David Salgado
A5063600106- Genomics and Rare Diseases
- Cancer Genomics and Diagnostics
- Biomedical Text Mining and Ontologies
- Congenital heart defects research
- Muscle Physiology and Disorders
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Cardiac Valve Diseases and Treatments
- COVID-19 diagnosis using AI
- Congenital Heart Disease Studies
- Genomic variations and chromosomal abnormalities
- AI in cancer detection
- Genetic and rare skin diseases.
- Bioinformatics and Genomic Networks
- Developmental Biology and Gene Regulation
- RNA and protein synthesis mechanisms
- Erythrocyte Function and Pathophysiology
- Cell Image Analysis Techniques
- SARS-CoV-2 detection and testing
- RNA Research and Splicing
- Neurogenetic and Muscular Disorders Research
- CRISPR and Genetic Engineering
- Gene expression and cancer classification
- Wind Turbine Control Systems
Dalhousie University
1982-2024
Queen Elizabeth II Health Sciences Centre
2024
Aix-Marseille Université
2014-2023
Inserm
2014-2023
Centre National de la Recherche Scientifique
2007-2023
Institut Français de Bioinformatique
2022-2023
Institut National de Recherche en Santé Publique
2017-2023
Centre de Génétique Médicale de Marseille
2019-2022
Escuela Politécnica del Ejército
2022
Génétique Médicale & Génomique Fonctionelle
2016-2021
Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, improved clinical care. Locus-specific databases allow collection, organization, storage, analysis genetic variants disease. Here, we describe development TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed data 7,149 held within database. A total 5,682 large were observed (80%...
Significance Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced genome a venomous snake, king cobra, and assessed composition venom gland expressed genes, small RNAs, secreted proteins. We show that regulatory components secretory system may have evolved from pancreatic origin toxin genes were co-opted by distinct genomic mechanisms. After co-option, important capture massively expanded gene...
The automatic extraction of chemical information from text requires the recognition entity mentions as one its key steps. When developing supervised named (NER) systems, availability a large, manually annotated corpus is desirable. Furthermore, large corpora permit robust evaluation and comparison different approaches that detect chemicals in documents. We present CHEMDNER corpus, collection 10,000 PubMed abstracts contain total 84,355 labeled by expert chemistry literature curators,...
Despite its high prevalence and mortality, little is known about the pathogenesis of rheumatoid arthritis-associated interstitial lung disease (RA-ILD). Given that familial pulmonary fibrosis (FPF) RA-ILD frequently share usual pattern pneumonia common environmental risk factors, we hypothesised two diseases might additional including FPF-linked genes. Our aim was to identify coding mutations FPF-risk genes associated with RA-ILD.We used whole exome sequencing (WES), followed by restricted...
With the rapidly developing high-throughput sequencing technologies known as next generation or NGS, our approach to gene hunting and diagnosis has drastically changed. In <10 years, these have moved from panel whole genome an exclusively research context clinical practice. Today, limit is not of one, many all genes but rather data analysis. Consequently, challenge efficiently identify disease-causing mutations within millions variants. To do so, we developed VarAFT software annotate...
Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address including how the end user would oversee generated output, for instance providing ranked results, textual evidence human interpretation or time savings using...
Background: Recent short-term clinical trials in patients with Duchenne Muscular Dystrophy (DMD) have indicated greater disease variability terms of progression than expected. In addition, as average life-expectancy increases, reliable data is req
Whole-exome sequencing (WES) is increasingly applied to research and clinical diagnosis of human diseases. It typically results in large amounts genetic variations. Depending on the mode inheritance, only one or two correspond pathogenic mutations responsible for disease present affected individuals. Therefore, it crucial filter out nonpathogenic variants limit downstream analysis a handful candidate mutations. We have developed new computational combinatorial system UMD-Predictor...
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These meant replace biocurators, instead assist them in one or more curation steps. To do so, the user interface is an important aspect that needs be considered for tool adoption. The BioCreative Interactive task (IAT) a track designed exploring user-system interactions, promoting development of useful TM tools, providing...
Deficiency in dihydropyrimidine dehydrogenase (DPD) enzyme is the main cause of severe and lethal fluoropyrimidine-related toxicity. Various approaches have been developed for DPD-deficiency screening, including DPYD genotyping phenotyping. The goal this prospective observational study was to perform exhaustive exome sequencing examine relationships between variants toxicity advanced breast cancer patients receiving capecitabine.Two-hundred forty-three were analysed (88.5% capecitabine...
Abstract Genetically modified mice have advanced our understanding of valve development and disease. Yet, human pathophysiological valvulogenesis remains poorly understood. Here we report that, by combining single cell sequencing in vivo approaches, a population pre-valvular endocardial cells (HPVCs) can be derived from pluripotent stem cells. HPVCs express gene patterns conforming to the E9.0 mouse atrio-ventricular canal (AVC) endocardium signature. treated with BMP2, cultured on AVC...
Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks recent progress genomics imaging technologies, systemic approaches now used parallel with small-scale studies establish links between genomic information phenotypes, often described at subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets different scales into a global view developmental program. Here,...
Duchenne muscular dystrophy (DMD) is an X-linked genetic disease, caused by the absence of dystrophin protein. Although many novel therapies are under development for DMD, there currently no cure and affected individuals often confined to a wheelchair their teens die in twenties/thirties. DMD rare disease (prevalence <5/10,000). Even largest countries do not have enough patients rigorously assess therapies, unravel complexities, determine patient outcomes. TREAT-NMD worldwide network...
The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. biocurator community, as an active user of biomedical literature, provides diverse engaged end group tools. Earlier challenges involved many teams in developing basic capabilities relevant curation, but they did not address issues system usage, insertion into workflow adoption by curators. Thus III (BC-III), InterActive Task (IAT) was...
Splenic diffuse red pulp lymphoma is an indolent small B-cell recognized as a provisional entity in the World Health Organization 2008 classification. Its precise relationship to other related splenic lymphomas with frequent leukemic involvement or lymphoproliferative disorders remains undetermined. We performed whole-exome sequencing explore genetic landscape of ten cases using paired tumor and normal samples. A selection 109 somatic mutations was then evaluated cohort including 42 samples...
As next-generation sequencing increases access to human genetic variation, the challenge of determining clinical significance variants becomes ever more acute. Germline in BRCA1 and BRCA2 genes can confer substantial lifetime risk breast ovarian cancer. Assessment variant pathogenicity is a vital part testing for these genes. A database observations BRCA critical resource that process. This article describes Share™, created by unique international alliance academic centers commercial...
Perturbation of addition second heart field (SHF) cardiac progenitor cells to the poles tube results in congenital defects (CHD). The transcriptional programs and upstream regulatory events operating different subpopulations SHF remain unclear. Here, we profile transcriptome chromatin accessibility anterior posterior sub-populations at genome-wide levels demonstrate that Hoxb1 negatively regulates differentiation SHF. Spatial mis-expression hypoplastic right ventricle. Activation embryonic...
Abstract Fusion of nascent myoblasts to pre-existing myofibres is critical for skeletal muscle growth and repair. The vast majority molecules known regulate myoblast fusion are necessary in this process. Here, we uncover, through high-throughput vitro assays vivo studies the chicken embryo, that TGFβ (SMAD2/3-dependent) signalling acts specifically uniquely as a molecular brake on fusion. While constitutive activation pathway arrests fusion, its inhibition leads striking over-fusion...