Inspired by: Bernhard Ø Palsson
Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of bacteria. In particular, these models correlate the genome with molecular physiology. Wikipedia (CC BY-SA 3.0)
2023 Articles
14 289 articles
The effective deficiency of biochemical networks
- Damoun Langary, Anika Küken, Zoran Nikoloski, …, Damoun Langary, Anika Küken, Zoran Nikoloski
- Sci Rep, 10.1038/s41598-023-41767-1
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways
- Zhitao Mao, Qianqian Yuan, Haoran Li, …, Shihui Yang, Xiaoping Liao, Hongwu Ma
- Nucleic Acids Res, 10.1093/nar/gkad360
Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction
- Puhua Niu, Maria J Soto, Shuai Huang, …, Francis J Alexander, Ian Blaby, Xiaoning Qian
- J Comput Biol, 10.1089/cmb.2022.0368
Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-Integer Linear Programming for Metabolite Production in Constraint-Based Models: gDel_minRN
- Takeyuki Tamura, Ai Muto-Fujita, Yukako Tohsato, …, Ai Muto-Fujita, Yukako Tohsato, Tomoyuki Kosaka
- J Comput Biol, 10.1089/cmb.2022.0352
CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities
- Alexandru Oarga, Bridget P Bannerman, Jorge Júlvez, …, Alexandru Oarga, Bridget P Bannerman, Jorge Júlvez
- Bioinformatics, 10.1093/bioinformatics/btad053
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli
- Joon Young Park, Sang-Mok Lee, Ali Ebrahim, …, Sang Woo Seo, Bernhard O Palsson, Donghyuk Kim
- None, 10.1093/nargab/lqad006
On the geometry of elementary flux modes
- Frederik Wieder, Martin Henk, Frederik Wieder, …, Frederik Wieder, Martin Henk, Alexander Bockmayr
- J Math Biol, 10.1007/s00285-023-01982-w
Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escherichia coli
- Yuki Kuriya, Masahiro Murata, Masaki Yamamoto, …, Masaki Yamamoto, Naoki Watanabe, Michihiro Araki
- None, 10.3390/bioengineering10060636
Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations
- Yoon-Mi Choi, Dong-Hyuk Choi, Yi Qing Lee, …, Nathan E Lewis, Meiyappan Lakshmanan, Dong-Yup Lee
- None, 10.1016/j.csbj.2023.07.025
FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models
- Anatoly Sorokin, Igor Goryanin, Anatoly Sorokin, Igor Goryanin, Anatoly Sorokin, Igor Goryanin
- Biomolecules, 10.3390/biom13030500
2022 Articles
1 418 articles
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
- Max van ‘t Hof, Omkar S Mohite, Jonathan M Monk, …, Tilmann Weber, Bernhard O Palsson, Morten O A Sommer
- BMC Bioinformatics, 10.1186/s12859-022-05108-9
Modeling the metabolic dynamics at the genome-scale by optimized yield analysis
- Hao Luo, Peishun Li, Boyang Ji, …, Peishun Li, Boyang Ji, Jens Nielsen
- Metab Eng, 10.1016/j.ymben.2022.12.001
Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data
- Saratram Gopalakrishnan, Chintan J Joshi, Miguel Valderrama Gomez, …, William Johnson, Cleo Kontoravdi, Nathan E Lewis
- Metab Eng, 10.1016/j.ymben.2022.12.003
Analysis of the Propionate Metabolism in Bacillus subtilis during 3-Indolacetic Production
- Freddy Castillo-Alfonso, Alejandro Quintana-Menéndez, Gabriel Vigueras-RamÃrez, …, Alfonso Mauricio Sales-Cruz, Luis Manuel Rosales-Colunga, Roberto Olivares-Hernández
- None, 10.3390/microorganisms10122352
Machine learning-guided prediction of potential engineering targets for microbial production of lycopene
- Chang Keun Kang, Jihoon Shin, YoonKyung Cha, …, TaeHo Kim, Young-Kwon Park, Yong Jun Choi
- Bioresour Technol, 10.1016/j.biortech.2022.128455
Navigating and expanding the roadmap of natural product genome mining tools
- Friederike Biermann, Sebastian L Wenski, Eric J N Helfrich, Friederike Biermann, Sebastian L Wenski, Eric J N Helfrich
- None, 10.3762/bjoc.18.178
An improved algorithm for flux variability analysis
- Dustin Kenefake, Erick Armingol, Nathan E Lewis, …, Erick Armingol, Nathan E Lewis, Efstratios N Pistikopoulos
- BMC Bioinformatics, 10.1186/s12859-022-05089-9
Application of comparative genomics of Acetobacter species facilitates genome-scale metabolic reconstruction of the Acetobacter ghanensis LMG 23848T and Acetobacter senegalensis 108B cocoa strains
- Rudy Pelicaen, Stefan Weckx, Didier Gonze, …, Stefan Weckx, Didier Gonze, Luc De Vuyst
- None, 10.3389/fmicb.2022.1060160
Predicting stress response and improved protein overproduction in Bacillus subtilis
- Juan D Tibocha-Bonilla, Cristal Zuñiga, Asama Lekbua, …, Kevin Rychel, Katie Short, Karsten Zengler
- NPJ Syst Biol Appl, 10.1038/s41540-022-00259-0
Systems Biology: New Insight into Antibiotic Resistance
- Piubeli Francine, Piubeli Francine, Piubeli Francine, Piubeli Francine
- None, 10.3390/microorganisms10122362