Search the literature by keyword, topic, or author. Filter to articles with full text available.
784 results
The pig (Sus scrofa) is both an economically important livestock species and a valuable biomedical model . Its genome bears regulatory features shaped by domestication and selection that are often poorly captured by genomic language …
Read PDFGenerative artificial intelligence (AI) is becoming a groundbreaking paradigm in the field of animal genomics and is providing the possibility to take a step towards intelligent agriculture, with better data integration, predictive modeling, and biological …
Read PDF<h4>Motivation</h4>The rapid accumulation of multi-omics data presents a valuable opportunity to advance our understanding of complex diseases and biological systems, driving the development of integrative computational methods. However, the complexity of biological processes, spanning multiple …
Read PDF<h4>Motivation</h4>Accurate cell type annotation is essential in scATAC-seq analysis, as it underpins the characterization of cellular heterogeneity, the identification of regulatory elements, and downstream biological discovery. However, current annotation methods still face major challenges. First, …
Read PDF<h4>Introduction</h4>Thyroid cancer, the most prevalent endocrine malignancy globally, poses challenges owing to the limited understanding of its molecular drivers. Previous research has highlighted collagen genes, such as COL13A1 and COL23A1, as key players in thyroid …
Read PDFRestoring CD8⁺T cell infiltration and potentiating anti-tumor immune responses in the tumor microenvironment (TME) is critical for developing effective immunotherapies against triple-negative breast cancer(TNBC), while the regulatory role of N⁶-methyladenosine (m⁶A)-modified circular RNAs (circRNAs) in …
Read PDF<h4>Summary</h4>Genome-wide association studies have revealed that many disease-associated genetic variants lie in non-coding regions of the genome. To prioritize these variants and clarify their functional roles, accurate classification of <i>cis</i>-regulatory elements is essential. Early approaches …
Read PDF<h4>Motivation</h4>Sequence-to-expression models typically do not consider chromatin accessibility, a major factor limiting gene regulation. We hypothesized that supplying accessibility as an input feature would allow a sequence-to-expression model to focus on important open regions of …
Read PDF<h4>Motivation</h4>Identifying pairwise associations between genomic loci is an important challenge for which large and diverse collections of epigenomic and transcription factor (TF) binding data can potentially be informative.<h4>Results</h4>We developed Learning Evidence of Pairwise Association from …
Read PDFN 6-methyladenosine (m6A), the most prevalent internal RNA modification, is an emerging key regulator of gene expression in the central nervous system, and its dysregulation is connected to psychiatric disorders. However, disentangling the causal links …
Read PDF<h4>Motivation</h4>Recent studies suggest that deep neural network models trained on thousands of human genomic datasets can accurately predict genomic features, including gene expression and chromatin accessibility. However, training these models is computation- and time-intensive, and …
Read PDF<h4>Motivation</h4>Illumina Infinium BeadChip technology for DNA methylation analysis continues to expand, with the latest EPICv2 arrays targeting about a million loci. As data volumes from this technology continue to grow, there is increasing demand for …
Read PDF<h4>Motivation</h4>Advances in high-throughput chromatin conformation capture have provided insight into the three-dimensional structure and organization of chromatin. While bulk Hi-C experiments capture spatio-temporally averaged chromatin interactions across millions of cells, single-cell Hi-C experiments report on …
Read PDF<h4>Summary</h4>Integration of exogenous DNA into host cell chromatin is a hallmark of many virus and transposon lifecycles and the foundational basis for many modern cellular and genetic therapies. Defining integration sites (ISs) in a population …
Read PDF<h4>Motivation</h4>Chromatin regulation is crucial for modulating gene expression and cellular function by altering DNA accessibility. Defining and understanding chromatin regulation across diverse biological conditions, including health and disease, requires quantification of both the presence and …
Read PDF<h4>Motivation</h4>DNA methylation (DNAme) is the best studied epigenetic mechanism that plays pivotal role in tissue differentiation and epigenetic disruption has been correlated to diverse disease types (e.g. cancer, metabolic disorders). While various DNAme array platforms …
Read PDF<h4>Summary</h4>DNA methylation (DNAm) of neighbouring CpG sites is highly correlated, making DNAm function in terms of blocks. DNAm patterns and functionality are linked to both chromatin structure of DNA and gene regulation. Defining biologically meaningful …
Read PDF<h4>Motivation</h4>5-Methylcytosine (5mC) plays an important role in gene regulation and development. Although nanopore sequencing has enabled direct detection of 5mC, existing methods still face several limitations, including poor generalization across species and sequence contexts (CpG/CHG/CHH), …
Read PDF<h4>Summary</h4>We developed slideimp, an R package that extends and optimizes K-nearest neighbor (K-NN) and Principal Component Analysis (PCA) imputation with grouped and sliding-window modes for accurate and efficient imputation of microarray and whole-genome DNA methylation …
Read PDF