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Related publications (29)

Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism

Vassily Hatzimanikatis, Anush Chiappino-Pepe, Matteo Lunghi, Damien Lionel Nicolas, Aarti Krishnan, Dominique Soldati-Favre

To survive and proliferate in diverse host environments with varying nutrient availability, the obligate intracellular parasite Toxoplasma gondii reprograms its metabolism. We have generated and curated a genome-scale metabolic model (iTgo) for the fast-re ...

CELL PRESS2020

Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Vassily Hatzimanikatis, Sofia Tsouka

Metabolism is a network of biotransformations that sustain life in cells. Over the past decades, metabolism has been studied in multiple contexts, ranging from medicine to industrial manufacturing. In particular, lipid metabolism has been linked to various ...

EPFL2020

Biogeography of microbial bile acid transformations along the murine gut

Rizlan Bernier-Latmani, Laure Menin, Solenne Anne Marie Marion, Lyne Desharnais

Bile acids, which are synthesized from cholesterol by the liver, are chemically transformed along the intestinal tract by the gut microbiota, and the products of these transformations signal through host receptors, affecting overall host health. These tran ...

AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2020

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

Didier Trono, George Coukos, Marion Leleu, Evaristo Jose Planet Letschert, Markus Müller, Florian Huber, Laia Simo Riudalbas, Delphine Yvette L Grun, Ioannis Xenarios, Lin Zhang, Alexandre Harari, Marion Arnaud

Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides derived from annotated ...

Nature Research2020

On the relevance of quality score metadata in genomic sequence data for omics applications

Ana Angelica Hernandez Lopez

High-throughput sequencing of DNA molecules has revolutionized biomedical research by enabling the quantitative analysis of the genome to study its function, structure and dynamics. It is driving sequencing-based experiments in life sciences as evidenced b ...

EPFL2019

The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism

Felix Naef, Cédric Gobet, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Jake Yeung

The circadian clock and associated feeding rhythms have a profound impact on metabolism and the gut microbiome. To what extent microbiota reciprocally affect daily rhythms of physiology in the host remains elusive. Here, we analyzed transcriptome and metab ...

Cell Press2019

Identifying microbial species by single-molecule DNA optical mapping and resampling statistics

Theo Lasser, Aleksandra Radenovic, Arno Pino Bouwens, Tomas Lukes, Adrien Charles-François Raymond Descloux, Kristin Stefanie Grussmayer, Jochem Deen

Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to p ...

2019

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Georgios Fengos, Tuure Eelis Hameri

Large-scale kinetic models are used for designing, predicting, and understanding the metabolic responses of living cells. Kinetic models are particularly attractive for the biosynthesis of target molecules in cells as they are typically better than other t ...

2019

Lysozyme-Induced Transcriptional Regulation of TNF-alpha Pathway Genes in Cells of the Monocyte Lineage

Paul Joseph Dyson, Romain Hamelin, Florence Armand, Isabelle Mireille Claude Schepens, Gianni Sava

Lysozyme is one of the most important anti-bacterial effectors in the innate immune system of animals. Besides its direct antibacterial enzymatic activity, lysozyme displays other biological properties, pointing toward a significant anti-inflammatory effec ...

2019

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