Cassan Océane

• PhD
• Editor at Ephyra Publishing

Gene expression is controlled by proximal and distal cis-regulatory elements (CREs), containing DNA motifs bound by various transcription factors (TFs). Other sequence features, such as specific k-mers or low complexity regions, have also been implicated. However, in a dynamic biological process such as cell differentiation, we lack an understandin...

With this very first Editorial, we would like to introduce a new actor in the field of aging research and communication. This new actor is Systems Aging, an open access peer-reviewed journal dedicated to advancing aging research through the use of computational and systems biology. It is published by Ephyra Publishing, a small new publisher intendi...

Motivations Gene Regulatory Networks (GRNs) are traditionally inferred from gene expression profiles monitoring a specific condition or treatment. In the last decade, integrative strategies have successfully emerged to guide GRN inference from gene expression with complementary prior data. However, datasets used as prior information and validation...

The elevation of atmospheric CO 2 leads to a decline in plant mineral content, which might pose a significant threat to food security in coming decades. Although few genes have been identified for the negative effect of elevated CO 2 on plant mineral composition, several studies suggest the existence of genetic factors. Here, we performed a large-s...

The elevation of atmospheric CO 2 leads to a decline in the plant mineral content, which might pose a significant threat to food security in the coming decades. To date, very few genes have been identified as having a role in the negative effect of elevated CO 2 on plant mineral composition. Yet, several studies have shown a certain degree of diver...

The elevation of atmospheric CO2 leads to a decline in the plant mineral content, which poses a major threat to food security in the coming decades. To date, very few genes have been identified as having a role in the negative effect of elevated CO2 on plant mineral composition. Yet, several studies have shown a certain degree of diversity in the i...

The elevation of atmospheric CO2 leads to a decline in the plant mineral content, which poses a major threat to food security in the coming decades. To date, very few genes have been identified as having a role in the negative effect of elevated CO2 on plant mineral composition. Yet, several studies have shown a certain degree of diversity in the i...

Gene Regulatory Networks (GRN) are traditionnally inferred from gene expression profiles monitoring a specific condition or treatment. In the last decade, integrative strategies have successfully emerged to guide GRN inference from gene expression with complementary prior data. However, datasets used as prior information and validation gold standar...

Gene Regulatory Networks (GRN) are traditionnally inferred from gene expression profiles monitoring a specific condition or treatment. In the last decade, integrative strategies have successfully emerged to guide GRN inference from gene expression with complementary prior data. However, datasets used as prior information and validation gold standar...

The elevation of atmospheric CO2 leads to a decline in the plant mineral content, which poses a major threat to food security in the coming decades. To date, very few genes have been identified as having a role in the negative effect of elevated CO2 on plant mineral composition. Yet, several studies have shown a certain degree of diversity in the i...

Human activity is causing an elevation of CO2 levels in the atmosphere, that are expected to rise from 420 ppm to approximately 1000 ppm by the end of the century.C3 plants, a major part of cultivated crops, are particularly affected by the rise of CO2levels. Even though a stimulation of biomass production is expected under elevatedCO2 (eCO2), this...

The elevation of CO2 in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO2 on plant growth and physiology, and to identi...

The elevation of atmospheric CO2 concentration has a strong impact on the physiology of C3 plants, far beyond photosynthesis and C metabolism. In particular, it reduces the concentrations of most mineral nutrients in plant tissues, posing major threats on crop quality, nutrient cycles, and carbon sinks in terrestrial agro-ecosystems. The causes of...

Polycomb-group (PcG) proteins are major chromatin complexes that regulate gene expression, mainly described as repressors keeping genes in a transcriptional silent state during development. Recent studies have nonetheless suggested that PcG proteins might have additional functions, including on targeting active genes or independently of gene expres...

Background High-throughput transcriptomic datasets are often examined to discover new actors and regulators of a biological response. To this end, graphical interfaces have been developed and allow a broad range of users to conduct standard analyses from RNA-seq data, even with little programming experience. Although existing solutions usually prov...

Background In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes. However, several questions remain regarding the conservation of these combinations among different gene classes, regulatory regions and cell types. Results We propose a new approach...

In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes. However, several questions remain regarding the conservation of these combina-tions among different gene classes, regulatory regions and cell types. We propose a new approach named TFcoop to inf...