Genome data, with underlying new knowledge, are accumulating at exponential rate thanks to ever-improving sequencing technologies and the parallel development of dedicated efficient Bioinformatics methods and tools. Advanced Education in Bioinformatics and Genome Analyses is to a large extent not accessible to students in developing countries where endeavors to set up Bioinformatics courses concern most often only basic levels. Here, we report a pioneering pilot experience concerning the design and implementation, from scratch, of a three-months advanced and extensive course in Bioinformatics and Genome Analyses in the Institut Pasteur de Tunis. Most significantly the outcome of the course was upgrading the participants' skills in Bioinformatics and Genome Analyses to recognized international standards. Here we detail the different steps involved in the implementation of this course as well as the topics covered in the program. The description of this pilot experience might be helpful for the implementation of other similar educational projects, notably in developing countries, aiming to go beyond basics and providing young researchers with high-level skills.
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http://dx.doi.org/10.1371/journal.pcbi.1006373 | DOI Listing |
STAR Protoc
January 2025
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:
Strand-optimized Smart-seq (So-Smart-seq) can capture a comprehensive transcriptome from low-input samples. This technique detects both polyadenylated and non-polyadenylated RNAs, inclusive of repetitive RNAs, while excluding highly abundant ribosomal RNAs. So-Smart-seq preserves strand information and minimizes 5' to 3' coverage bias.
View Article and Find Full Text PDFHGG Adv
January 2025
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Inherited genetics represents an important contributor to risk of esophageal adenocarcinoma (EAC), and its precursor Barrett's esophagus (BE). Genome-wide association studies have identified ∼30 susceptibility variants for BE/EAC, yet genetic interactions remain unexamined. To address challenges in large-scale G×G scans, we combined knowledge-guided filtering and machine learning approaches, focusing on genes with (A) known/plausible links to BE/EAC pathogenesis (n=493) or (B) prior evidence of biological interactions (n=4,196).
View Article and Find Full Text PDFSci Rep
January 2025
Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India.
COVID-19 has proved to be a global health crisis during the pandemic, and the emerging JN.1 variant is a potential threat. Therefore, finding alternative antivirals is of utmost priority.
View Article and Find Full Text PDFTransl Psychiatry
January 2025
Genetic Epidemiology Group, Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
Experiencing a traumatic event may lead to Posttraumatic Stress Disorder (PTSD), including symptoms such as flashbacks and hyperarousal. Individuals suffering from PTSD are at increased risk of cardiovascular disease (CVD), but it is unclear why. This study assesses shared genetic liability and potential causal pathways between PTSD and CVD.
View Article and Find Full Text PDFBMC Oral Health
January 2025
Beijing Institute of Dental Research, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China.
Background: Low-intensity pulsed ultrasound (LIPUS) has been used as an effective noninvasive method for treating fractures and osteoarthrosis, but the application in the field of oral implantation is in its infancy. This study aimed to clarify the effect and mechanism of LIPUS on the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) and implant osseointegration, and to provide an experimental basis for future clinical applications.
Methods: Dental implants were inserted into Wistar rat femurs, and LIPUS was performed for 4 weeks.
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