A5042127372- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Probiotics and Fermented Foods
- RNA Research and Splicing
- FOXO transcription factor regulation
- GaN-based semiconductor devices and materials
- Cancer-related molecular mechanisms research
- Protein Structure and Dynamics
- Bacillus and Francisella bacterial research
- Ga2O3 and related materials
- Esophageal Cancer Research and Treatment
- Urological Disorders and Treatments
- Protein Degradation and Inhibitors
- Innovative Microfluidic and Catalytic Techniques Innovation
- Aldose Reductase and Taurine
- Wnt/β-catenin signaling in development and cancer
- Semiconductor materials and devices
- Immune Cell Function and Interaction
- Cell Image Analysis Techniques
- Cancer Cells and Metastasis
- Marine Ecology and Invasive Species
- Machine Learning in Materials Science
National Institute of Arthritis and Musculoskeletal and Skin Diseases
2017-2024
National Institutes of Health
2017-2024
University of Chinese Academy of Sciences
2011-2024
Chinese Academy of Sciences
2010-2024
Guangzhou Institutes of Biomedicine and Health
2024
Mayo Clinic in Florida
2016-2022
Army Medical University
2019-2022
Xinqiao Hospital
2019-2022
Army Medical College
2022
Jacksonville College
2020
With the rapid development of DNA sequencing technology, increasing bacteria genome data enable biologists to dig evolutionary and genetic information prokaryotic species from pan-genome sight. Therefore, high-efficiency pipelines for analysis are mostly needed. We have developed a new pipeline (PGAP), which can perform five analytic functions with only one command, including cluster functional genes, profile analysis, variation evolution function enrichment gene clusters. PGAP's performance...
Abstract Summary: Pan-genome analyses have shed light on the dynamics and evolution of bacterial genome from point population. The explosive growth sequence also brought an extremely big challenge to pan-genome profile analysis. We developed a tool, named PanGP, complete analysis for large-scale strains efficiently. PanGP has integrated two sampling algorithms, totally random (TR) distance guide (DG). DG algorithm drew sample strain combinations basis diversity performance these algorithms...
Panax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four P. strains, which are Damaya (DMY), Ermaya (EMY), Gaolishen (GLS) Yeshanshen (YSS). The total sequence length DMY, EMY GLS was 156,354 bp, while that YSS 156,355 bp. Comparative genomic analysis of indicate gene content, GC order DMY quite similar to its relative...
Mycobacterium abscessus (Ma) is an emerging human pathogen that causes both soft tissue infections and systemic disease. We present the first comparative whole-genome study of Ma strains isolated from patients wide geographical origin. found a high proportion accessory strain-specific genes indicating open, non-conservative pan-genome structure, clear evidence rapid phage-mediated evolution. Although we fewer virulence factors in compared to M. tuberculosis, our data indicated evolves...
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across variety of species and provides an interactive browser for visualization methylation data. Here, we present updated implementation (version 3.0) by incorporating more from multiple equipping with enhanced functionalities data annotation friendly web interfaces presentation, search visualization. 3.0 features large-scale integration methylomes, involving 34 consensus reference derived...
Functional FOXA1 targeting is mostly unique to each of the four human cancer cell lines HepG2, LNCaP, MCF7, and T47D.
Discontinuous transcription is evolutionarily conserved and a fundamental feature of gene regulation; yet, the exact mechanisms underlying transcriptional bursting are unresolved. Analyses transcriptome-wide have focused on role cis-regulatory elements, but other factors that regulate this process remain elusive. We applied mathematical modeling to single-cell RNA sequencing data infer dynamics under multiple conditions identify possible molecular mechanisms. found Mediator complex subunit...
Since PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed bacterial genomics research. Though integrated several modules for pan-genomics analysis, how to properly and effectively interpret visualize the results data is still a challenge. To well present genomic characteristics, novel cross-platform software developed, named PGAP-X. Four kinds of were developed integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile...
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict map in eukaryote the past years, data is increasing dramatically. To facilitate usage published across studies, we developed a database named (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental from 477 samples 15 species. With series functional modules, users can search profile at promoter region...
Defense systems are vital weapons for prokaryotes to resist heterologous DNA and survive from the constant invasion of viruses, they widely used in biochemistry investigation antimicrobial drug research. So far, numerous types defense have been discovered, but there is no comprehensive database organize prokaryotic gene datasets. To fill this gap, we unveil antiviral system (PADS) Arsenal (https://bigd.big.ac.cn/padsarsenal), a public dedicated gathering, storing, analyzing visualizing The...
An astronomical increase in microbial genome data recent years has led to strong demand for bioinformatic tools pan-genome analysis within and across species. Here, we present PGAweb, a user-friendly, web-based tool bacterial analysis, which is composed of two main modules, PGAP PGAP-X. PGAweb provides key interactive customizable functions that include orthologous clustering, profiling, sequence variation evolution functional classification. presents features genomic structural dynamics...
Salmonella Paratyphi A (S. A) is a highly adapted, human-specific pathogen that causes paratyphoid fever. Cases of fever have recently been increasing, and the disease becoming major public health concern, especially in Eastern Southern Asia. To investigate genomic variation evolution S. A, pan-genomic analysis was performed on five newly sequenced strains two other reference strains. whole genome comparison revealed seven genomes are collinear their organization conserved. The high rate...
The transcription factor forkhead box protein A1 (FOXA1) plays a critical role in the proliferation of human breast cancer cells, particularly estrogen receptor alpha (ERα)-positive luminal cells. However, genetic studies requirement for Foxa1 mammary tumor formation mice have been hampered by lack conditional gene ablation. We examined three mouse models mammary-specific ablation ductal epithelial cells to identify best system complete and Foxa1. found that MMTV-Cre MMTV-rtTA;Tet-On-Cre led...
Abstract Explainable artificial intelligence aims to interpret how machine learning models make decisions, and many model explainers have been developed in the computer vision field. However, understanding of applicability these biological data is still lacking. In this study, we comprehensively evaluated multiple by interpreting pre-trained for predicting tissue types from transcriptomic identifying top contributing genes each sample with greatest impacts on prediction. To improve...
We report a selective area growth (SAG) method to define the p-GaN gate of AlGaN/GaN high electron mobility transistors (HEMTs) by metal-organic chemical vapor deposition. Compared with Schottky HEMTs, SAG HEMTs show more positive threshold voltage (Vth) and better control ability. The influence Cp2Mg flux on has also been studied. With increasing from 0.16 μmol/min 0.20 μmol/min, Vth raises −0.67 V −0.37 V. maximum transconductance HEMT at drain 10 is 113.9 mS/mm while that value 51.6...
The safety and efficacy of endoscopic submucosal dissection (ESD) radiofrequency ablation for early esophageal cancer (EEC) in cirrhotic patients has not been thoroughly investigated to date. present study aimed establish a standard treatment strategy EEC with varices. Six flat-type EECs (high-grade intraepithelial neoplasia) on or adjacent varices were enrolled. Esophageal varix ligation (EVL) transjugular intrahepatic portosystemic shunt (TIPS) used the initial management Follow-up...
The data released by the 1000 Genomes Project contain an increasing number of genome sequences from different nations and populations with a large genetic variations. As result, focus human studies is changing single static to complex dynamic. currently available reference (GRCh37) based on sequencing 13 anonymous Caucasian volunteers, which might limit scope genomics, transcriptomics, epigenetics, wide association studies. We used massive amount published Consortium construct Virtual...
In mammals, transcriptional factors (TFs) drive gene expression by binding to regulatory elements in a cooperative manner. Deciphering the rules of such cooperation is crucial obtain full understanding cellular homeostasis and development. Although this long-standing topic, there no comprehensive database for biologists access syntax TF sites. Here we present TFSyntax (https://tfsyntax.zhaopage.com), focusing on arrangement maps motif 1299 human TFs 890 mouse across 382 cells tissues,...