A5036539061- Music Technology and Sound Studies
- Music and Audio Processing
- Algorithms and Data Compression
- Neuroscience and Music Perception
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Diverse Musicological Studies
- Chronic Lymphocytic Leukemia Research
- Lymphoma Diagnosis and Treatment
- Machine Learning in Bioinformatics
- Acute Lymphoblastic Leukemia research
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Animal Disease Management and Epidemiology
- Musicology and Musical Analysis
- Viral Infections and Immunology Research
- semigroups and automata theory
- DNA and Biological Computing
- Natural Language Processing Techniques
- Speech and Audio Processing
- RNA Research and Splicing
- Genetics, Bioinformatics, and Biomedical Research
- Research Data Management Practices
- Publishing and Scholarly Communication
- Chromosomal and Genetic Variations
Centre de Recherche en Informatique
2016-2025
Université de Lille
2016-2025
Ommic (France)
2015-2024
Direction Générale de l'Armement
2024
Centre National de la Recherche Scientifique
2011-2023
Centre de Recherche en Informatique, Signal et Automatique de Lille
2015-2022
École Centrale de Lille
2018-2022
Centre de recherche Inria Lille - Nord Europe
2008-2016
Institut national de recherche en informatique et en automatique
2006-2014
Laboratoire d'Informatique Fondamentale de Lille
2006-2014
Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification quantification minimal residual disease (MRD) in lymphoid neoplasms has been the focus intense research, development application. However, standardization validation a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay design, including bioinformatics, was performed within EuroClonality-NGS...
The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called V(D)J recombinations, is specific to each lymphocyte, enables recognition antigenes. Today, with new sequencing techniques, one can get billions DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it now possible picture population lymphocytes, monitor more accurately immune response as well pathologies such leukemia.Vidjil an open-source...
The diversity of the immune repertoire is grounded on V(D)J recombinations in several loci. Many algorithms and software detect designate these high-throughput sequencing data. To improve their efficiency, we propose a multi-loci seed identification through an Aho-Corasick like automaton as well seed-based gene filtration. These were implemented into Vidjil-algo, used routinely by labs for analysis hematologic malignancies. We benchmark results Vidjil-algo MiXCR five datasets, evaluating...
Abstract Background Dogs and rats have a highly developed capability to detect identify odorant molecules, even at minute concentrations. Previous analyses shown that the olfactory receptors (ORs) specifically bind molecules are encoded by largest gene family sequenced in mammals so far. Results We identified five amino acid patterns characteristic of ORs recently boxer dog brown Norway rat genomes. Using these patterns, we retrieved 1,094 genes 1,493 from shotgun sequences. The sequences...
V(D)J recombinations in lymphocytes are essential for immunological diversity. They also useful markers of pathologies. In leukemia, they used to quantify the minimal residual disease during patient follow-up. However, full breadth lymphocyte diversity is not fully understood. We propose new algorithms that process high-throughput sequencing (HTS) data extract unnamed junctions and gather them into clones quantification. This analysis based on a seed heuristic fast scalable because first...
Abstract Analysis and interpretation of Ig TCR gene rearrangements in the conventional, low-throughput way have their limitations terms resolution, coverage, biases. With advent high-throughput, next-generation sequencing (NGS) technologies, a deeper analysis and/or (IG/TR) is now within reach, which impacts on all main applications IG/TR immunogenetic analysis. To bridge generation gap from low- to high-throughput analysis, EuroClonality-NGS Consortium has been formed, with objectives...
Accurate and rapid identification of viruses is crucial for an effective medical diagnosis when dealing with infections. Conventional methods, including DNA amplification techniques or lateral-flow assays, are constrained to a specific set targets search for. In this study, we introduce novel tandem mass spectrometry proteotyping-based method that offers universal approach the pathogenic other components, eliminating need priori knowledge sample composition. Our protocol relies on time...
Automatic harmonic analysis has been an enduring focus of the MIR community, and enjoyed a particularly vigorous revival interest in machine-learning age. We here on specific case Roman numeral which, by virtue requiring key/functional information addition to chords, may be viewed as acutely challenging use case. report three main developments. First, we provide new meta-corpus bringing together all existing datasets; this offers greater scale diversity, not only music represented, but also...
In November 2006, six symptomatic cases of hepatitis A in pupils a secondary school Upper Normandy, France, were reported to the district health service. This paper describes outbreak investigation undertaken with aim identify vehicle and source infection, implement control measures estimate size outbreak. primary case at was defined as pupil or member staff IgM anti-HAV detected serum onset symptoms between 12 21 2006; contact who developed had two seven weeks later. We performed study...
Summary High‐throughput sequencing ( HTS ) is considered a technical revolution that has improved our knowledge of lymphoid and autoimmune diseases, changing approach to leukaemia both at diagnosis during follow‐up. As part an immunoglobulin/T cell receptor‐based minimal residual disease MRD assessment acute lymphoblastic patients, we assessed the performance feasibility replacement first steps based on DNA isolation Sanger sequencing, using protocol combined with bioinformatics analysis...
The musical analysis of large-scale structures, such as the classical sonata form, requires to integrate multiple analyses local events into a global coherent analysis. Modelling structures is still challenging task for research community. It includes building large and accurate annotated corpora, well developing practical efficient tools in order visualize these corpora. finally conception effective properly evaluated MIR algorithms.We propose machine learning approach form structure on 32...
Musical co-creativity aims at making humans and computers collaborate to compose music. As an MIR team in computational musicology, we experimented with when writing our entry the "AI Song Contest 2020". Artificial intelligence was used generate song's structure, harmony, lyrics, hook melody independently as a basis for human composition. It challenge from both creative technical point of view: very short time-frame, had adapt its own simple models, or experiment existing ones, related yet...
One of the pinnacles form in classical Western music, fugue is often used teaching music analysis and composition. Fugues alternate between instances a subject other patterns modulatory sections, called episodes. Musicological analyses are generally built on these sections. We have developed several algorithms to perform an automated fugue, starting from score which all voices separated. By focusing diatonic similarities pitch intervals, we detect subjects countersubjects, as well partial...
Walnut blight, due to Xanthomonas arboricola pv. juglandis (Xaj), is one of the most important diseases walnut trees (Juglans regia). It responsible for significant crop losses which can reach more than 50% nut drops. In south western France, disease management has relied upon 3 4 copper compound sprays applied from bud break female flowering. However, this strategy often ineffective and no other solution yet been found. Moreover, there a lack knowledge on development. Thus, we tried better...
Abstract B cell receptor (BcR) immunoglobulins (IG) display a tremendous diversity due to complex DNA rearrangements, the V(D)J recombination, further enhanced by somatic hypermutation process. In chronic lymphocytic leukemia (CLL), mutational load of clonal BcR IG expressed leukemic cells constitutes an important prognostic and predictive biomarker. Here, we provide reliable methodology capable determining status genes in CLL using high-throughput sequencing, starting from or RNA.
Abstract Within the EuroClonality-NGS group, immune repertoire analysis for target identification in lymphoid malignancies was initially developed using two-stage amplicon approaches, essentially as a progressive modification of preceding methods Sanger sequencing. This approach has, however, limitations with respect to sample handling, adaptation automation, and risk contamination by products. We therefore one-step PCR individual barcoding batched IGH, IGK, TRD, TRG, TRB rearrangements,...