Small molecule metabolites: discovery of biomarkers and therapeutic targets

S Qiu, Y Cai, H Yao, C Lin, Y Xie, S Tang… - Signal Transduction and …, 2023 - nature.com
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite
accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite …

Recent advances in mass spectrometry-based computational metabolomics

TMD Ebbels, JJJ van der Hooft, H Chatelaine… - Current opinion in …, 2023 - Elsevier
The computational metabolomics field brings together computer scientists, bioinformaticians,
chemists, clinicians, and biologists to maximize the impact of metabolomics across a wide …

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 …

Machine learning for the advancement of genome-scale metabolic modeling

P Kundu, S Beura, S Mondal, AK Das, A Ghosh - Biotechnology Advances, 2024 - Elsevier
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the
interrelations between genotype, phenotype, and external environment. The recent …

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

D Chicco, F Cumbo, C Angione - PLOS Computational Biology, 2023 - journals.plos.org
Data are the most important elements of bioinformatics: Computational analysis of
bioinformatics data, in fact, can help researchers infer new knowledge about biology …

The Warburg effect explained: integration of enhanced glycolysis with heterogeneous mitochondria to promote cancer cell proliferation

L Alberghina - International Journal of Molecular Sciences, 2023 - mdpi.com
The Warburg effect is the long-standing riddle of cancer biology. How does aerobic
glycolysis, inefficient in producing ATP, confer a growth advantage to cancer cells? A new …

Gene signatures for cancer research: A 25-year retrospective and future avenues

W Liu, H He, D Chicco - PLOS Computational Biology, 2024 - journals.plos.org
Over the past two decades, extensive studies, particularly in cancer analysis through large
datasets like The Cancer Genome Atlas (TCGA), have aimed at improving patient therapies …

Metagenome-scale community metabolic modelling for understanding the role of gut microbiota in human health

S Beura, P Kundu, AK Das, A Ghosh - Computers in biology and medicine, 2022 - Elsevier
Metabolic activities of the microbial population are important to maintain the balance of
almost all the ecosystems on earth. In the human gut environment, these microbial …

Recreating metabolic interactions of the tumour microenvironment

R Curvello, N Berndt, S Hauser, D Loessner - Trends in Endocrinology & …, 2024 - cell.com
Tumours are heterogeneous tissues containing diverse populations of cells and an
abundant extracellular matrix (ECM). This tumour microenvironment prompts cancer cells to …

Construction of multiscale genome-scale metabolic models: Frameworks and challenges

X Bi, Y Liu, J Li, G Du, X Lv, L Liu - Biomolecules, 2022 - mdpi.com
Genome-scale metabolic models (GEMs) are effective tools for metabolic engineering and
have been widely used to guide cell metabolic regulation. However, the single gene–protein …