Pouyan Ghaffari

TL;DR: The CASINO (Community And Systems-level INteractive Optimization) toolbox is described, a comprehensive computational platform for analysis of microbial communities through metabolic modeling that could quantitatively describe altered fecal and serum amino acid levels in response to diet intervention.

TL;DR: Investigating how the gut microbiota modulates the global metabolic differences in duodenum, jejunum, ileum, colon, liver, and two white adipose tissue depots obtained from conventionally raised (CONV‐R) and germ‐free (GF) mice revealed that the gut microbiome influences host amino acid and glutathione metabolism in mice.

TL;DR: Cancer-associated reprogramming of metabolism is reviewed and the capability of genome-scale metabolic modeling approaches in perceiving a system-level perspective of cancer metabolism and in detecting novel selective drug targets is highlighted.

TL;DR: This work reconstructed Genome scale metabolic models for eleven cell lines based on RNA-Seq data and validated the functionality of these models with data from metabolite profiling, and predicted 85 antimetabolites that can inhibit growth of, or even kill, any of the cell lines, while at the same time not being toxic for 83 different healthy human cell types.

TL;DR: In this article , the authors proposed a new perspective on using data-driven approach and applying computational modelling and machine learning to design microbiome-aware personalized treatment for Irritable Bowel Syndrome (IBS).