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Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.
J Hered
January 2025
Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, 5A, Oester Farimagsgade, Copenhagen, 1353, Denmark.
The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species.
View Article and Find Full Text PDFEarly-life Exposure to Tobacco Smoke and the Risk of Idiopathic Pulmonary Fibrosis: A Population-based Cohort Study.
Ann Am Thorac Soc
January 2025
Hangzhou Medical College, Hangzhou, China;
Rationale: Tobacco smoking is a well-established risk factor for idiopathic pulmonary fibrosis (IPF), yet the influence of early-life tobacco exposure on future IPF risk remains poorly understood.
Objectives: To test the hypothesis that early-life tobacco exposure may elevate the risk of developing IPF, with this effect potentially modified by genetic susceptibility to IPF and mediated through accelerated biological aging.
Methods: Using data from over 430,000 participants in the UK Biobank, we performed a prospective cohort study to examine the associations of maternal smoking around birth and age of smoking initiation with IPF risk.
Study of the role of transmembrane emp24 domain-containing protein 2 in oral squamous cell carcinoma.
J Appl Oral Sci
January 2025
Ningde Hospital Affiliated to Ningde Normal University, Department of Stomatology, Fujian, China.
Objective: This study aimed to investigate the role of transmembrane emp24 domain-containing protein 2 (TMED2) in oral squamous cell carcinoma (OSCC).
Methodology: A bioinformatics analysis was first conducted to explore TMED2 expression in OSCC and its relation with overall survival. The analysis results were further verified by assessing TMED2 expression levels in human normal oral keratinocyte cells and human OSCC cell lines using quantitative real-time polymerase chain reaction and the Western blot.
Classification-based pathway analysis using GPNet with novel P-value computation.
Brief Bioinform
November 2024
Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, United States.
Pathway analysis plays a critical role in bioinformatics, enabling researchers to identify biological pathways associated with various conditions by analyzing gene expression data. However, the rise of large, multi-center datasets has highlighted limitations in traditional methods like Over-Representation Analysis (ORA) and Functional Class Scoring (FCS), which struggle with low signal-to-noise ratios (SNR) and large sample sizes. To tackle these challenges, we use a deep learning-based classification method, Gene PointNet, and a novel $P$-value computation approach leveraging the confusion matrix to address pathway analysis tasks.
View Article and Find Full Text PDFInferring the genetic relationships between unsupervised deep learning-derived imaging phenotypes and glioblastoma through multi-omics approaches.
Brief Bioinform
November 2024
Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
This study aimed to investigate the genetic association between glioblastoma (GBM) and unsupervised deep learning-derived imaging phenotypes (UDIPs). We employed a combination of genome-wide association study (GWAS) data, single-nucleus RNA sequencing (snRNA-seq), and scPagwas (pathway-based polygenic regression framework) methods to explore the genetic links between UDIPs and GBM. Two-sample Mendelian randomization analyses were conducted to identify causal relationships between UDIPs and GBM.
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