Genome-scale models in human metabologenomics

A Mardinoglu, BØ Palsson - Nature Reviews Genetics, 2024 - nature.com
Metabologenomics integrates metabolomics with other omics data types to comprehensively
study the genetic and environmental factors that influence metabolism. These multi-omics …

Critical challenges and advances in recombinant adeno‐associated virus (rAAV) biomanufacturing

Q Fu, A Polanco, YS Lee, S Yoon - Biotechnology and …, 2023 - Wiley Online Library
Gene therapy is a promising therapeutic approach for genetic and acquired diseases
nowadays. Among DNA delivery vectors, recombinant adeno‐associated virus (rAAV) is one …

Recon3D enables a three-dimensional view of gene variation in human metabolism

E Brunk, S Sahoo, DC Zielinski, A Altunkaya… - Nature …, 2018 - nature.com
Genome-scale network reconstructions have helped uncover the molecular basis of
metabolism. Here we present Recon3D, a computational resource that includes three …

Recon 2.2: from reconstruction to model of human metabolism

N Swainston, K Smallbone, H Hefzi, PD Dobson… - Metabolomics, 2016 - Springer
Introduction The human genome-scale metabolic reconstruction details all known metabolic
reactions occurring in humans, and thereby holds substantial promise for studying complex …

A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolism

H Hefzi, KS Ang, M Hanscho, A Bordbar… - Cell systems, 2016 - cell.com
Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are
widely used in mammalian cell line engineering research. To elucidate metabolic …

A systematic evaluation of methods for tailoring genome-scale metabolic models

S Opdam, A Richelle, B Kellman, S Li, DC Zielinski… - Cell systems, 2017 - cell.com
Genome-scale models of metabolism can illuminate the molecular basis of cell phenotypes.
Since some enzymes are only active in specific cell types, several algorithms use omics data …

Low carbon fuels and commodity chemicals from waste gases–systematic approach to understand energy metabolism in a model acetogen

E Marcellin, JB Behrendorff, S Nagaraju… - Green …, 2016 - pubs.rsc.org
Gas fermentation using acetogenic bacteria offers a promising route for the sustainable
production of low carbon fuels and commodity chemicals from abundant, inexpensive C1 …

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

JM Gutierrez, A Feizi, S Li, TB Kallehauge… - Nature …, 2020 - nature.com
Abstract In mammalian cells,> 25% of synthesized proteins are exported through the
secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion …

Human systems biology and metabolic modelling: a review—from disease metabolism to precision medicine

C Angione - BioMed research international, 2019 - Wiley Online Library
In cell and molecular biology, metabolism is the only system that can be fully simulated at
genome scale. Metabolic systems biology offers powerful abstraction tools to simulate all …

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal

CJ Fritzemeier, D Hartleb, B Szappanos… - PLoS computational …, 2017 - journals.plos.org
Energy metabolism is central to cellular biology. Thus, genome-scale models of
heterotrophic unicellular species must account appropriately for the utilization of external …