Search PubMedSearch

Biomedical subjects

Shuo Liu

Publications and source records attributed to Shuo Liu.

3 recordsLinked to original sources

Quantile Tensor Regression for Integrative Genomic Analysis of Oesophageal Carcinoma.

Recent integrative genomic studies have increasingly exploited the tensor structure of multi-omics data to develop statistical methods that jointly model the relationship between clinical outcomes and multiple genomes. However, genomic measurements and clinical outcomes are frequently contaminated by outliers or heavy-tailed noise, necessitating robust tensor-based inference approaches. In this paper, we investigate the quantile tensor regression with an emphasis on the region selection problem. We introduce a novel estimator that integrates quantile regression for robustness with a nonconvex penalty to encourage sparsity in the tensor coefficient, thereby enabling the identification of localized genomic regions that significantly influence the clinical response. To solve the resulting optimization problem, we devise an effective algorithm tailored to the nonconvex objective and tensor architecture. We establish the asymptotic properties of the proposed nonconvex penalized estimator. Extensive simulations demonstrate the excellent finite-sample performance of the proposed estimator. We further illustrate the practical utility of the proposed estimator through an application to esophageal carcinoma data, providing empirical validation.

Humans

Chromosomal level genome assembly of medicinal plant Chrysosplenium macrophyllum.

Chrysosplenium macrophyllum Oliv., a perennial herb native to China, is widely used in traditional medicine for its notable therapeutic properties. However, the absence of a reference genome has constrained its full potential for research and application. This study presents the first chromosome-level de novo genome assembly of C. macrophyllum, constructed by integrating long reads from Oxford Nanopore Technologies (ONT), short reads from BGI, and Hi-C data. The final assembly spans 2.55 Gb, with a scaffold N50 of 93.38 Mb, and 83.70% of the genome has been assigned to 22 chromosomes. The mapping rate of the BGI short reads to the genome is approximately 97.94%, and BUSCO analysis reveals that 97.94% of the predicted genes are complete. A total of 62,921 protein-coding genes were predicted, with functional annotations for 93.67% of them. This chromosome-level genome assembly represents an important resource for expanding our understanding of Chrysosplenium species and supports future genomic studies and applications.

Genome, Plant

Characterizing the gut microbiome of diarrheal mink under farmed conditions: A metagenomic analysis.

This study aimed to comprehensively characterize the gut microbiota in diarrheal mink. We conducted Shotgun metagenomic sequencing on samples from five groups of diarrheal mink and five groups of healthy mink. The microbiota α-diversity and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology did not show significant differences between the groups. However, significant differences were observed in microbiota β-diversity and the function of carbohydrate-active enzymes (CAZymes) between diarrheal and healthy mink. Specifically, The relative abundance of Firmicutes was lower, whereas that of Bacteroidetes was higher in diarrheal mink. Fusobacteria were enriched as invasive bacteria in the gut of diarrheal mink compared with healthy mink. In addition, Escherichia albertii was identified as a new bacterium in diarrheal mink. Regarding functions, nicotinate and nicotinamide metabolism and glycoside hydrolases 2 (GH2) family were the enhanced KEGG orthology and CAZymes in diarrheal mink. Furthermore, the diversity and number of antibiotic-resistant genes were significantly higher in the diarrheal mink group than in the healthy group. These findings enhance our understanding of the gut microbiota of adult mink and may lead to new approaches to the diagnosis and treatment of mink diarrhea.

Animals