A5008600556- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Earthquake Detection and Analysis
- Geophysics and Gravity Measurements
- Ionosphere and magnetosphere dynamics
- Gene expression and cancer classification
- RNA modifications and cancer
- Geographic Information Systems Studies
- Molecular Biology Techniques and Applications
- Cell Image Analysis Techniques
- Tuberculosis Research and Epidemiology
- RNA and protein synthesis mechanisms
- Literature, Language, and Rhetoric Studies
- Network Security and Intrusion Detection
- Data-Driven Disease Surveillance
- Advanced Computational Techniques and Applications
- Cancer Genomics and Diagnostics
- Anomaly Detection Techniques and Applications
- Gene Regulatory Network Analysis
- Renal and related cancers
- Sarcoma Diagnosis and Treatment
- Pluripotent Stem Cells Research
- Genetic Syndromes and Imprinting
- Text and Document Classification Technologies
- Data Stream Mining Techniques
University of Missouri
2021-2025
Qilu Hospital of Shandong University
2024
Baylor College of Medicine
2022-2023
Allen Institute
2023
Allen Institute for Brain Science
2023
First Affiliated Hospital of Anhui Medical University
2023
Anhui Medical University
2023
Huazhong Agricultural University
2011-2022
Texas Children's Hospital
2022
Ministry of Agriculture and Rural Affairs
2021
The mammalian brain consists of millions to billions cells that are organized into many cell types with specific spatial distribution patterns and structural functional properties1-3. Here we report a comprehensive high-resolution transcriptomic cell-type atlas for the whole adult mouse brain. was created by combining single-cell RNA-sequencing (scRNA-seq) dataset around 7 million profiled (approximately 4.0 passing quality control), approximately 4.3 using multiplexed error-robust...
Abstract Single-cell multi-omics (scMulti-omics) allows the quantification of multiple modalities simultaneously to capture intricacy complex molecular mechanisms and cellular heterogeneity. Existing tools cannot effectively infer active biological networks in diverse cell types response these external stimuli. Here we present DeepMAPS for network inference from scMulti-omics. It models scMulti-omics a heterogeneous graph learns relations among cells genes within both local global contexts...
Lung cancer, of which 85% is non-small-cell (NSCLC), the leading cause cancer-related death in United States. We used genome-wide analysis tumor tissue to investigate whether single nucleotide polymorphisms (SNPs) tumors are prognostic factors early-stage NSCLC.
Spatially resolved transcriptomics provides a new way to define spatial contexts and understand the pathogenesis of complex human diseases. Although some computational frameworks can characterize context via various clustering methods, detailed architectures functional zonation often cannot be revealed localized due limited capacities associating information. We present RESEPT, deep-learning framework for characterizing visualizing tissue architecture from spatially transcriptomics. Given...
Abstract Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression corresponding spatial coordinates two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results often cannot handle three-dimensional transcriptomic data. Here we introduce BSP (big-small patch), a non-parametric model...
ABSTRACT Emerging spatial omics technologies empower comprehensive exploration of biological systems from multi-omics perspectives in their native tissue location two and three- dimensional space. However, sparse sequencing capacity growing resolution present significant computational challenges identifying biologically meaningful molecules that exhibit variable distributions across different omics. We introduce scBSP, an open-source, versatile, user-friendly package for spatially features...
We present an enhancer AAV toolbox for accessing and perturbing striatal cell types circuits. Best-in-class vectors were curated major neuron populations including medium spiny neurons (MSNs), direct indirect pathway MSNs, as well Sst-Chodl, Pvalb-Pthlh, cholinergic interneurons. Specificity was evaluated by multiple modes of molecular validation, three different routes virus delivery, with diverse transgene cargos. Importantly, we provide detailed information necessary to achieve reliable...
Active DNA demethylation occurs after a sperm enters an egg. However, the mechanisms for active remain poorly understood. Ten-eleven translocation enzymes were recently shown to catalyze conversion of 5-methylcytosine 5-hydroxymethylcytosine (5hmC). Thus, we decided investigate role 5hmC in demethylation. We analyzed methylation and hydroxymethylation status metaphase II oocytes as well 1-cell stage cleavage embryos. In zygotes, was mainly detected paternal pronucleus it increased from...
DNA methylation and histone modifications are essential epigenetic marks that can significantly affect the mammalian somatic cell nuclear transfer (SCNT) embryo development. However, mechanisms by which affects reprogramming have not been fully elucidated.In our study, we used quantitative polymerase chain reaction (qPCR), Western blotting, immunofluorescence staining (IF) sodium bisulfite genomic sequencing to examine effects of RG108, a methyltransferase inhibitor (DNMTi), on dynamic...
Associative classification (AC) which is based on association rules has shown great promise over many other techniques static dataset.Meanwhile, a new challenge have been proposed in that the increasing prominence of data streams arising wide range advanced application.This paper describes and evaluates associative algorithm for AC-DS, estimation mechanism Lossy Counting (LC) landmark window model.And AC-DS was applied to mining several datasets obtained from UCI Machine Learning Repository...
// Yihao Yang 1, * , Ya Zhang Xin Qu Junfeng Xia 1 Dongqi Li Xiaojuan Yu Wang Zewei He Su Yonghong Zhou Lin Xie Zuozhang Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department Orthopaedics, The Third Affiliated Hospital Kunming Medical University (Tumor Province), Kunming, 650118, China These authors contributed equally to this work co-first Correspondence to: Yang, email: yangzuozhang@163.com zuozhangyang1326@sohu.com Xie, xielinyanghan@163.com Keywords: differentially...
Although Mycobacterium tuberculosis (MTB) has existed for thousands of years, its immune escape mechanism remains obscure. Increasing evidence signifies that microRNAs (miRNAs) play pivotal roles in the progression (TB). RNA sequencing was used to sequence miRNAs human acute monocytic leukemia cells (THP-1) infected by virulent MTB-1458 strain and avirulent vaccine bovis Bacillus Calmette-Guérin (BCG). Sets differentially expressed (DE-miRNAs) between MTB-1458/BCG-infected groups uninfected...
Abstract Spatially resolved transcriptomics provides a new way to define spatial contexts and understand biological functions in complex diseases. Although some computational frameworks can characterize context via various clustering methods, the detailed architectures functional zonation often cannot be revealed localized due limited capacities of associating information. We present RESEPT, deep-learning framework for characterizing visualizing tissue architecture from spatially...
Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression corresponding spatial coordinates two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results often cannot handle three-dimensional transcriptomic data. Here we introduce BSP (big-small patch), a granularity-guided...
Abstract We present DeepMAPS (Deep learning-based Multi-omics Analysis Platform for Single-cell data) biological network inference from single-cell multi-omics (scMulti-omics). includes both cells and genes in a heterogeneous graph to simultaneously infer cell-cell, cell-gene, gene-gene relations. The multi-head attention mechanism transformer considers the relation among within local global context, making robust data noise scale. benchmarked on 18 scMulti-omics datasets cell clustering...
Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected processed starting from raw sequencing reads in a uniform analysis pipeline. To address the heterogeneity different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map expressions into latent space adapted standard...
Tuberculosis is the second cause in infectious diseases leading to human death. Understanding virulence mechanism inevitable if disease needs be fully cured. Therefore, this study aimed reveal by comparing proteomic profiles of intracellular and extracellular virulent strain M.tb bacille Calmette-Guérin (BCG) from infected THP-1cells. First, BCG THP-1 at MOI 10:1. Twelve hours postinfection, bacteria were collected, whereas two bacilli cultured 7H9 broth media used as control. Then four...
Wilms tumor (WT) is the most common malignancy of genitourinary system in children. Currently, Integration single-cell RNA sequencing (scRNA-Seq) and Bulk (RNA-Seq) analysis heterogeneity between different cell types pediatric WT tissues could more accurately find prognostic markers, but this lacking. RNA-Seq clinical data related to were downloaded from Therapeutically Applicable Research Generate Effective Treatments (TARGET) database. Small nucleolar host gene 15 (SNHG15) was identified...
Abstract Neural tuning for visual words is essential fluent reading across various scripts. This study investigated the emergence and development of N170 Chinese characters its cognitive–linguistic correlates. Electroencephalogram data from 48 adult L2 learners 23 native readers were collected using a color detection task. The real characters, pseudo-characters, false stroke combinations line drawings recorded. We found beginner showed larger compared to (coarse neural tuning)....
Mycobacteria encounter a number of environmental changes during infection and respond using different mechanisms. Small RNA (sRNA) is post-transcriptionally regulatory system for gene functions has been investigated in many other bacteria. This study used Mycobacterium tuberculosis bovis Bacillus Calmette-Guérin (BCG) models sequenced whole bacterial RNAs before after host cell infection. A comparison differentially expressed sRNAs Gene Ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG)...