Cyril Matthey-Doret

Swiss Federal Institute of Technology in Lausanne | EPFL · Swiss Data Science Center

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investiga...

The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high-quality genome sequences for two extensively studied A. castell...

Over the last decade, genomic proximity ligation approaches have reshaped our vision of chromosomes 3D organizations, from bacteria nucleoids to larger eukaryotic genomes. The different protocols (3Cseq, Hi-C, TCC, MicroC [XL], Hi-CO, etc.) rely on common steps (chemical fixation digestion, ligation…) to detect pairs of genomic positions in close p...

Numerous bacteria and viruses use cells from another species to ensure their proliferation. This mode of reproduction implies the pathogen must escape the host immune system and reprogram its metabolism to sustain its own needs. These changes are often detrimental to the host cell and cause pathologies or death. The intracellular bacteria which use...

The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high quality genome sequences for two extensively studied A. castell...

Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here w...

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Chromosomes of all species studied so far display a variety of higher-order organizational features such as domains, loops, or compartments. Many of these structures have been characterized from the genome-wide contact maps generated by chromosome conformation capture approaches (Hi-C, ChIA-PET,...). Indeed, DNA 3D structures translate as distinct...

Sex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, the large inse...

Sex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, a large insect...

Changes from sexual reproduction to female-producing parthenogenesis (thelytoky) have great evolutionary and ecological consequences, but how many times parthenogenesis evolved in different animal taxa is unknown. We present the first exhaustive database covering 765 cases of parthenogenesis in haplodiploid (arrhenotokous) arthropods, and estimate...

Figure S1. Frequency of parthenogenesis in Chalcidoidea. Phylogeny from Heraty, et al. (1). Total number of species per family was taken from Noyes (2). Figure S2. Frequency of parthenogenesis in Symphyta. Phylogeny from Klopfstein, et al. (3) and the total number of species was taken from Taeger and Blank (4). 14 families with fewer than 80 speci...

Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs...