In recent years, metal–organic frameworks (MOFs) have been extensively studied as candidate enzyme immobilization platforms. However, conventional MOF–enzyme composites usually exhibit low controllability and reusability. this study, a novel stable strategy for was designed by use of ZIF-8 to encapsulate in situ DNA–enzyme on the surface magnetic particles (MPs). The mechanism encapsulation discussed detail. It found that immobilized enzymes were involved growth ZIF-8, DNA cross-linking...

Gene regulatory elements, including promoters, enhancers, silencers, etc., control transcriptional programs in a spatiotemporal manner. Though these elements are known to be able induce either positive or negative control, the community has been mostly studying enhancers which amplify transcription initiation, with less emphasis given silencers repress gene expression. To facilitate study of and investigation their potential roles we developed SilencerDB...

<title>Abstract</title> Large-scale foundation models have recently opened a new avenue to artificial general intelligence for life sciences, showing great promise in the analysis of single-cell transcriptomic data. Nevertheless, such challenges as tremendous number signaling regions, extreme data sparsity, and nearly binary nature epigenomic prevented construction model epigenomics thus far, though it is evident that abundant properties chromatin accessibility provide more decisive insights...

Recent advances in spatial epigenomic techniques have given rise to assay for transposase-accessible chromatin using sequencing (spATAC-seq) data, enabling the characterization of heterogeneity and information simultaneously. Integrative analysis multiple spATAC-seq samples, which no method has been developed, allows effective identification elimination unwanted non-biological factors within comprehensive exploration tissue structures providing a holistic landscape, thereby facilitating...

We aim to estimate impact and projection of the COVID-19 pandemic on burden stroke at global, regional, national levels METHODS: Utilizing standardized GBD methodologies, we conducted a comprehensive analysis prevalence, incidence, mortality, disability-adjusted life years (DALYs) associated with across 204 countries regions spanning periods from 1990 2019, 2019 2021, 2021. Our study provides detailed estimates accompanied by corresponding 95% uncertainty intervals (UIs), stratified age sex....

Abstract Spatially resolved sequencing technologies have revolutionized the characterization of biological regulatory processes within microenvironment by simultaneously accessing states genomic regions, genes and proteins, along with spatial coordinates cells, necessitating advanced computational methods for cross-modality multi-sample integrated analysis omics datasets. To address this gap, we propose PRESENT, an effective scalable contrastive learning framework, representation spatially...

Abstract The inherent similarities between natural language and biological sequences have inspired the use of large models in genomics, but current struggle to incorporate chromatin interactions or predict unseen cellular contexts. To address this, we propose EpiGePT, a transformer-based model designed for predicting context-specific human epigenomic signals. By incorporating transcription factor activities 3D genome interactions, EpiGePT outperforms existing methods signal prediction tasks,...

Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are predominantly sequence-based typically focus on individual types, limiting insights into their cell-type-specific functions dynamics. Here, we present CREATE, a multimodal deep learning framework based Vector Quantized Variational AutoEncoder,...

The inherent similarities between natural language and biological sequences have given rise to great interest in adapting the transformer-based large models (LLMs) underlying recent breakthroughs processing (references), for applications genomics. However, current LLMs genomics suffer from several limitations such as inability include chromatin interactions training data, make prediction new cellular contexts not represented data. To mitigate these problems, we propose EpiGePT, a pretrained...

Abstract Summary Chromatin accessibility serves as a critical measurement of physical contact between nuclear macromolecules and DNA sequence, providing valuable insights into the comprehensive landscape regulatory mechanisms, thus we previously developed OpenAnnotate web server. However, an increasing number epigenomic analysis software tools emerged, web-based annotation often faced limitations inconveniences when integrated these pipelines. To address issues, here develop two packages...

Abstract Cell–cell communication (CCC) through ligand–receptor (L–R) pairs forms the cornerstone for complex functionalities in multicellular organisms. Deciphering such intercellular signaling can contribute to unraveling disease mechanisms and enable targeted therapy. Nonetheless, notable biases inconsistencies are evident among inferential outcomes generated by current methods inferring CCC network. To fill this gap, we developed collectNET (http://health.tsinghua.edu.cn/collectnet) as a...

In recent years, Scratch has been a popular programming platform for young children. To help children express emotions projects, provides with music module to create desirable background music. However, in Scratch, there is not tool helping recognize the emotion of Besides, as Scratch-generated differs from regular music, existing recognition models perform poor overcome it, this paper, we propose novel model First, build dataset by main melody extraction algorithm. Then, each extract their...

This paper makes use of the characteristics initial sensitivity and randomness chaotic map to design an image encryption algorithm based on sine tent map. The is used improve map; then, improved sine-tent proposed. traditional proposed in this has expanded control parameter range better chaos. In algorithm, bit rearrangement adopted further map, which can reconstruct output value expand parameters are connected with generate key. step, a method replacing most significant scrambling-diffusion...

Abstract Single-cell sequencing technology has enabled the characterization of cellular heterogeneity at an unprecedented resolution. To analyze single-cell RNA-sequencing data, numerous tools have been proposed for various analytic tasks, which systematically summarized and concluded in a comprehensive database called scRNA-tools. Although epigenomic data can effectively reveal chromatin regulatory landscape that governs transcription, analysis presents assay-specific challenges, abundance...

From 2018 to 2019, two Chinese Sparrowhawks (Bird 01, male; Bird 02, female), Accipiter soloensis, were captured and fitted with Global Positioning System (GPS) loggers in order identify summering wintering sites, migration routes, stop-over sites. The first backpack solar GPS satellite trackers China explore their routes. successfully completed from southern China, through Nanning city of Guangxi province, Vietnam, Laos, Myanmar, Thailand, Malaysia, Singapore finally arriving Indonesia,...

The mitogenome was sequenced through whole-genome shotgun sequencing using the Illumina platform, and phylogenetic analysis carried out on basis of 13 PCGs two rRNAs. complete T. cardis comprised 16,761 bp, MN865118. organization location genes in were consistent with those reported for other Turdidae species. Phylogenetic relationships based Bayesian inference Maximum likelihood method revealed that closely related to Turdus hortulorum, indicating molecular taxonomy is its current...

Abstract Summary Cell-cell communication through ligand-receptor pairs forms the cornerstone for complex functionalities in multicellular organisms. Deciphering such intercellular signaling can contribute to un-raveling disease mechanisms and enables targeted therapy. Nonetheless, notable biases inconsistencies are evident among inferential outcomes generated by current methods inferring cell-cell network. To fill this gap, we developed collectNET ( http://health.tsing-hua.edu.cn/collectnet...

The highly pathogenic avian influenza 2.3.4.4b H5 viruses have been a cause for concern recently, as they responsible continuous outbreaks since 2021. In China, the H5N6 subtype has predominantly circulating in domestic poultry but rarely detected wild birds over past 3 years. December 2023, novel reassortant were resurgent and ducks Eastern Asia. reassorted with those of currently prevalent H5N1 bird origin worldwide, well that caused human infections 2022 low viruses, such H9N2 virus,...

Spatial epigenomic technologies enable simultaneous capture of spatial location and chromatin accessibility cells within tissue slices. Identifying peaks that display variation cellular heterogeneity is the key analytic task for characterizing landscape complex tissues. Here, we propose an efficient iterative model, Descart, spatially variable identification based on graph inter-cellular correlations. Through comprehensive benchmarking, demonstrate superiority Descart in revealing capturing...

Abstract Recent advances in spatial epigenomic techniques have given rise to assay for transposase-accessible chromatin using sequencing (spATAC-seq) data, enabling the characterization of heterogeneity and information simultaneously. Integrative analysis multiple spATAC-seq samples, which no method has been developed, allows effective identification elimination unwanted non-biological factors within comprehensive exploration tissue structures providing a holistic landscape, thereby...