This study evaluates the symmetry of data distributions after normalization, focusing on various statistical tests, including a few explored test named Rp. We apply normalization techniques, such as variance stabilizing transformations, to ribonuclei...
Polycystic ovary syndrome (PCOS) is a complex endocrine disorder affecting reproductive-aged women. Previous studies have identified genomic associations at chromosome 12q13.2, but the functional mechanisms underlying these associations remain unclea...
Insights from public DNA methylation data derived from cancer or normal tissues from cancer patients or healthy people can be obtained by machine learning. The goal is to determine methylation patterns that could be useful for predicting the prognosi...
Next Generation Sequencing technologies have produced a substantial increase of publicly available genomic data and related clinical/biospecimen information. New models and methods to easily access, integrate and search them effectively are needed. A...
Copy number variation (CNV) detection based on second-generation sequencing technology is the basis of much gene research, but the read depth is affected by mapping errors, repeated reads, and GC bias. The existing methods have low sensitivity to var...
Sea star wasting disease (SSWD) is a condition that has affected asteroids for over 120 years, yet mechanistic understanding of this wasting etiology remains elusive. We investigated temporal virome variation in two Pisaster ochraceus specimens that...
The number of patients diagnosed with cancer continues to increasingly rise, and has nearly doubled in 20 years. Therefore, predicting cancer occurrence has a significant impact on reducing medical costs, and preventing cancer early can increase surv...
Genomic imprinting refers to the epigenetic silencing of one of both alleles in a parent-of-origin-specific manner, particularly in genes regulating growth and development. Impaired genomic imprinting leading to the activation of the silenced allele,...
A growing body of evidence currently proposes that deep learning approaches can serve as an essential cornerstone for the diagnosis and prediction of Alzheimer’s disease (AD). In light of the latest advancements in neuroimaging and genomics, numerous...
Genomic selection (GS) accelerates plant breeding by predicting complex traits using genomic data. This study compares genomic best linear unbiased prediction (GBLUP), quantile mapping (QM)—an adjustment to GBLUP predictions—and four outl...
Human and other annotated genome sequences have facilitated generation of vast amounts of correlative data, from human/animal genetics, normal and disease-affected tissues from complex diseases such as arthritis using gene/protein chips and SNP ana...
DNA replication is a fundamental process ensuring the maintenance of the genome each time cells divide. This is particularly relevant early in development when cells divide profusely, later giving rise to entire organs. Here, we analyze and compare t...
Trisomy 7 is the most frequently observed type of rare autosomal trisomies in genome-wide non-invasive prenatal screening (NIPS). Currently, the clinical significance of trisomy 7 NIPS-positive results is still unknown. We reviewed two independent co...
It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensio...
Potatoes destined for crisping are normally stored above 8 degrees; below this glucose accumulates leading to very dark fry colors and potential acrylamide build up. Unfortunately, sprouting occurs above 4 degrees and impacts product quality, necessi...
The human mitochondrial DNA (mtDNA) encodes 37 genes, including thirteen proteins essential for the respiratory chain, and RNAs functioning in the mitochondrial translation apparatus. The total number of mtDNA molecules per cell (mtDNA content) is va...
The correct establishment and maintenance of DNA methylation patterns are critical for mammalian development and the control of normal cell growth and differentiation. DNA methylation has profound effects on the mammalian genome, including transcript...
CXCR3 is a chemokine receptor with two well-characterized isoforms that have unique, context-dependent roles: CXCR3-A and CXCR3-B, which are produced through alternative 3′ splice site selection (A3SS). RNA-seq data from The Cancer Genome Atlas (TCGA...
Background: Mass spectrometry-based metabolomics approaches provide an immense opportunity to enhance our understanding of the mechanisms that underpin the cellular reprogramming of cancers. Accurate comparative metabolic profiling of heterogeneous c...
The formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during the development and maintenance...
Complex human diseases, including cancer, are linked to genetic factors. Genome-wide association studies (GWASs) are powerful for identifying genetic variants associated with cancer but are limited by their reliance on case–control data. We pro...
Copy number variation (CNV) is a common type of structural variation in the human genome. Accurate detection of CNVs from tumor genomes can provide crucial information for the study of tumor genesis and cancer precision diagnosis. However, the contam...
Genomic selection (GS) is a groundbreaking statistical machine learning method for advancing plant and animal breeding. Nonetheless, its practical implementation remains challenging due to numerous factors affecting its predictive performance. This r...
Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but...
Asthma and obesity are two of the most common chronic conditions in children and adolescents. There is increasing evidence that sphingolipid metabolism is altered in childhood asthma and is linked to airway hyperreactivity. Dysregulated sphingolipid...
Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of ‘open’ chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal ti...
Mast cells are the major effector cells that mediate IgE-dependent allergic reactions. We sought to use integrated network analysis to identify genomic biomarkers associated with high response in IgE-mediated activation of primary human mast cells. P...
Cervical cancer remains a significant global health concern, impacting over half a million women annually. The primary cause is a persistent infection with hr-HPV, which disrupts various cellular processes crucial for normal function. This disruption...
Human endogenous retroviruses (HERVs) have been implicated in a variety of human diseases including cancers. However, technical challenges in analyzing HERV sequence data have limited locus-specific characterization of HERV expression. Here, we use t...
Genome instability in cancer cells causes not only point mutations but also structural variations of the genome, including copy number variations (CNVs). It has recently been proposed that CNVs arise in cancer to adapt to a given microenvironment to...
Proteus mirabilis is a component of the normal intestinal microflora of humans and animals, but can cause urinary tract infections and even sepsis in hospital settings. In recent years, the number of multidrug-resistant P. mirabilis isolates, includi...
Chronic lymphocytic leukemia (CLL) is a very common and mostly incurable B-cell malignancy. Recent studies revealed high interpatient mutational heterogeneity and worsened therapy response and survival of patients with complex genomic aberrations. In...
Functional data analysis has demonstrated significant success in time series analysis. In recent biomedical research, it has also been used to analyze sequence variations in genome-wide association studies (GWAS). The observations of genetic variants...
Background: Esotropia and exotropia are two major phenotypes of comitant strabismus. It remains controversial whether esotropia and exotropia would share common genetic backgrounds. In this study, we used a quantitative trait locus (QTL)-sequencing p...
For cancer diagnosis, many DNA methylation markers have been identified. However, few studies have tried to identify DNA methylation markers to diagnose diverse cancer types simultaneously, i.e., pan-cancers. In this study, we tried to identify DNA m...
Grain and flour quality traits affect marketing potential and milling and baking properties. Trait means varied in fourteen wheat grain and flour quality traits for a population of 188 diverse soft winter wheat varieties harvested from 2020 to 2023 a...
For accurate gene expression quantification, normalization of gene expression data against reliable reference genes is required. It is known that the expression levels of commonly used reference genes vary considerably under different experimental co...
Structural variants drive tumorigenesis by disrupting normal gene function through insertions, inversions, translocations, and copy number changes, including deletions and duplications. Detecting structural variants is crucial for revealing their rol...
The mitochondrial genome and 5S rDNA are powerful tools for exploring and confirming species identity and understanding evolutionary trajectories. In addition, evaluating the nutritional value of Cambaroides dauricus by determining and analyzing the...
The size of viral genomes is limited, thus the majority of encoded proteins possess multiple functions. The main function of tobamoviral movement protein (MP) is to perform plasmodesmata gating and mediate intercellular transport of the viral RNA. MP...
The breast cancer susceptibility gene 1 (BRCA1) has been well established as a tumor suppressor and functions primarily by maintaining genome integrity. Genome stability is compromised when cells are exposed to oxidative stress. Increasing evidence s...
The most frequent DNA lesion resulting from an oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoG). 8-oxoG is a premutagenic base modification due to its capacity to pair with adenine. Thus, the repair of 8-oxoG is critical for the preservation of...
Genetic biomarkers have played a pivotal role in the classification, prognostication, and guidance of clinical cancer therapies. Large-scale and multi-dimensional analyses of entire cancer genomes, as exemplified by projects like The Cancer Genome At...
Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. LINEs replicate using an RNA intermediate followed by reverse transcription and are typically a few kilobases in length. LINE acti...
The search for new therapeutic principles is essential for treating relapsed/refractory (r/r) acute myeloid leukemia (AML). Novel principles include genome-agnostic differentiation induction, controlling AML-triggering inflammation, potentiating the...
Cytochrome P450 monooxygenases (P450s) have a variety of functions, including involvement in the metabolism of exogenous substances and the synthesis and degradation of endogenous substances, which are important for the growth and development of inse...
Background: Curcuma bakerii is a species of the family Zingiberaceae, endemic to Bangladesh. This genus of rhizomatous plants is widely distributed in tropical regions worldwide and is valued for its medicinal, aromatic, and culinary properties. Meth...
Tumor suppressor genes (TSGs) are essential for normal cellular function in multicellular organisms, but many TSGs and tumor-suppressing mechanisms remain unknown. Planarian flatworms exhibit particularly robust tumor suppression, yet the specific me...
Colorectal cancer (CRC) is the third leading cause of cancer deaths. Advances within bioinformatics, such as machine learning, can improve biomarker discovery and ultimately improve CRC survival rates. There are clear sex differences in CRC character...
Peroxiredoxins have a long-established cellular function as regulators of redox metabolism by catalyzing the reduction of peroxides (e.g., H2O2, lipid peroxides) with high catalytic efficiency. This activity is also critical to the initiation and rel...
of 13