Big data analytics in healthcare

A Belle, R Thiagarajan… - BioMed research …, 2015‏ - Wiley Online Library
The rapidly expanding field of big data analytics has started to play a pivotal role in the
evolution of healthcare practices and research. It has provided tools to accumulate, manage …

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0

L Heirendt, S Arreckx, T Pfau, SN Mendoza… - Nature protocols, 2019‏ - nature.com
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …

A community-driven global reconstruction of human metabolism

I Thiele, N Swainston, RMT Fleming, A Hoppe… - Nature …, 2013‏ - nature.com
Multiple models of human metabolism have been reconstructed, but each represents only a
subset of our knowledge. Here we describe Recon 2, a community-driven, consensus' …

Integrative approaches for finding modular structure in biological networks

K Mitra, AR Carvunis, SK Ramesh, T Ideker - Nature Reviews Genetics, 2013‏ - nature.com
A central goal of systems biology is to elucidate the structural and functional architecture of
the cell. To this end, large and complex networks of molecular interactions are being rapidly …

Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas

SR Rosario, MD Long, HC Affronti, AM Rowsam… - Nature …, 2018‏ - nature.com
Understanding metabolic dysregulation in different disease settings is vital for the safe and
effective incorporation of metabolism-targeted therapeutics in the clinic. Here, using …

Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism

D Machado, M Herrgård - PLoS computational biology, 2014‏ - journals.plos.org
Constraint-based models of metabolism are a widely used framework for predicting flux
distributions in genome-scale biochemical networks. The number of published methods for …

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

C Jo, J Zhang, JM Tam, GM Church, AS Khalil… - Materials Today Bio, 2023‏ - Elsevier
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through
its interactions with growing and decaying flora and their constituent microbiomes. The …

[HTML][HTML] Integrating omics data in genome-scale metabolic modeling: a methodological perspective for precision medicine

P Sen, M Orešič - Metabolites, 2023‏ - mdpi.com
Recent advancements in omics technologies have generated a wealth of biological data.
Integrating these data within mathematical models is essential to fully leverage their …

Fast reconstruction of compact context-specific metabolic network models

N Vlassis, MP Pacheco, T Sauter - PLoS computational biology, 2014‏ - journals.plos.org
Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of
context-specific metabolic network models. The reconstruction of such a model from high …