Genome and pan-genome analysis to classify emerging bacteria
International audience
Gene connectivity and enzyme evolution in the human metabolic network
Published in Biology Direct
BackgroundDetermining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic genes to explore the associations between network structure and the presence and strength of natural selection in the genes whose ...
Integration of molecular features with clinical information for predicting outcomes for neuroblastoma patients
Published in Biology Direct
BackgroundNeuroblastoma is one of the most common types of pediatric cancer. In current neuroblastoma prognosis, patients can be stratified into high- and low-risk groups. Generally, more than 90% of the patients in the low-risk group will survive, while less than 50% for those with the high-risk disease will survive. Since the so-called “high-risk...
The role of synthetic biology in climate change mitigation
Published in Biology Direct
AbstractThere is growing agreement that the aim of United Nations Framework Convention on Climate Change, which is to avoid dangerous anthropogenic interference with the climate system, is not likely to be met without inclusion of methods to physically remove atmospheric carbon. A number of approaches have been suggested, but the community appears ...
Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of c...
Published in Biology Direct
BackgroundThe availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles.ResultsHere we use a transformation of the conventional bacterial strain or gene ...
Application of machine learning techniques for creating urban microbial fingerprints
Published in Biology Direct
BackgroundResearch has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communities remain poorly studied. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) I...
Massive metagenomic data analysis using abundance-based machine learning
Published in Biology Direct
BackgroundMetagenomics is the application of modern genomic techniques to investigate the members of a microbial community directly in their natural environments and is widely used in many studies to survey the communities of microbial organisms that live in diverse ecosystems. In order to understand the metagenomic profile of one of the densest in...
Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data
Published in Biology Direct
BackgroundMetagenomic data of whole genome sequences (WGS) from samples across several cities around the globe may unravel city specific signatures of microbes. Illumina MiSeq sequencing data was provided from 12 cities in 7 different countries as part of the 2018 CAMDA “MetaSUB Forensic Challenge”, including also samples from three mystery sets. W...
Associating expression and genomic data using co-occurrence measures
Published in Biology Direct
AbstractRecent technological evolutions have led to an exponential increase in data in all the omics fields. It is expected that integration of these different data sources, will drastically enhance our knowledge of the biological mechanisms behind genomic diseases such as cancer. However, the integration of different omics data still remains a cha...
MDA19, a novel CB2 agonist, inhibits hepatocellular carcinoma partly through inactivation of AKT signaling pathway
Published in Biology Direct
BackgroundCB2 (cannabinoid receptor 2) agonists have been shown to exert anti-tumor activities in different tumor types. However, there is no study exploring the role of MDA19 (a novel CB2 agonist) in tumors. In this study we aimed to investigate the effects of MDA19 treatment on HCC cell lines, Hep3B and HepG2 and determine the relevant mechanisms...
