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With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks. Here, we describe our experience with the organization of a course in one of the longest-running extended bioinformatics series of workshops, the Evomics Workshop on Population and Speciation Genomics that takes place biennially in the UNESCO world heritage town of Český Krumlov, Czech Republic. We list the key ingredients that make this workshop successful in our view, explain the routine for workshop organization that we have optimized over the years, and describe the most important lessons that we have learned from it. We report the results of a survey conducted among past workshop participants that quantifies measures of effective teaching and provide examples of how the workshop setting has led to the cross-fertilisation of ideas and ultimately scientific progress. We expect that our account may be useful for other groups aiming to set up their own extended bioinformatics courses.
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http://dx.doi.org/10.1186/s12052-023-00182-w | DOI Listing |
Plant Commun
September 2025
College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China. Electronic address:
Molecular phylogenetics illustrates the evolution and divergence of green plants by employing sequence data from various sources. Interestingly, phylogenetic reconstruction based on mitochondrial genes tends to exhibit incongruence with those derived from nuclear and chloroplast genes. Although the uniparental inheritance and conservatively retained protein-coding genes of mitochondrial genomes inherently exclude certain potential factors that affect phylogenetic reconstruction, such as hybridization and gene loss, the utilization of mitochondrial genomes for phylogeny and divergence time estimation remains limited.
View Article and Find Full Text PDFTheriogenology
September 2025
Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand; Multi-Omics for Functional Products in Food, Cosmetics and Animals Research Unit, Chulalongkorn University, Bangkok, 10330, Thailand. Electronic address: Morakot
Boar semen quality and age are vital for successful fertility management in the swine industry. Understanding how seminal plasma (SP) metabolites vary with semen quality and age is essential for optimizing breeding strategies. This study aimed to determine whether SP metabolite profiles and semen quality are associated with Duroc boar age.
View Article and Find Full Text PDFLife Sci Alliance
November 2025
Immunoregulation Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
Amino acid (AA) detection is fundamental for cellular function, balancing translation demands, biochemical pathways, and signaling networks. Although the GCN2 and mTORC1 pathways are known to regulate AA sensing, the global cellular response to AA deprivation remains poorly understood, particularly in non-transformed cells, which may exhibit distinct adaptive strategies compared with cancer cells. Here, we employed murine pluripotent embryonic stem (ES) cells as a model system to dissect responses to AA stress.
View Article and Find Full Text PDFEnviron Pollut
September 2025
Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China; Key Laboratory of Post-Trauma Neuro-Repair and Regeneration in Central Nervous System, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin Neurol
This study systematically investigated the association between triclosan (TCS) exposure and Alzheimer's disease (AD) risk via integrated bioinformatics approaches. TCS-AD-related genes were identified using bioinformatics tools and public databases, followed by the screening of key genes through multi-model machine learning algorithms (LASSO, SVM-RFE, RF) to mitigate random errors in small sample sizes. DRD2 was confirmed as the most robust core gene by LASSO confidence interval analysis and SHAP evaluation, while APP and SLC6A3 were validated through cross-method intersection.
View Article and Find Full Text PDFMol Cell
September 2025
Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA. Electronic address:
In animal germ cells, PIWI proteins use piRNAs to detect active selfish genetic elements. Base-pairing to a piRNA defines transposon recognition, but how this interaction triggers a defensive response remains unclear. Here, we identify a transposon recognition complex composed of the silkworm proteins Siwi, GTSF1, and Maelstrom.
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