A5014679436- Genetic and phenotypic traits in livestock
- Gene expression and cancer classification
- Animal Genetics and Reproduction
- Bioinformatics and Genomic Networks
- Reconstructive Surgery and Microvascular Techniques
- Cleft Lip and Palate Research
- Animal Nutrition and Physiology
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Genetic Mapping and Diversity in Plants and Animals
- Craniofacial Disorders and Treatments
- Adipose Tissue and Metabolism
- Regulation of Appetite and Obesity
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- Insect and Pesticide Research
- Insect and Arachnid Ecology and Behavior
- Bayesian Methods and Mixture Models
- Head and Neck Cancer Studies
- Facial Trauma and Fracture Management
- Reconstructive Facial Surgery Techniques
- Animal Virus Infections Studies
- Aquaculture disease management and microbiota
- Gut microbiota and health
- Plant Virus Research Studies
Génétique Animale et Biologie Intégrative
2016-2025
Universitätsmedizin Greifswald
2021-2025
AgroParisTech
2016-2025
Université Paris-Saclay
2016-2025
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2018-2025
Bellvitge University Hospital
2024
Universität Greifswald
2022-2023
Université de Lille
2020-2023
Université de Picardie Jules Verne
2020-2023
University of Tübingen
2023
During the last 3 years, a number of approaches for normalization RNA sequencing data have emerged in literature, differing both type bias adjustment and statistical strategy adopted. However, as continue to accumulate, there has been no clear consensus on appropriate method be used or impact chosen downstream analysis. In this work, we focus comprehensive comparison seven recently proposed methods differential analysis RNA-seq data, with an emphasis use varied real simulated datasets...
Abstract Motivation: RNA sequencing is now widely performed to study differential expression among experimental conditions. As tests are on a large number of genes, stringent false-discovery rate control required at the expense detection power. Ad hoc filtering techniques regularly used moderate this correction by removing genes with low signal, little attention paid their impact downstream analyses. Results: We propose data-driven method based Jaccard similarity index calculate threshold...
Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, functional annotation of genomes is a critical step to decipher genotype-to-phenotype relationships livestock animals. As part Functional Annotation Animal Genomes (FAANG) action, FR-AgENCODE project aimed create reference maps domesticated animals by profiling landscape transcription (RNA-seq), chromatin accessibility (ATAC-seq) conformation (Hi-C) species representing...
Abstract Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact ruminant production. In this study, rumen microbiome from Holstein cows was characterized through a combination 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH 4 ) dry matter intake (DMI) were individually measured over 4–6 weeks to calculate CH yield y = /DMI) per cow. We implemented clustering, multivariate mixed model analyses identify set operational taxonomic unit...
Abstract Because of its high requirements on dexterity and microsurgical skills the need complete understanding flap anatomy, microvascular free transfer belongs to most demanding surgical procedures. Therefore, courses for raising exercise are considered a prerequisite prepare clinical practise. To achieve teaching conditions as realistic possible we used novel cadaver embalming method enabling tissue dissection comparable living body. Thirty cadavers which were offered us by Institute...
Abstract To differentiate between the contribution of mammary epithelial cells (MEC) and infiltrating immune to gene expression profiles tissue during early stage mastitis, we investigated in goats vivo transcriptional response MEC an experimental intra infection (IMI) with Staphylococcus aureus , using a non-invasive RNA sampling method from milk fat globules (MFG). Microarrays were used record patterns first 24 hours post-infection (hpi). This approach was combined laser capture...
Abstract Motivation: In recent years, gene expression studies have increasingly made use of high-throughput sequencing technology. turn, research concerning the appropriate statistical methods for analysis digital (DGE) has flourished, primarily in context normalization and differential analysis. Results: this work, we focus on question clustering DGE profiles as a means to discover groups co-expressed genes. We propose Poisson mixture model using rigorous framework parameter estimation well...
Abstract Although a large number of clustering algorithms have been proposed to identify groups co-expressed genes from microarray data, the question if and how such methods may be applied RNA-seq data remains unaddressed. In this work, we investigate use transformations in conjunction with Gaussian mixture models for co-expression analyses, as well penalized model selection criterion select both an appropriate transformation clusters present data. This approach has advantage accounting...
Abstract Background Mature sperm carry thousands of RNAs, including mRNAs, lncRNAs, tRNAs, rRNAs and sncRNAs, though their functional significance is still a matter debate. Growing evidence suggests that especially are selectively retained during spermiogenesis or specifically transferred epididymis maturation, thus delivered to the oocyte at fertilization, providing resources for embryo development. However , deep characterization sncRNA content bull its expression profile across breeds...
Chemical communication is a widely used mode of for social insects and has been demonstrated to be involved in many behaviours physiological processes such as reproduction, nutrition or the fight against parasites pathogens. In honey bee, Apis mellifera , release chemical compounds by brood plays role worker behaviour, physiology, foraging activities colony health whole. Several have already described pheromones, components ester pheromone (E)-β-ocimene. other originating from diseased...
Nasoalveolar molding (NAM) has gained wide acceptance and evidence in cleft therapy. However, standardized treatment protocols experiences recorded from European centres are lacking. The results of 40 infants with lip palate treated presurgical NAM according to the Grayson technique were analyzed. Standardized parameters width nasal symmetry measured pre- posttreatment plaster casts digitalized 3-dimensional STL models. Statistical analyses performed by using Student´s t-test a per-protocol...
Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most them based on similar frameworks after normalization, differing primarily in choice data distribution, mean and variance estimation strategy filtering. We propose an evaluation impact these choices when few biological replicates through use synthetic sets. This framework is real sets allows exploration various scenarios proportion non-differentially...
Gene regulatory networks refer to the interactions that occur among genes and other cellular products. The topology of these can be inferred from measurements changes in gene expression over time. However, because measurement device (i.e., microarrays) typically yields information on thousands few biological replicates, systems are quite difficult elucidate. An approach with proven effectiveness for inferring is Dynamic Bayesian Network. We have developed an iterative empirical procedure a...
Summary Plant domestication has led to considerable phenotypic modifications from wild species modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as reduction of diversity or global gene co‐expression patterns. In this study, we used a combination expression and population genetics crop tomato decipher footprints domestication. We found set 1729 differentially expressed genes ( DEG ) between two...
Abstract In contrast to mammals, adult fish display a remarkable ability fully regenerate central nervous system (CNS) axons, enabling functional recovery from CNS injury. Both and mammals normally undergo developmental downregulation of axon growth activity as neurons mature. Fish are able damage-induced “reprogramming” through re-expression genes necessary for guidance, however, the gene regulatory mechanisms remain unknown. Here we present first comprehensive analysis reprogramming in...
Klebsiella pneumoniae causes severe diseases including sepsis, pneumonia and wound infections is differentiated into hypervirulent (hvKp) classic (cKp) pathotypes. hvKp isolates are characterized clinically by invasive multiple site infection phenotypically in particular through hypermucoviscosity increased siderophore production, enabled the presence of respective virulence genes, which partly carried on plasmids.Here, we analyzed two K. a human patient that caused infection. By applying...
(1) Background: Evaluation of impact adjuvant radiation therapy (RT) in patients with oral squamous cell carcinoma the cavity/oropharynx (OSCC) up to 4 cm (pT1/pT2) and solitary ipsilateral lymph node metastasis (pN1). A non-irradiated group clinical follow-up was chosen for control, survival quality life (QL) were compared; (2) Methods: This prospective multicentric comprehensive cohort study included resected OSCC (pT1/pT2, pN1, cM0) who allocated into or observation. The primary endpoint...
Abstract Controversy exists over how long a free flap is dependent on its pedicle and if neovascularization different between types, recipient sites, irradiated nonirradiated patients. An understanding of the timing this process should optimize safety secondary procedures involving flap. In prospective clinical study, hemoglobin oxygenation capillary flow were measured in 50 flaps (25 forearm flaps, 15 osteocutaneous fibula 10 anterolateral thigh flaps) 4 12 weeks postoperatively. The...
The parasite Varroa destructor represents a significant threat to honeybee colonies. Indeed, development of infestation within colonies, if left untreated, often leads the death colony. Although its impact on bees has been extensively studied, less is known about biology and functional processes governing adult life cycle adaptation host. We therefore developed full transcriptomic catalogue in females included pairwise comparisons with males, artificially-reared non-reproducing (10 stages...