Avoiding the Enumeration of Infeasible Elementary Flux Modes by Including Transcriptional Regulatory Rules in the Enumeration Process Saves Computational Costs.

Autor: Christian Jungreuthmayer, David E Ruckerbauer, Matthias P Gerstl, Michael Hanscho, Jürgen Zanghellini

Publikováno v: PLoS ONE, Vol 10, Iss 6, p e0129840 (2015)

Despite the significant progress made in recent years, the computation of the complete set of elementary flux modes of large or even genome-scale metabolic networks is still impossible. We introduce a novel approach to speed up the calculation of ele

Externí odkaz: https://doaj.org/article/2f4cdded027f48bbb00f8cddac5fa4a1

Towards rational glyco-engineering in CHO: from data to predictive models

Autor: Jürgen Zanghellini, Nicole Borth, David E. Ruckerbauer, Diana Széliová, Jerneja Štor

Publikováno v: Current Opinion in Biotechnology. 71:9-17

Metabolic modeling strives to develop modeling approaches that are robust and highly predictive. To achieve this, various modeling designs, including hybrid models, and parameter estimation methods that define the type and number of parameters used i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::418daf0750dddc4b9b52de7aee67f3d9
https://doi.org/10.1016/j.copbio.2021.05.003

A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes

Autor: Lasse Ebdrup Pedersen, Karen Julie la Cour Karottki, Helene Faustrup Kildegaard, Alex Thomas, Hooman Hefzi, Nathan E. Lewis, Songyuan Li, Chintan Joshi, Philipp Spahn, Juan A. Hernandez Bort, Gyun Min Lee, David E. Ruckerbauer, Nicole Borth, Jae Seong Lee

Publikováno v: Metab Eng
Karottki, K J L C, Hefzi, H, Li, S, Pedersen, L E, Spahn, P N, Joshi, C, Ruckerbauer, D, Bort, J A H, Thomas, A, Lee, J S, Borth, N, Lee, G M, Kildegaard, H F & Lewis, N E 2021, ' A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes ', Metabolic Engineering, vol. 66, pp. 114-122 . https://doi.org/10.1016/j.ymben.2021.03.017

Over the past decades, optimization of media formulation and feeding strategies have fueled a many-fold improvement in CHO-based biopharmaceutical production. While Design of Experiments (DOE) and media screens have led to many advances, genome editi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::55d3a308807be59b6b5c1d42a0a54b70
https://pubmed.ncbi.nlm.nih.gov/33813034

What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines

Autor: Hanne Bjerre Christensen, David E. Ruckerbauer, Gunda Koellensperger, Nathan E. Lewis, Lars B. Petersen, Tim J. Causon, Klaus Natter, Christina Troyer, Sarah N. Galleguillos, Stephan Hann, Diana Széliová, Lars K. Nielsen, Nicole Borth, Dong-Yup Lee, Jürgen Zanghellini, Michael Hanscho, Harald Schoeny

Publikováno v: Metabolic engineering. 61

Background Cell line-specific, genome-scale metabolic models enable rigorous and systematic in silico investigation of cellular metabolism. Such models have recently become available for Chinese hamster ovary (CHO) cells. However, a key ingredient, n

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::39d6373673652ca593f924d5d026c2fe
https://pubmed.ncbi.nlm.nih.gov/32619503

Robust Analytical Methods for the Accurate Quantification of the Total Biomass Composition of Mammalian Cells

Autor: David E. Ruckerbauer, Stephen Hann, Špela Knez, Robert Ahrends, Nicole Borth, Christina Troyer, Gunda Koellensperger, Diana Széliová, Jürgen Zanghellini, Cristina Coman, Harald Schoeny, Evelyn Rampler

Publikováno v: Methods in Molecular Biology ISBN: 9781071601587

Biomass composition is an important input for genome-scale metabolic models and has a big impact on their predictive capabilities. However, researchers often rely on generic data for biomass composition, e.g. collected from similar organisms. This le

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::603977ae59e13a00a2664d390ff4d669
https://doi.org/10.1007/978-1-0716-0159-4_7