A5046031524- Genome Rearrangement Algorithms
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Algorithms and Data Compression
- DNA and Biological Computing
- Enzyme Production and Characterization
- Metabolomics and Mass Spectrometry Studies
- Advanced Proteomics Techniques and Applications
- Advanced Graph Theory Research
- Mass Spectrometry Techniques and Applications
- Phytase and its Applications
- Complexity and Algorithms in Graphs
- Plant Pathogens and Fungal Diseases
- Yeasts and Rust Fungi Studies
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Plant Molecular Biology Research
- Microbial Community Ecology and Physiology
- Plant nutrient uptake and metabolism
- Genetic Mapping and Diversity in Plants and Animals
- RNA modifications and cancer
- Graph Labeling and Dimension Problems
- Cancer-related molecular mechanisms research
- Plant Disease Resistance and Genetics
- Protist diversity and phylogeny
Laboratoire des Sciences du Numérique de Nantes
2017-2025
Nantes Université
2016-2025
Centre National de la Recherche Scientifique
2014-2024
École Centrale de Nantes
2018-2024
Génomique Bioinformatique et Applications
2017-2022
IMT Atlantique
2018
Memorial Sloan Kettering Cancer Center
2014-2015
Max Planck Society
2010-2015
Friedrich Miescher Laboratory
2010-2015
European Molecular Biology Laboratory
2014
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete components with high success rates but assembly complete isoform structures poses a major challenge even when all constituent elements identified. Expression-level estimates also varied widely across methods, based on similar models. Consequently,...
Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive phenotypic variation, and until now these have been interpreted largely in context of annotated reference accession Col-0. Here we report sequencing, assembly annotation genomes 18 natural A. accessions, their transcriptomes. When assessed on basis annotation, one-third protein-coding genes are predicted to be disrupted at least one accession. However, re-annotation each genome revealed that...
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent which this occurs, nor mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited transposons, where CHH was found increase with temperature. Genome-wide association studies (GWAS) revealed that extensive strongly associated...
Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and consequences its ancestral duplication, leaving evolution entire class hemiascomycetes only partly explored. We concentrate here five species Saccharomycetaceae , a large subdivision hemiascomycetes, that we call “protoploid” because they diverged from S. lineage prior to genome duplication. determined complete sequences three these species: Kluyveromyces (Lachancea)...
Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge microbial ecology. In this work, we compared two co-occurrence networks representing soil communities from different sections of pH, temperature and humidity gradient occurring along western slope Andes Atacama Desert. doing so, topological graph alignment was used to determine impact shift environmental variables on OTUs taxonomic composition their relationships. We observed...
SpecPeptidOMS directly aligns peptide fragmentation spectra to whole and undigested protein sequences. The algorithm was specifically initially designed for peptidomics, where the aim is identify peptides that do not result from hydrolysis of a known therefore, whose termini cannot be predicted. Thus, can perform alignments starting ending anywhere in sequence. underlying computational method SpecPeptidOMS, which based on dynamic programming approach, drastically optimized. As result,...
Next-generation sequencing technologies have revolutionized genome and transcriptome sequencing. RNA-Seq experiments are able to generate huge amounts of sequence reads at a fraction the cost Sanger Reads produced by these relatively short error prone. To utilize such for reconstruction gene-structure identification, one needs be accurately align over intron boundaries. In this unit, we describe PALMapper, fast easy-to-use tool that is designed compute both unspliced spliced alignments...
Combinatorial works on genome rearrangements have so far ignored the influence of intergene sizes, i.e. number nucleotides between consecutive genes, although it was recently shown decisive for accuracy inference methods (Biller et al. in Genome Biol Evol 8:1427–39, 2016; Biller Beckmann A, Bienvenu L, Jonoska N, editors. Proceedings Pursuit Universal-12th conference computability Europe, CiE 2016, Lecture notes computer science, vol 9709, Paris, France, June 27–July 1, 2016. Berlin:...
During the evolutionary process, genomes are affected by various genome rearrangements, that is, events modify large stretches of genetic material. In literature, a number models have been proposed to estimate occurred during evolution; most them represent as an ordered sequence genes, and, in particular, disregard material between consecutive genes. However, recent studies showed taking into account genes can enhance distance estimations. Reversal and transposition rearrangements widely...
As one of the most studied genome rearrangements, tandem repeats have a considerable impact on genetic backgrounds inherited diseases. Many methods designed for repeat detection reference sequences obtain high quality results. However, in case de novo context, where no sequence is available, remains difficult problem. The short reads obtained with second-generation sequencing are not long enough to span regions that contain repeats. This length limitation was tackled by third-generation...
Abstract We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that is integrated in Galaxy. Its distinguishing features include customizable computational workflows and a modular pipeline architecture facilitates comparative assessment of tool data quality. Oqtans integrates assortment machine learning-powered tools into Galaxy, which show superior or equal performance to state-of-the-art tools. Implemented comprise complete analysis workflow: short-read...
Abstract Background In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, limited number false positives, and huge search space allowing any without priori. The scientific community needs new developments in this area aid discovery novel post-translational that may play important roles disease. Results To make progress on issue, we...
The study of evolutionary mechanisms is made more and accurate by the increase in number fully sequenced genomes. One main problems to reconstruct plausible ancestral genome architectures based on comparison contemporary Current methods have largely focused finding complete for genomes, and, due computational difficulty problem, stop after a small equivalent minimal solutions been found. Recent results suggest, however, that set minimum very large heterogeneous. In fact these are collections...
Genome rearrangements are mutations affecting large portions of a genome, and reversal is one the most studied genome in literature through Sorting by Reversals (SbR) problem. SbR solvable polynomial time on signed permutations (i.e., gene orientation known), it NP-hard unsigned permutations. This problem (and many others considering rearrangements) models as list its genes order they appear, ignoring all other information present genome. Recent works claimed that incorporation size...
The evolutionary distance between two genomes can be estimated by computing a minimum length sequence of operations, called genome rearrangements, that transform one into another. Usually, is modeled as an ordered genes, and most the studies in rearrangement literature consist shaping biological scenarios mathematical models. For instance, allowing different rearrangements operations at same time, adding constraints to these (e.g., each affect given number genes), considering implies cost...
Abstract Background Mass spectrometry remains the privileged method to characterize proteins. Nevertheless, most of spectra generated by an experiment remain unidentified after their analysis, mostly because modifications they carry. Open Modification Search (OMS) methods offer a promising answer this problem. However, assessing quality OMS identifications difficult task. Methods Aiming at better understanding relationship between (1) similarity pairs provided and (2) relevance corresponding...
Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two based on genome rearrangements. However, most them focused (order the) genes a genome, disregarding other important elements in it. Recently, researchers shown considering regions each pair genes, called <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">intergenic...
Genomes present various types of repeated structures having important roles in the mechanism evolution. In particular, tandem repeats are analysed for their impact on genetic backgrounds inherited diseases. However, main objective today's de novo assemblers is to output long, high-quality, assembled sequences; this end, they use heuristic-based assembling procedures, which can leave many regions unassembled - and particular exact due genomes complexity. paper, we propose an effective method,...
Current methods for detecting synteny work well genomes with high degrees of inter- and intra-species chromosomal homology, such as mammals. This paper presents a new algorithm computation that is suited to covering large evolutionary span. It based on three-step process: identification initial microsyntenic homologous regions, extension boundaries reconstruction syntenic blocks by groups genomic segments are conserved in every subject genome. Our method performs GRIMM-Synteny mammalian...
Background The current revolution in sequencing technologies allows us to obtain a much more detailed picture of transcriptomes via deep RNA Sequencing (RNA-Seq). In considering the full complement transcripts that comprise transcriptome, two important analytical questions emerge: what is abundance and which genes or are differentially expressed. parallel with developing technologies, data analysis software also constantly updated improve accuracy sensitivity while minimizing run times....