi. 10.3390/antiox12051100

By:

Bertola, Nadia;
Regis, Stefano;
Bruno, Silvia;
Mazzarello, Andrea Nicola;
Serra, Martina;
Lupia, Michela;
Sabatini, Federica;
Corsolini, Fabio;
Ravera, Silvia;
Cappelli, Enrico

Publication type:

Article

Single-Cell Kinetic Modeling of β-Lapachone Metabolism in Head and Neck Squamous Cell Carcinoma.

Published in:

Antioxidants, 2023, v. 12, n. 3, p. 741, doi. 10.3390/antiox12030741

By:

Raddatz, Andrew D.;
Furdui, Cristina M.;
Bey, Erik A.;
Kemp, Melissa L.

Publication type:

Article

Dietary Mg Supplementation Decreases Oxidative Stress, Inflammation, and Vascular Dysfunction in an Experimental Model of Metabolic Syndrome with Renal Failure.

Published in:

Antioxidants, 2023, v. 12, n. 2, p. 283, doi. 10.3390/antiox12020283

By:

López-Baltanás, Rodrigo;
Rodríguez-Ortiz, María E.;
Díaz-Tocados, Juan M.;
Martinez-Moreno, Julio M.;
Membrives, Cristina;
Rodelo-Haad, Cristian;
Pendón Ruiz de Mier, M. Victoria;
Rodríguez, Mariano;
Canalejo, Antonio;
Almadén, Yolanda;
Muñoz-Castañeda, Juan R.

Publication type:

Article

Modelos animales en el estudio del síndrome metabólico.

Published in:

TIP Revista Especializada en Ciencias Químico-Biológicas, 2021, v. 24, p. 1, doi. 10.22201/fesz.23958723e.2021.373

By:

Escalona Mugica, José Rene;
Barajas Martínez, Antonio;
Alfaro Becerril, Orlando A.;
Estrada Rojo, Francisco;
Ángeles Castellanos, Manuel;
Ubaldo-Reyes, Laura M.

Publication type:

Article

Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models.

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.87406

By:

Vezina, Ben;
Watts, Stephen C.;
Hawkey, Jane;
Cooper, Helena B.;
Judd, Louise M.;
Jenney, Adam W. J.;
Monk, Jonathan M.;
Holt, Kathryn E.;
Wyres, Kelly L.

Publication type:

Article

Development and validation of metabolic models for predicting survival and immune status of hepatocellular carcinoma patients.

Published in:

Advances in Clinical & Experimental Medicine, 2023, v. 32, n. 12, p. 1423, doi. 10.17219/acem/162819

By:

Xueying Li;
Mengli Gu;
Qiying Hu;
Yihui Weng;
Xianlei Cai

Publication type:

Article

Simulating metabolic pathways to enhance interpretations of metabolome genome-wide association studies.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-01634-7

By:

Kodate, Shun;
Sato, Mitsuharu;
Hishinuma, Eiji;
Kojima, Kaname;
Motoike, Ikuko N.;
Abe, Hikaru;
Abe, Michiaki;
Abe, Momoka;
Abe, Naomi;
Abe, Noriko;
Abe, Tomomi;
Abe, Yuto;
Ahiko, Shizuko;
Aiki, Kayo;
Aizawa, Hiromi;
Akiyama, Yukari;
Anzawa, Hayato;
Aoki, Eri;
Aoki, Yuichi;
Arai, Hiroko

Publication type:

Article

Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii.

Published in:

Frontiers in Plant Science, 2015, p. 1, doi. 10.3389/fpls.2015.00474

By:

Chapman, Stephen P.;
Paget, Caroline M.;
Johnson, Giles N.;
Schwartz, Jean-Marc

Publication type:

Article