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dna2bit: high performance genomic distance estimation software for microbial genome analysis.
Front Microbiol
December 2024
Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
dna2bit is an ultra-fast software specifically engineered for microbial genome analysis, particularly adept at calculating genome distances within metagenome and single amplified genome datasets. Distinguished from existing software such as Mash and Dashing, dna2bit employs feature hashing technique and Hamming distance to achieve enhanced speed and memory utilization, without sacrifice in the accuracy of average nucleotide identity calculations. dna2bit has promising applications in various domains such as average nucleotide identity approximation, metagenomic sequence clustering, and homology querying.
View Article and Find Full Text PDFTranscriptome-Wide Association Study of Metabolic Dysfunction-Associated Steatotic Liver Disease Identifies Relevant Gene Signatures.
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Department of Emergency Medicine, Shandong University, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Qingdao, China.
Metabolic dysfunction-associated steatotic liver disease (MASLD) is considered the most widespread chronic liver condition globally. Genome-wide association studies (GWAS) have pinpointed several genetic loci correlated to MASLD, yet the biological significance of these loci remains poorly understood. Initially, we applied Functional Mapping and Annotation (FUMA) to conduct a functional annotation of the MASLD GWAS summary statistics, which included data from 3242 cases and 707 631 controls.
View Article and Find Full Text PDFIntegrated proteogenomic characterization of ampullary adenocarcinoma.
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Center for Cell and Gene Therapy, Clinical Research Center for Cell-based Immunotherapy, Shanghai Pudong Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200433, China.
Ampullary adenocarcinoma (AMPAC) is a rare and heterogeneous malignancy. Here we performed a comprehensive proteogenomic analysis of 198 samples from Chinese AMPAC patients and duodenum patients. Genomic data illustrate that 4q loss causes fatty acid accumulation and cell proliferation.
View Article and Find Full Text PDFPRDM9 drives the location and rapid evolution of recombination hotspots in salmonid fish.
PLoS Biol
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Institut de Génétique Humaine, Univ Montpellier, Centre National de la Recherche Scientifique, Montpellier, France.
In many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called recombination hotspots. In various lineages, recombination hotspots are located in regions with promoter-like features and are evolutionarily stable. Conversely, in some mammals, hotspots are driven by PRDM9 that targets recombination away from promoters.
View Article and Find Full Text PDFSurvival and immune microenvironment prediction of glioma based on MRI imaging genomics method: a retrospective observational study.
Neurosurg Rev
January 2025
Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China.
Glioma is characterized by high heterogeneity and poor prognosis. Attempts have been made to understand its diversity in both genetic expressions and radiomic characteristics, while few integrated the two omics in predicting survival of glioma. This study was intended to investigate the connection between glioma imaging and genome, and examine its predictive value in glioma mortality risk and tumor immune microenvironment (TIME).
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