基因组学
Gene set enrichment analyses of 8,405 genes linked with 35,074 human-specific (hs) regulatory single-nucleotide changes (SNCs) revealed the staggering breadth of significant associations with morphological structures, physiological…
Our view of the universe of genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) has been markedly expanded in recent years. To infer the evolutionary origins of loci harboring HSRS, analyses of…
Molecular and genetic definitions of human-specific changes to genomic regulatory networks (GRNs) contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of…
Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Here, conservation…
Despite significant progress in structural and functional characterization of human genome, understanding of mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. We report that non-randomly distributed…
DNA language models have advanced genomics, but their downstream performance varies widely due to differences in tokenization, pretraining data, and architecture. We argue that a major bottleneck lies in tokenizing sparse and unevenly…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…
Chromatin conformation capture technologies such as Hi-C have revealed that the genome is organized in a hierarchy of structures spanning multiple scales observed at different resolutions. Current algorithms often focus on specific…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
Motivation: PCR is more economical and quicker than Next Generation Sequencing for detecting target organisms, with primer design being a critical step. In epidemiology with rapidly mutating viruses, designing effective primers is…
Predicting the sensitivity of cancer cell lines to PLX-4720, a preclinical BRAF inhibitor, requires models capable of capturing the multilayered regulation of oncogenic signaling. Single-omics predictors are often insufficient because drug…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell…
Next-Generation Sequencing (NGS) has become a cornerstone of genomic research, yet the complexity of downstream analysis-ranging from differential expression gene (DEG) identification to biological interpretations-remains a significant…
Large Language Models are increasingly popular in genomics due to their potential to decode complex biological sequences. Hence, researchers require a standardized benchmark to evaluate DNA Language Models (DNA LMs) capabilities. However,…
Summary: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks.…
Personalized neoantigen vaccines represent a promising immunotherapy approach that harnesses tumor-specific antigens to stimulate anti-tumor immune responses. However, the design of these vaccines requires sophisticated computational…
Summary: We present needLR, a structural variant (SV) annotation tool that can be used for filtering and prioritization of candidate pathogenic SVs from long-read sequencing data using population allele frequencies, annotations for genomic…
Accurate variant descriptions are of paramount importance in the field of genomics. The domain is confronted with increasingly complex variants, e.g., combinations of multiple indels, making it challenging to generate proper variant…
Numerous diseases, particularly autoimmune disorders, are associated with the human leukocyte antigen (HLA), a small genomic region located on human chromosome 6. Adequate characterization of linkage disequilibrium (LD) in the HLA across…