Undisclosed, unmet and neglected challenges in multi-omics studies

S Tarazona, A Arzalluz-Luque, A Conesa - Nature Computational …, 2021 - nature.com
Multi-omics approaches have become a reality in both large genomics projects and small
laboratories. However, the multi-omics research community still faces a number of issues …

Microalgal heterotrophic and mixotrophic culturing for bio-refining: from metabolic routes to techno-economics

O Perez-Garcia, Y Bashan - Algal Biorefineries: Volume 2: Products and …, 2015 - Springer
In comparison with conventional photo-autotrophic cultivation, heterotrophic and mixotrophic
cultivations of microalgae offers a feasible strategy to produce biomass and valuable …

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PD Karp, SM Paley, M Krummenacker… - Briefings in …, 2010 - academic.oup.com
Pathway Tools is a production-quality software environment for creating a type of model-
organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc …

Environments that induce synthetic microbial ecosystems

N Klitgord, D Segrè - PLoS computational biology, 2010 - journals.plos.org
Interactions between microbial species are sometimes mediated by the exchange of small
molecules, secreted by one species and metabolized by another. Both one-way …

PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases

T Liu, P Salguero, M Petek… - Nucleic Acids …, 2022 - academic.oup.com
PaintOmics is a web server for the integrative analysis and visualisation of multi-omics
datasets using biological pathway maps. PaintOmics 4 has several notable updates that …

[HTML][HTML] Multi-omics and metabolic modelling pipelines: challenges and tools for systems microbiology

M Fondi, P Liò - Microbiological research, 2015 - Elsevier
Integrated-omics approaches are quickly spreading across microbiology research labs,
leading to (i) the possibility of detecting previously hidden features of microbial cells like …

Metabolic network modeling of microbial interactions in natural and engineered environmental systems

O Perez-Garcia, G Lear, N Singhal - Frontiers in microbiology, 2016 - frontiersin.org
We review approaches to characterize metabolic interactions within microbial communities
using Stoichiometric Metabolic Network (SMN) models for applications in environmental and …

Metabolic engineering for enhancing microbial biosynthesis of advanced biofuels

M Das, P Patra, A Ghosh - Renewable and Sustainable Energy Reviews, 2020 - Elsevier
Increasing global energy demand and environmental concerns associated with petroleum
have raised interest in biofuels for reducing dependency on crude oil and promote carbon …

The application of flux balance analysis in systems biology

EP Gianchandani, AK Chavali… - … : Systems Biology and …, 2010 - Wiley Online Library
An increasing number of genome‐scale reconstructions of intracellular biochemical
networks are being generated. Coupled with these stoichiometric models, several systems …

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

C Huthmacher, A Hoppe, S Bulik, HG Holzhütter - BMC systems biology, 2010 - Springer
Background Despite enormous efforts to combat malaria the disease still afflicts up to half a
billion people each year of which more than one million die. Currently no approved vaccine …