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11 papers found.
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Integrative analysis of somatic mutations and transcriptomic data to functionally stratify breast cancer patients

Background Somatic mutations can be used as potential biomarkers for subtyping and predicting outcomes for cancer patients. However, cancer patients often carry many somatic mutations, which do not always concentrate on specific genomic loci, suggesting that the mutations may affect common pathways or gene interaction networks instead of common genes. The challenge is thus to ...

Analysis of gene expression in the midgut of Bombyx mori during the larval molting stage

Background Insects can be models for understanding human intestinal infection and pathology. Molting, a special period during which the old insect cuticle is shed and a new one is produced, is crucial for insect development. Holometabolous insects may experience several larva-to-larva moltings to become larger, a pupal molt and adult eclosion to become adults. During the larval ...

A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.)

Background Pumpkin (Cucurbita maxima Duch.) is an economically important crop belonging to the Cucurbitaceae family. However, very few genomic and genetic resources are available for this species. As part of our ongoing efforts to sequence the pumpkin genome, high-density genetic map is essential for anchoring and orienting the assembled scaffolds. In addition, a saturated genetic ...

Mining the tissue-tissue gene co-expression network for tumor microenvironment study and biomarker prediction

Background Recent discovery in tumor development indicates that the tumor microenvironment (mostly stroma cells) plays an important role in cancer development. To understand how the tumor microenvironment (TME) interacts with the tumor, we explore the correlation of the gene expressions between tumor and stroma. The tumor and stroma gene expression data are modeled as a weighted ...

Redistribution of H3K4me2 on neural tissue specific genes during mouse brain development

Background Histone modification plays an important role in cell differentiation and tissue development. A recent study has shown that the dimethylation of lysine 4 residue on histone 3 (H3K4me2) marks the gene body area of tissue specific genes in the human CD4+ T cells and neural cells. However, little is known of the H3k4me2 distribution dynamics through the cell differentiation ...

Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study

Background Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gallstone patients as well as the gut of 38 normal individuals, ...

De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode

BackgroundAegilops variabilis No.1 is highly resistant to cereal cyst nematode (CCN). However, a lack of genomic information has restricted studies on CCN resistance genes in Ae. variabilis and has limited genetic applications in wheat breeding.ResultsUsing RNA-Seq technology, we generated a root transcriptome at a sequencing depth of 4.69 gigabases of Ae. variabilis No. 1 from a ...

Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins

Background Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. The 454 pyrosequencing technology provides a promising opportunity for finding novel genes that participate in plant metabolism. Consequently, this technology may ...

The Odorant Binding Protein Gene Family from the Genome of Silkworm, Bombyx mori

Background Chemosensory systems play key roles in the survival and reproductive success of insects. Insect chemoreception is mediated by two large and diverse gene superfamilies, chemoreceptors and odorant binding proteins (OBPs). OBPs are believed to transport hydrophobic odorants from the environment to the olfactory receptors. Results We identified a family of OBP-like genes in ...

Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans

Background Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses ...

Structural and functional annotation of the porcine immunome

Harry D Dawson Jane E Loveland Graldine Pascal James GR Gilbert Hirohide Uenishi Katherine M Mann Yongming Sang Jie Zhang Denise Carvalho-Silva Toby Hunt Matthew Hardy Zhiliang Hu 0 Shu-Hong Zhao