A5101531536- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Bacteriophages and microbial interactions
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- RNA Research and Splicing
- Plant Virus Research Studies
- MicroRNA in disease regulation
- Optical Systems and Laser Technology
- Gene expression and cancer classification
- Connexins and lens biology
- Adaptive optics and wavefront sensing
- Insect Resistance and Genetics
- Microbial Community Ecology and Physiology
- Cancer-related molecular mechanisms research
- Advanced biosensing and bioanalysis techniques
- Retinal Development and Disorders
- Molecular Biology Techniques and Applications
- Circular RNAs in diseases
- Plant Molecular Biology Research
- Adipokines, Inflammation, and Metabolic Diseases
- Advanced optical system design
- Image Processing Techniques and Applications
- Cytomegalovirus and herpesvirus research
Miami University
2016-2025
Hong Kong University of Science and Technology
2025
University of Hong Kong
2025
Second Military Medical University
2012-2018
University of Miami
2017
Institute of Plant Protection
2012-2016
Chinese Academy of Agricultural Sciences
2013-2016
Shanghai Changzheng Hospital
2011-2016
Nanjing University of Aeronautics and Astronautics
2008-2013
Xiamen University
2012
Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation animals and plants. However, the extent of sense antisense APA at genome level is not known. We developed a deep-sequencing protocol that queries junctions 3′UTR poly(A) tails confidently maps tags annotated genome. The results this mapping show 70% Arabidopsis genes use more than one site, excluding microheterogeneity. Analysis reveal extensive introns coding sequences, which can...
The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, ecological evolutionary genomics, pest control a plethora other topics. RNA interference (RNAi), transgenesis genome editing are well established resources genome-wide RNAi screening have become available this model. All these techniques depend on high quality assembly precise models. However, first version was generated by Sanger sequencing, with...
Comprehensive and accurate annotation of the repeatome, including transposons, is critical for deepening our understanding repeat origins, biogenesis, regulatory mechanisms, roles. Here, we developed Generic Repeat Finder (GRF), a tool genome-wide detection based on fast, exhaustive numerical calculation algorithms integrated with optimized dynamic programming strategies. GRF sensitively identifies terminal inverted repeats (TIRs), direct (TDRs), interspersed that bear both repeats. also...
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNA primarily expressed in germ cells that can silence transposons at the post-transcriptional level. Accurate prediction piRNAs remains significant challenge.We developed program for piRNA annotation (Piano) using piRNA-transposon interaction information. We downloaded 13,848 Drosophila and 261,500 transposons. The were aligned to with maximum three mismatches. Then, interactions predicted by RNAplex. Triplet elements combining...
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cpf1 system has been successfully applied in genome editing. However, target efficiency of the CRISPR-Cpf1 varies among different guide RNA (gRNA) sequences.
Apomixis, asexual reproduction through seed, is widespread among angiosperm families. Gametophytic apomixis in Pennisetum squamulatum and Cenchrus ciliaris controlled by the apospory-specific genomic region (ASGR), which highly conserved macrosyntenic between these species. Thirty-two ASGR bacterial artificial chromosomes (BACs) isolated from both species one ASGR-recombining BAC P. squamulatum, together cover approximately 2.7 Mb of DNA, were used to investigate structure this region. Phrap...
Drought stress is the principal cause of seedling mortality in pine forests southeastern United States and many other forested regions around globe. As part a larger effort to discover loblolly genes, this study subjected rooted cuttings three unrelated genotypes watering regimens. Expressed sequence tags (ESTs) were obtained from both 3' 5' ends 12,918 randomly selected cDNAs generated root tissues. These ESTs clustered identify 6,765 unique transcripts (UniScripts) derived 6,202 putative...
Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only few SSRs (simple sequence repeats), also known simple tandem repeats or microsatellites, mapped in P. taeda. The objective this study was to integrate large set SSR markers from sources published cDNA into composite map constructed two reference mapping pedigrees. A dense that incorporates loci will benefit complete genome...
Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on sequenced gene annotations 31 plant algal species Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs a genome-wide scale, characterized their distributions motif features, explored putative biological functions. Among species, no significant correlation was detected between TR density genome size. Interestingly, green alga Chlamydomonas reinhardtii (42,059 bp/Mbp) castor bean Ricinus...
Abstract Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes, including plants and animals. Classified as a type of non-autonomous DNA elements, they play important roles genome organization evolution. Comprehensive accurate genome-wide detection MITEs various genomes can improve our understanding their origins, transposition processes, regulatory mechanisms biological relevance with regard to gene structures, expression regulation. In this paper, we...
To study whether miR-214 is regulated in coronary artery disease (CAD) patients and placental growth factor (PLGF) a possible target for atherosclerosis.Circulating was measured by quantitative PCR using RNA isolated from 40 with CAD, including 12 stable angina pectoris, 16 unstable pectoris acute myocardial infarction, 15 controls without CAD. Plasma level of PLGF ELISA.The significantly lower CAD compared that (P < 0.01). Compared to controls, (UAP, 38.6±9.1 pg/mL) infarction (AMI,...
Abstract Microsatellite instability (MSI) is characterized by high degree of polymorphism in microsatellite lengths due to deficiency mismatch repair (MMR) system. MSI associated with several tumor types and its status can be considered as an important indicator for patient prognosis. Conventional clinical diagnosis examines PCR products a panel markers using electrophoresis (MSI-PCR), which laborious, costly, time consuming. We developed MSIpred, python package automatic classification...
Abstract Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that variations such as isomiRs and “arm switching” are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on variations. To deepen our understanding of variability, we developed a new tool called “mirPRo”...
Improved knowledge of the sorghum transcriptome will enhance basic understanding how plants respond to stresses and serve as a source genes value agriculture. Toward this goal, Sorghum bicolor L. Moench cDNA libraries were prepared from light- dark-grown seedlings, drought-stressed plants, Colletotrichum-infected seedlings ovaries, embryos, immature panicles. Other with meristems propinquum (Kunth) Hitchc. that had been photoperiodically induced flower, rhizomes S. johnsongrass (Sorghum...
To understand nuclear mRNA polyadenylation mechanisms in the model alga Chlamydomonas reinhardtii, we generated a data set of 16,952 silico-verified poly(A) sites from EST sequencing traces based on Genome Assembly v.3.1. Analysis this revealed unique and complex signal profile that is setting apart other organisms. In contrast to high-AU content 3'-UTRs organisms, shows high-guanylate transits high-cytidylate around site. The average length 3'-UTR 595 nucleotides (nt), significantly longer...
Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to hosts. Despite this importance, metagenomic CRISPR detection remains major challenge. Here we present reference-guided ( Meta genomic Reference-Aided Search...
Piwi-interacting RNAs (piRNAs) are the largest class of small non-coding discovered in germ cells. Identifying piRNAs from RNA data is a challenging task due to lack conserved sequences and structural features piRNAs. Many programs have been developed identify piRNA data. However, these limitations. They either rely on extracting complicated features, or only demonstrate strong performance transposon related Here we proposed new program called piRNN for identification. For our software,...
The CRISPR system holds much promise for successful genome engineering, but therapeutic, industrial, and research applications will place high demand on improving the specificity efficiency of this tool. CT-Finder (http://bioinfolab.miamioh.edu/ct-finder) is a web service to help users design guide RNAs (gRNAs) optimized specificity. accommodates original single-gRNA Cas9 two specificity-enhancing paired-gRNA systems: D10A nickases (Cas9n) dimeric RNA-guided FokI nucleases (RFNs). Optimal...
Abstract Long non-coding RNAs (lncRNAs) play an essential role in diverse biological processes and disease development. Accurate classification of lncRNAs mRNAs is important for the identification tissue- or disease-specific lncRNAs. Here, we present our tool LncDC (Long RNA detection) that able to accurately predict with XGBoost model using features extracted from sequences, secondary structures, translated proteins. Benchmarking experiments showed consistently outperformed six...
Coronary artery disease (CAD) is a multigenic condition influenced by both nature and nurture (60% to 40%). Prognosis of CAD based on familial patterns. This study examined analyzed the susceptibility genetic variants in various Pakistani families. A total 50 families, 308 participants (79 affected 229 unaffected were genotyped for NOS3 (rs1799983, rs2070744), PON1 (rs662), LPA-PLA2 (rs105193, rs1805017), APOE (rs429358, rs7412), PCSK9 (rs505151), MEF2A (rs325400), TNF (rs1800629) LDLR...
Background: Understanding the role of repetitive elements (REs) in cancer development is crucial for identifying novel biomarkers and therapeutic targets. Methods: This study investigated locus-specific dysregulation REs, including differential expression methylation across 12 TCGA types stratified by their genomic context (i.e., genic intergenic REs). Results: We found uniquely dysregulated REs co-regulated with corresponding transcripts associated distinct biological functions different...
Abstract Summary CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has reported as a tool for RNA Here we describe CRISPR-RT (CRISPR RNA-Targeting), first web application to help biologists design crRNAs with improved target specificity system. allows users set up wide range of parameters, making it highly flexible current and future research CRISPR-based covers major model organisms can be easily extended cover other species. will empower...
Abstract Alternative polyadenylation has been recognized as a key contributor of gene expression regulation by generating different transcript isoforms with altered 3′ ends. Although is well known for marking the end UTR, an increasing number studies have reported previously less-addressed events located in other parts genes many eukaryotic organisms. These locations include 5′ UTRs, introns and coding sequences (termed herein non-3UTR), antisense intergenic polyadenlation. Focusing on n on-...