Publications related to Omics | EPFL Graph Search

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provi ...

NATURE RESEARCH2021

ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses

Bart Deplancke, Vincent Roland Julien Gardeux, Maria Litovchenko

Single-cell omics enables researchers to dissect biological systems at a resolution that was unthinkable just 10 years ago. However, this analytical revolution also triggered new demands in 'big data' management, forcing researchers to stay up to speed wit ...

OXFORD UNIV PRESS2020

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Vassily Hatzimanikatis, Sofia Tsouka

Over the last decades, yeast has become a key model organism for the study of lipid biochemistry. Because the regulation of lipids has been closely linked to various physiopathologies, the study of these biomolecules could lead to new diagnostics and treat ...

OXFORD UNIV PRESS2020

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Noushin Hadadi, Vikash Kumar Pandey, Anush Chiappino-Pepe, Merten Morales, Florence Mehl

Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation re ...

NATURE PUBLISHING GROUP2020

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

Vassily Hatzimanikatis, Matteo Lunghi, Damien Lionel Nicolas, Anush Chiappino-Pepe, 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 ...

2020

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Omics

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer

ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

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

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

Biogeography of microbial bile acid transformations along the murine gut

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

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

Graph Chatbot

Chat with Graph Search

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer

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

Biogeography of microbial bile acid transformations along the murine gut

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

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses

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

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