STRsensor: a computationally efficient method for STR allele-typing from massively parallel sequencing data.

Short tandem repeats (STRs) represent one of the most polymorphic variations in the human genome, finding extensive applications in forensics, population genetics and medical genetics. In contrast to the traditional capillary electrophoresis (CE) method, genotyping STRs using massive parallel sequencing technology offers enhanced sensitivity and accuracy. However, current methods are mainly designed for target sequencing with higher coverage for a specific STR locus, thereby constraining the utility of STRs in low- and medium-coverage whole genome sequencing (WGS) data.

A methylation panel of 10 CpGs for accurate age inference via stepwise conditional epigenome-wide association study.

Estimating individual age from DNA methylation at age associated CpG sites may provide key information facilitating forensic investigations. Systematic marker screening and feature selection play a critical role in ensuring the performance of the final prediction model. In the discovery stage, we screened for 811876 CpGs from whole blood of 2664 Chinese individuals ranging from 18 to 83 years of age based on a stepwise conditional epigenome-wide association study (SCEWAS).

Classification of Dog Breeds Using Convolutional Neural Network Models and Support Vector Machine.

When classifying breeds of dogs, the accuracy of classification significantly affects breed identification and dog research. Using images to classify dog breeds can improve classification efficiency; however, it is increasingly challenging due to the diversities and similarities among dog breeds. Traditional image classification methods primarily rely on extracting simple geometric features, while current convolutional neural networks (CNNs) are capable of learning high-level semantic features.

Alzheimer's Disease from Modeling to Mechanism Research.

As our population continues to age, the search for effective therapeutic strategies to combat neurodegenerative diseases, particularly Alzheimer's disease (AD), has become more pressing than ever. For over a decade, researchers have focused on the amyloid cascade hypothesis in their pursuit of new drugs for AD. However, with numerous drugs targeting this hypothesis failing in clinical trials, it is clear that AD's pathogenesis is complex, and each individual may display significant heterogeneity.

[Artificial intelligence model for diagnosis of coronary artery disease based on facial photos].

To develop and validate an artificial intelligence (AI) diagnostic model for coronary artery disease based on facial photos. This study was a cross-sectional study. Patients who were scheduled to undergo coronary angiography (CAG) at Beijing Anzhen Hospital and Beijing Daxing Hospital from August 2022 to November 2023 were included consecutively.

Immunological face of megakaryocytes.

Megakaryocytes (MKs), which are traditionally known for their role in platelet production, are now emerging as unique immune cells with diverse capabilities. They express immune receptors, participate in pathogen recognition and response, phagocytose pathogens, contribute to antigen presentation, and interact with various immune cell types. When encountering inflammatory challenges, MKs exhibit intricate immune functions that can either promote or inhibit inflammation.

VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences.

The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable, universal, and automated preliminary taxonomic framework for comprehensive virus studies. Here, we introduce VISTA (Virus Sequence-based Taxonomy Assignment), a computational tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for virus taxonomy. Leveraging physio-chemical property sequences, k-mer profiles, and machine learning techniques, VISTA constructs a robust distance-based framework for taxonomic assignment.

iDog: a multi-omics resource for canids study.

iDog (https://ngdc.cncb.ac.

Automatic construction of Petri net models for computational simulations of molecular interaction network.

Petri nets are commonly applied in modeling biological systems. However, construction of a Petri net model for complex biological systems is often time consuming, and requires expertise in the research area, limiting their application. To address this challenge, we developed GINtoSPN, an R package that automates the conversion of multi-omics molecular interaction network extracted from the Global Integrative Network (GIN) into Petri nets in GraphML format.

Spatial transcriptomic landscape unveils immunoglobin-associated senescence as a hallmark of aging.

To systematically characterize the loss of tissue integrity and organ dysfunction resulting from aging, we produced an in-depth spatial transcriptomic profile of nine tissues in male mice during aging. We showed that senescence-sensitive spots (SSSs) colocalized with elevated entropy in organizational structure and that the aggregation of immunoglobulin-expressing cells is a characteristic feature of the microenvironment surrounding SSSs. Immunoglobulin G (IgG) accumulated across the aged tissues in both male and female mice, and a similar phenomenon was observed in human tissues, suggesting the potential of the abnormal elevation of immunoglobulins as an evolutionarily conserved feature in aging.

An EED/PRC2-H19 Loop Regulates Cerebellar Development.

EED (embryonic ectoderm development) is a core subunit of the polycomb repressive complex 2 (PRC2), which senses the trimethylation of histone H3 lysine 27 (H3K27). However, its biological function in cerebellar development remains unknown. Here, we show that EED deletion from neural stem cells (NSCs) or cerebellar granule cell progenitors (GCPs) leads to reduced GCPs proliferation, cell death, cerebellar hypoplasia, and motor deficits in mice.

Progressive polyadenylation and m6A modification of Ighg1 mRNA maintain IgG1 antibody homeostasis in antibody-secreting cells.

Antigen-specific antibodies are generated by antibody-secreting cells (ASCs). How RNA post-transcriptional modification affects antibody homeostasis remains unclear. Here, we found that mRNA polyadenylations and N6-methyladenosine (m6A) modifications maintain IgG1 antibody production in ASCs.

VDGE: a data repository of variation database for gene-edited animals across multiple species.

Gene-edited animals are crucial for addressing fundamental questions in biology and medicine and hold promise for practical applications. In light of the rapid advancement of gene editing technologies over the past decade, a dramatically increased number of gene-edited animals have been generated. Genome editing at off-target sites can, however, introduce genomic variations, potentially leading to unintended functional consequences in these animals.

CancerSCEM 2.0: an updated data resource of single-cell expression map across various human cancers.

The field of single-cell RNA sequencing (scRNA-seq) has advanced rapidly in the past decade, generating significant amounts of valuable data for researchers to study complex tumor profiles. This data is crucial for gaining innovative insights into cancer biology. CancerSCEM (https://ngdc.

Splicing dysregulation in glioblastoma alters the function of cell migration-related genes.

Glioblastoma (GBM) has a poor prognosis with a high recurrence and low survival rate. Previous RNA-seq analyses have revealed that alternative splicing (AS) plays a role in GBM progression. Here, we present a novel AS analysis method (Semi-Q) and describe its use to identify GBM-specific AS events.

SMART: STR Mixture Analysis and Resolution Tools.

The analysis of STR mixture profiles derived from mixed DNA samples plays a critical role in criminal investigations and legal proceedings. In this article, we present SMART, a novel software developed within the fully continuous model framework to analyze STR mixture profiles. SMART incorporates the peak height model, stutter model, drop-in/drop-out model, and population genetics model, offering various functionalities such as calculating likelihood ratios (LR), resolving genotypes of individual contributors, and performing direct database searches using mixed DNA profiles.

EryDB: A Transcriptomic Profile Database for Erythropoiesis and Erythroid-related Diseases.

Erythropoiesis is a finely regulated and complex process that involves multiple transformations from hematopoietic stem cells to mature red blood cells at hematopoietic sites from the embryonic to the adult stages. Investigations into its molecular mechanisms have generated a wealth of expression data, including bulk and single-cell RNA sequencing data. A comprehensively integrated and well-curated erythropoiesis-specific database will greatly facilitate the mining of gene expression data and enable large-scale research of erythropoiesis and erythroid-related diseases.