Genetics

CrosSplice: A Pipeline for Identifying Rare Splice-Site Creating Variants from Cross-Tissue Transcriptome Data

Despite their profound impact on patients’ lives, most rare and intractable diseases still lack established treatments. Genomic variants that disrupt normal splicing by creating novel splice sites (splice-site creating variants, SSCVs) substantially contribute to the pathogenesis of those conditions. Deep intronic SSCVs are particularly amenable to antisense oligonucleotide (ASO)-mediated splice m...

ML-Guided GWAS Reveals Genetic Architectures for MASLD for Overweight and Lean Individuals in the All of Us Cohort

Metabolic dysfunction-associated steatotic liver disease (MASLD) arises from excessive hepatic fat accumulation that triggers inflammation and liver injury. It is the most prevalent chronic liver disease worldwide, affecting more than one quarter of adults. Despite this, MASLD is often underdiagnosed, making it more difficult to perform genome-wide association studies (GWAS). In this paper, we imp...

Machine Learning and Micro Capture-C resolve GWAS associations revealing endothelial stress pathways in Coronary Artery Disease

Resolving the gene targets of non-coding genetic variation is the major bottleneck in translating genome wide association studies into mechanistic und...

A Pathway-Based Machine Learning Approach Identifies Region-Specific Markers and Patterns in Alzheimer’s Disease Patients Based on Spatial and Severity Metadata

Alzheimer’s disease (AD) exhibits profound spatial heterogeneity in its molecular and pathological features, yet the basis of this regional selectivit...

Heterogeneous epigenetic variation converges on splicing dysregulation in opioid addiction

Disease heterogeneity presents a major challenge for genetic and epigenetic dissection of complex traits. Neuropsychiatric traits, such as opioid use ...

Artificial Intelligence-Driven Precision Oncology Uncovers Prognostic Significance of RTK-RAS Alterations in FOLFOX-Treated Early-Onset Colorectal Cancer

The incidence of early-onset colorectal cancer (EOCRC; <50 years) is rising rapidly among populations. Although alterations in the RTK-RAS signaling p...

Conversational Artificial Intelligence-Based Integration of Clinical and Genomic Data Identifies MAPK Alterations in Colorectal Cancer

Colorectal cancer (CRC) exhibits marked heterogeneity across age, ancestry, and treatment context, underscored by the rising incidence of early-onset ...

GENPHIRE: Enhancing Disease Risk Prediction Using Large Language Model

Estimating an individual’s liability to a disease is a fundamental problem in genome research. By exploiting findings from genome-wide association stu...

Estrogen upregulates NF-κB and TNF signaling in B cells to cause sex and age differences in antibody responses to seasonal influenza vaccination

Sex differences in the humoral immune responses to the seasonal quadrivalent influenza vaccine (QIV) in young adults (YA; 18-49yo) or high dose QIV in...

DRB1 Subtyping Reveals Divergent Risk and Protection for Type 1 Diabetes in Middle Eastern Populations

Type 1 diabetes (T1D) is strongly influenced by HLA variation, yet current genetic risk models developed largely in European cohorts perform suboptima...

Infectious diseases, imposing density-dependent mortality on MHC/HLA variation, can account for balancing selection and MHC/HLA polymorphism

The human MHC transplantation loci (HLA-A, -B, -C, -DPB1, -DQB1, -DRB1) are the most polymorphic in the human genome. It is generally accepted this ...

Characterizing hub biomarkers for metabolic-induced endothelial dysfunction and unveiling their regulatory roles in EndMT through RNA sequencing and machine learning approaches.

BACKGROUND: Metabolic disorder and endothelial dysfunction (ED) are key events in the development and pathophysiology of atherosclerosis and are assoc...

Identification of hub immune-related genes and construction of predictive models for systemic lupus erythematosus by bioinformatics combined with machine learning.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that involves multiple systems. SLE is characterized by the production of autoantib...

Deciphering mitochondrial dysfunction in keratoconus: Insights into ACSL4 from machine learning-based bulk and single-cell transcriptome analyses and experimental validation.

Keratoconus (KC) is a prevalent ectatic corneal disease and the leading cause of corneal transplantation globally. Despite evidence of mitochondrial a...

Integration of T cell repertoire, CyTOF, genotyping and symptomatology data reveals subphenotypic variability in COVID-19 patients.

COVID-19 manifests a broad spectrum of clinical outcomes, from asymptomatic cases to severe disease. While several biomarkers have been proposed, comp...

RNA knowledge-graph analysis through homogeneous embedding methods.

MOTIVATION: We recently introduced RNA-knowledge graph (KG), an ontology-based KG that integrates biological data on RNAs from over 60 public database...

Intimate partner violence and stress-related disorders: from epigenomics to resilience.

Intimate Partner Violence (IPV) is a major public health problem to be addressed with innovative and interconnecting strategies for ensuring the psych...

Prediction of KRAS gene mutations in colorectal cancer using a CT-based radiomic model.

BACKGROUND: Determining the KRAS gene mutation status in colorectal cancer (CRC) before surgery is highly important for an individualized clinical tre...

Ligand-receptor dynamics in heterophily-aware graph neural networks for enhanced cell type prediction from single-cell RNA-seq data.

Graph Neural Networks (GNNs) have emerged as powerful tools for analyzing structured data, particularly in domains where relationships and interaction...

m5CStack: An integrated framework for m5C site prediction using multi-feature stacking.

RNA 5-methylcytosine (m5C) modification sites are essential for understanding the regulation of RNA functions in various biological processes. However...