基因组学
Biological age, which may be older or younger than chronological age due to factors such as genetic predisposition, environmental exposures, serves as a meaningful biomarker of aging processes and can inform risk stratification, treatment…
Alternative splicing creates complex bubbles in splicing graphs where more than two transcript paths compete, challenging methods designed for simple binary events. We present a unified framework that compares paths using distinct exonic…
The discovery of genetic risk factors has transformed human genetics, yet the pace of new gene identification has slowed despite the exponential expansion of sequencing and biobank resources. Current approaches are optimized for the…
Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have…
Nucleotide sequence variation can induce significant shifts in functional fitness. Recent nucleotide foundation models promise to predict such fitness effects directly from sequence, yet heterogeneous datasets and inconsistent preprocessing…
Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step…
Transformers have revolutionized nucleotide sequence analysis, yet capturing long-range dependencies remains challenging. Recent studies show that autoregressive transformers often exhibit Markovian behavior by relying on fixed-length…
Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research…
DNA methylation can be associated with phenotypic plasticity, yet how temperature shapes DNA methylation diversity in natural populations is unclear. Analyzing whole-genome bisulfite sequencing from 1075 Arabidopsis thaliana accessions…
Introduction: Epigenomic datasets from high-throughput sequencing experiments are commonly summarized as genomic intervals. As the volume of this data grows, so does interest in analyzing it through deep learning. However, the heterogeneity…
Summary: We present AmpliconHunter2 (AHv2), a highly scalable in silico PCR engine written in C that can handle degenerate primers and uses a highly accurate melting temperature model. AHv2 implements a bit-mask IUPAC matcher with AVX2 SIMD…
Sequencing of PCR amplicons generated using degenerate primers (typically targeting a region of the 16S ribosomal gene) is widely used in metagenomics to profile the taxonomic composition of complex microbial samples. To reduce taxonomic…
Single-cell RNA-seq foundation models achieve strong performance on downstream tasks but remain black boxes, limiting their utility for biological discovery. Recent work has shown that sparse dictionary learning can extract concepts from…
Background: Patients carrying MEF2C haploinsufficiency develop a recognizable neurodevelopmental syndrome featuring intellectual disability, treatment-resistant seizures, and autism spectrum behaviors. While MEF2C's critical roles in…
The identification of homologous gene families across multiple genomes is a central task in bacterial pangenomics traditionally requiring computationally demanding all-against-all comparisons. PanDelos addresses this challenge with an…
The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility…
Aging is a highly complex and heterogeneous process that progresses at different rates across individuals, making biological age (BA) a more accurate indicator of physiological decline than chronological age. While previous studies have…
Arsenic (As), a widespread environmental toxin, poses major health risks due to its inorganic forms (iAs), which are linked to cancer, cardiovascular disease, and endocrine disruption. Although its toxic effects have been extensively…
Motivation: Standard genome-wide association studies in cancer genomics rely on statistical significance with multiple testing correction, but systematically fail in underpowered cohorts. In TCGA breast cancer (n=967, 133 deaths), low event…
Sequence data, such as DNA, RNA, and protein sequences, exhibit intricate, multi-scale structures that pose significant challenges for conventional analysis methods, particularly those relying on alignment or purely statistical…