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The strong correlation between reproductive life cycle type and chromosome numbers in green plants has been a long-standing mystery in evolutionary biology. Within green plants, the derived condition of heterosporous reproduction has emerged from the ancestral condition of homospory in disparate locations on the phylogenetic tree at least 11 times, of which three lineages are extant. In all green plant lineages where heterospory has emerged, there has been a significant downsizing in chromosome numbers.
View Article and Find Full Text PDFComputational epitope-based vaccine design with bioinformatics approach; a review.
Heliyon
January 2025
Tehran Azad University of Medical Sciences, Faculty of Pharmaceutical Sciences, Iran.
The significance of vaccine development has gained heightened importance in light of the pandemic. In such critical circumstances, global citizens anticipate researchers in this field to swiftly identify a vaccine candidate to combat the pandemic's root cause. It is widely recognized that the vaccine design process is traditionally both time-consuming and costly.
View Article and Find Full Text PDFEpigenetic variation in light of population genetic practice.
Nat Commun
January 2025
Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.
The evolutionary impact of epigenetic variation depends on its transgenerational stability and source - whether genetically determined, environmentally induced, or due to spontaneous, genotype-independent mutations. Here, we evaluate current approaches for investigating an independent role of epigenetics in evolution, pinpointing methodological challenges. We further identify opportunities arising from integrating epigenetic data with population genetic analyses in natural populations.
View Article and Find Full Text PDFNetSDR: Drug repurposing for cancers based on subtype-specific network modularization and perturbation analysis.
Biochim Biophys Acta Mol Basis Dis
January 2025
MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics and Computational Biology, School of Life Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China; Key Laboratory of Alkene-carbon Fibres-based Technology & Application for Detection of Major Infectious Diseases, Soochow University, Suzhou 215123, China; Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou 215123, China. Electronic address:
Cancer, a heterogeneous disease, presents significant challenges for drug development due to its complex etiology. Drug repurposing, particularly through network medicine approaches, offers a promising avenue for cancer treatment by analyzing how drugs influence cellular networks on a systemic scale. The advent of large-scale proteomics data provides new opportunities to elucidate regulatory mechanisms specific to cancer subtypes.
View Article and Find Full Text PDFRecipes and ingredients for deep learning models of 3D genome folding.
Curr Opin Genet Dev
January 2025
Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA. Electronic address:
Three-dimensional genome folding plays roles in gene regulation and disease. In this review, we compare and contrast recent deep learning models for predicting genome contact maps. We survey preprocessing, architecture, training, evaluation, and interpretation methods, highlighting the capabilities and limitations of different models.
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