The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years.
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| http://dx.doi.org/10.1093/nar/gku380 | DOI Listing |
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Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing.
Nat Genet
January 2025
Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
Crop genomes accumulate deleterious mutations-a phenomenon known as the cost of domestication. Precision genome editing has been proposed to eliminate such potentially harmful mutations; however, experimental demonstration is lacking. Here we identified a deleterious mutation in the tomato transcription factor SUPPRESSOR OF SP2 (SSP2), which became prevalent in the domesticated germplasm and diminished DNA binding to genome-wide targets.
View Article and Find Full Text PDFGender and geographical bias in the editorial decision-making process of biomedical journals: a case-control study.
BMJ Evid Based Med
December 2024
BMJ Publishing Group, London, UK.
Objectives: To assess whether the gender (primary) and geographical affiliation (post-hoc) of the first and/or last authors are associated with publication decisions after peer review.
Design: Case-control study.
Setting: Biomedical journals.
Bridging Wright-Fisher and Moran models.
J Theor Biol
February 2025
Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland. Electronic address:
The Wright-Fisher model and the Moran model are both widely used in population genetics. They describe the time evolution of the frequency of an allele in a well-mixed population with fixed size. We propose a simple and tractable model which bridges the Wright-Fisher and the Moran descriptions.
View Article and Find Full Text PDFsnRNA-seq stratifies multiple sclerosis patients into distinct white matter glial responses.
Neuron
December 2024
Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, Basel, Switzerland. Electronic address:
Poor understanding of the cellular and molecular basis of clinical and genetic heterogeneity in progressive multiple sclerosis (MS) has hindered the search for new effective therapies. To address this gap, we analyzed 632,000 single-nucleus RNA sequencing profiles from 156 brain tissue samples of MS and control donors to examine inter- and intra-donor heterogeneity. We found distinct cell type-specific gene expression changes between MS gray and white matter, highlighting clear pathology differences.
View Article and Find Full Text PDFDesign, validation, and implementation of multiplex digital PCR assays for simultaneous quantification of multiple targets.
Lett Appl Microbiol
January 2025
Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600, Dübendorf, Switzerland.
Quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) are applied for quantifying molecular targets in disease diagnostics, pathogen detection, and ecological monitoring. Uptake of dPCR is increasing due to its higher quantification accuracy relative to qPCR, which stems from its independence from standard curves and its increased resistance to PCR inhibitors. Throughput can be increased through multiplexing, which allows simultaneous quantification of multiple targets.
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