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112 papers found.
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Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Background With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected...

antiCODE: a natural sense-antisense transcripts database

at its websites http://bioinfo.ibp.ac.cn/ ANTICODE or http://www.anticode.org Authors' contributions Yifei Yin and Yi Zhao carried out the design and the collection of data. Jie Wang carried for

Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics

Background Long-established protein-coding genes may lose their coding potential during evolution (“unitary gene loss”). Members of the Poaceae family are a major food source and represent an ideal model clade for plant evolution research. However, the global pattern of unitary gene loss in Poaceae genomes as well as the evolutionary fate of lost genes are still less-investigated...

Evaluation of high-risk clinicopathological indicators in gastrointestinal stromal tumors for prognosis and imatinib treatment outcome

Background Although the clinical benefit of imatinib adjuvant therapy for high-risk patients with gastrointestinal stromal tumor (GIST) has been proven, the recurrence rate still remains high. This study aimed to sub-divide high-risk GIST patients with some “very high-risk” factors for more precise prognostic indicator, and possible association with efficiency of imatinib...

Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis)

Background Major secondary metabolites, including flavonoids, caffeine, and theanine, are important components of tea products and are closely related to the taste, flavor, and health benefits of tea. Secondary metabolite biosynthesis in Camellia sinensis is differentially regulated in different tissues during growth and development. Until now, little was known about the...

Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes

Xiang-Yang Lou 0 Jian-Yi Zhao 1 0 Department of Biostatistics and Bioinformatics, Tulane University , 1440 Canal St., Suite 2001, New Orleans, LA 70112-2632 , USA 1 State Key Laboratory Breeding Base

Transcriptomic analyses reveal the adaptive features and biological differences of guts from two invasive whitefly species

Background The gut of phloem feeding insects is critical for nutrition uptake and xenobiotics degradation. However, partly due to its tiny size, genomic information for the gut of phloem feeding insects is limited. Results In this study, the gut transcriptomes of two species of invasive whiteflies in the Bemisia tabaci complex, Middle East Asia Minor 1 (MEAM1) and Mediterranean...

The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex

Background The whiteflies under the name Bemisia tabaci (Gennadius) (Aleyrodidae: Hemiptera) are species complex of at least 31 cryptic species some of which are globally invasive agricultural pests. Previously, the mitochondrial genome (mitogenome) of the indigenous New World B. tabaci species was sequenced and major differences of gene order from the postulated whitefly...

Global transcriptome profiles of Camellia sinensis during cold acclimation

Background Tea is the most popular non-alcoholic health beverage in the world. The tea plant (Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in tea plants. To elucidate the molecular mechanisms of cold...

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

Background Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the...

dbDEMC: a database of differentially expressed miRNAs in human cancers

(InCoB2010): Computational Biology. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/11?issue=S4. Authors contributions Haitao Zhao, Yi Zhao and Yang Zhong

Exploring hierarchical and overlapping modular structure in the yeast protein interaction network

Changning Liu 0 Jing Li 0 Yi Zhao 0 0 Bioinformatics Group, Key Laboratory of Intelligent Information Processing, Center for Advanced Computing Research, Institute of Computing Technology, Chinese

Alu-directed transcriptional regulation of some novel miRNAs

Background Despite many studies on the biogenesis, molecular structure and biological functions of microRNAs, little is known about the transcriptional regulatory mechanisms controlling the spatiotemporal expression pattern of human miRNA gene loci. Several lines of experimental results have indicated that both polymerase II (Pol-II) and polymerase III (Pol-III) may be involved...

MicroRNA-encoding long non-coding RNAs

Background Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs). Whereas the functional properties of these ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts. Results A few ml-ncRNA have been shown to have genomic loci that...

Date of origin of the SARS coronavirus strains

Background A new respiratory infectious epidemic, severe acute respiratory syndrome (SARS), broke out and spread throughout the world. By now the putative pathogen of SARS has been identified as a new coronavirus, a single positive-strand RNA virus. RNA viruses commonly have a high rate of genetic mutation. It is therefore important to know the mutation rate of the SARS...

Transient filament occlusion of the middle cerebral artery in rats: does the reperfusion method matter 24 hours after perfusion?

Background There are two widely used transient middle cerebral artery occlusion (MCAO) methods, which differ in the use of unilateral or bilateral carotid artery reperfusion (UNICAR and BICAR). Of the two methods, UNICAR is easier to perform. This study was designed to comprehensively compare the two reperfusion methods to determine if there are any differences in outcomes...

The association between medical students’ lifestyles and their attitudes towards preventive counseling in different countries

1 Yi Zhao 7 Shen Yuan 4 Ruijuan Zhang 4 Matthew Sebranek 0 Lennert Veerman 6 Mu Li 5 Enying Gong 9 Shu Chen 9 Wenjie Ma 9 Liping Huang 5 KaWing Cho 9 Stephen Leeder 8 Lijing Yan 0 0 Duke Global Health

Modeling miRNA-mRNA interactions: fitting chemical kinetics equations to microarray data

Background The miRNAs are small non-coding RNAs of roughly 22 nucleotides in length, which can bind with and inhibit protein coding mRNAs through complementary base pairing. By degrading mRNAs and repressing proteins, miRNAs regulate the cell signaling and cell functions. This paper focuses on innovative mathematical techniques to model gene interactions by algorithmic analysis...

Clustered microRNAs' coordination in regulating protein-protein interaction network

Background MicroRNAs (miRNAs), a growing class of small RNAs with crucial regulatory roles at the post-transcriptional level, are usually found to be clustered on chromosomes. However, with the exception of a few individual cases, so far little is known about the functional consequence of this conserved clustering of miRNA loci. In animal genomes such clusters often contain non...

10-Year experience regarding the reliability and morbidity of radio guided lymph node biopsy in penile cancer patients and the associated radiation exposure of medical staff in this procedure

Background The guidelines of the European Association of Urologists (EAU), of the German Society of Nuclear Medicine (DGN), and the European Society for Medical Oncology (ESMO) recommend sentinel lymph node biopsy (SLNB) for lymph node staging in penile cancer with non-palpable inguinal lymph nodes as one diagnostic method. Despite this, the method is neither widely nor regularly...