22 documents found, page 1 of 3
FROG analysis ensures the reproducibility of genome scale metabolic models
Raman, Karthik; Kratochvil, Miroslav; Olivier, Brett G.; Konig, Matthias; Sengupta, Pratyay; Baskaran, Dinesh Kumar Kuppa; Nguyen, Tung V NGenome scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting a...
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms metabolism under different conditions1. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Geneproteinreaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with ...
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Excess all-cause mortality during the COVID-19 pandemic in Europe – preliminary...
Vestergaard, Lasse S.; Nielsen, Jens; Richter, Lukas; Schmid, Daniela; Bustos, Natalia; Braeye, Toon; Denissov, Gleb; Veideman, Tatjana; Luomala, OskariA remarkable excess mortality has coincided with the COVID-19 pandemic in Europe. We present preliminary pooled estimates of all-cause mortality for 24 European countries/federal states participating in the European monitoring of excess mortality for public health action (EuroMOMO) network, for the period March–April 2020. Excess mortality particularly affected ≥ 65 year olds (91% of all excess deaths), but al...
Turnover dependent phenotypic simulation: a quantitative constraint-based simul...
Pereira, Rui Miguel Pinheiro Silva; Vilaça, P.; Maia, Paulo; Nielsen, Jens; Rocha, I.The uncertain relationship between genotype and phenotype can make strain engineering an arduous trial and error process. To identify promising gene targets faster, constraint-based modelling methodologies are often used, although they remain limited in their predictive power. Even though the search for gene knock-outs is fairly established in constraint-based modelling, most strain design methods still model g...
European all-cause excess and influenza-attributable mortality in the 2017/18 s...
Nielsen, Jens; Vestergaard, Lasse; Richter, L.; Schmid, D.; Bustos, N.; Asikainen, T.; Trebbien, R.; Denissov, G.; Innos, K.; Virtanen, M.J.Objectives: Weekly monitoring of European all-cause excess mortality, the EuroMOMO network, observed high excess mortality during the influenza B/Yamagata dominated 2017/18 winter season, especially among elderly. We describe all-cause excess and influenza-attributable mortality during the season 2017/18 in Europe. Methods: Based on weekly reporting of mortality from 24 European countries or sub-national region...
Guidelines and recommendations on yeast cell death nomenclature
Carmona-Gutierrez, Didac; Bauer, Maria Anna; Zimmermann, Andreas; Aguilera, Andrés; Austriaco, Nicanor; Ayscough, Kathryn; Balzan, RenaElucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cel-lular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the defi-nition of accide...
Metabolite secretion in microorganisms: the theory of metabolic overflow put to...
Pinu, Farhana R.; Granucci, Ninna; Daniell, James; Han, Ting-Li; Carneiro, Sónia; Rocha, I.; Nielsen, Jens; Villas-Boas, Silas G.Introduction Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. Materials and Methods The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete differ...
Screening of 2A peptides for polycistronic gene expression in yeast
Souza-Moreira, Tatiana M. [UNESP]; Navarrete, Clara; Chen, Xin; Zanelli, Cleslei F. [UNESP]; Valentini, Sandro R. [UNESP]; Furlan, Maysa [UNESP]Made available in DSpace on 2018-12-11T17:21:52Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-08-01; A complexity of pathway expression in yeast compared to prokaryotes is the need for separate promoters and terminators for each gene expressed. Single transcript expression and separated protein production is possible via the use of 2A viral peptides, but detailed characterization to assess their suitab...
Excess all-cause and influenza-attributable mortality in Europe, December 2016 ...
Vestergaard, Lasse S; Nielsen, Jens; Krause, Tyra G; Espenhain, Laura; Tersago, Katrien; Bustos Sierra, Natalia; Denissov, Gleb; Innos, KaireSince December 2016, excess all-cause mortality was observed in many European countries, especially among people aged ≥ 65 years. We estimated all-cause and influenza-attributable mortality in 19 European countries/regions. Excess mortality was primarily explained by circulation of influenza virus A(H3N2). Cold weather snaps contributed in some countries. The pattern was similar to the last major influenza A(H3...