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Search: authors:"Dapeng Wang"

11 papers found.
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Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs

Plastids carry their own genetic material that encodes a variable set of genes that are limited in number but functionally important. Aside from orthology, the lineage-specific order and orientation of these genes are also relevant. Here, we develop a database, Plastid-LCGbase (http://lcgbase.big.ac.cn/plastid-LCGbase/), which focuses on organizational variability of plastid...

KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation

Background The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. Results To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a...

Total arsenic and speciation analysis of saliva and urine samples from individuals living in a chronic arsenicosis area in China

Background It is generally acknowledged that the determination of harmful chemical compounds excreted into saliva is useful for assessing their exposure levels. The aim of the present study was to compare the total arsenic and its species in saliva and urine samples collected from the people residing in an arsenic-contaminated area of China and to further verify the feasibility...

Both Size and GC-Content of Minimal Introns Are Selected in Human Populations

Background We previously have studied the insertion and deletion polymorphism by sequencing no more than one hundred introns in a mixed human population and found that the minimal introns tended to maintain length at an optimal size. Here we analyzed re-sequenced 179 individual genomes (from African, European, and Asian populations) from the data released by the 1000 Genome...

Functional Networking of Human Divergently Paired Genes (DPGs)

Divergently paired genes (DPGs), also known as bidirectional (head-to-head positioned) genes, are conserved across species and lineages, and thus deemed to be exceptional in genomic organization and functional regulation. Despite previous investigations on the features of their conservation and gene organization, the functional relationship among DPGs in a given species and...

The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology

Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we...

Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes

Background Mammalian genome sequence data are being acquired in large quantities and at enormous speeds. We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what their particular functions and evolutionary dynamics are, through comparative genomics. Results We chose human and eleven other high-coverage mammalian genome...

Biomechanism of adhesion in gecko setae

The study of the adhesion of millions of setae on the toes of geckos has been advanced in recent years with the emergence of new technology and measurement methods. The theory of the mechanism of adhesion by van der Waals forces is now accepted and broadly understood. However, this paper presents limitations of this theory and gives a new hypothesis of the biomechanism of gecko...

Distinct Genomic Aberrations between Low-Grade and High-Grade Gliomas of Chinese Patients

Background Glioma is a type of tumor that develops in the central nerve system, mainly the brain. Alterations of genomic sequence and sequence segments (such as copy number variations or CNV and copy neutral loss of heterozygosities or cnLOH) are thought to be a major determinant of the tumor grade. Methods We mapped genomic variations between low-grade and high-grade gliomas...

A Novel Role for Minimal Introns: Routing mRNAs to the Cytosol

Background Introns and their splicing are tightly coupled with the subsequent mRNA maturation steps, especially nucleocytoplasmic export. A remarkable fraction of vertebrate introns have a minimal size of about 100 bp, while majority of introns expand to several kilobases even megabases in length. Principal Findings We carried out analyses on the evolution and function of minimal...

Therapeutic potential of human umbilical cord mesenchymal stem cells in the treatment of rheumatoid arthritis

Introduction Rheumatoid arthritis (RA) is a T-cell-mediated systemic autoimmune disease, characterized by synovium inflammation and articular destruction. Bone marrow mesenchymal stem cells (MSCs) could be effective in the treatment of several autoimmune diseases. However, there has been thus far no report on umbilical cord (UC)-MSCs in the treatment of RA. Here, potential...