Showing papers in "Genomics in 2011"

TL;DR: The ability to determine genome-wide methylation patterns will rapidly advance methylation research.

TL;DR: Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines and can reliably identify barcodes and assign the reads to the original samples.

TL;DR: The development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that is used to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH).

TL;DR: An in-depth review of the gene set analysis procedures, along with parameter choices and the particular methodology challenges at each stage, and classify the analysis methods into larger categories and discuss their strengths and limitations.

TL;DR: Medicinal Salvia miltiorrhiza is a Chinese herb commonly used for treating cardiovascular diseases and neuroasthenic insomnia, and its transcriptome is obtained by performing Solexa deep sequencing over the entire growing cycle to benefit research into its molecular genetics and functional genomics.

TL;DR: Four custom Axiom genotyping arrays were designed for a genome-wide association study of 100,000 participants from the Kaiser Permanente Research Program on Genes, Environment and Health and are valuable additions for large-scale GWA studies.

TL;DR: The current literature regarding features conserved among miRNA promoters useful for their detection and the current novel methodologies available to enable researchers to advance the understanding of the transcriptional regulation of miRNA genes are reviewed.

TL;DR: Efficient tools for PCR primer and probe design are developed, which also predict oligonucleotide properties based on experimental studies of PCR efficiency, and the in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs.

TL;DR: A comprehensive survey of the TIFY family allowed us to discover a new group within the JAZ subfamily and to identify several novel conserved motifs via phylogenetic analysis.

TL;DR: The transcriptome analysis might provide some useful insights into salt-mediated signal transduction pathways in cotton and offer a number of candidate genes as potential markers of tolerance to salt stress.

TL;DR: The top three phthalate toxicity categories were found to be cardiotoxicity, hepatotoxicity and nephrotoxicity, and the top 20 diseases included cardiovascular, liver, urologic, endocrine and genital diseases.

TL;DR: A comparative analysis between the identified sheepCNVRs and those reported in cattle and goat genomes indicated that overlaps between sheep and both other species CNVRs are highly significant, suggesting that several chromosome regions might contain recurrent interspecies CNVs.

TL;DR: This work introduces the genome theory which calls for the departure of gene-centric genomic research and acknowledges the importance of new genome-based biological concepts and to establish new technology platforms to decode the genome beyond sequencing.

TL;DR: The identification and characterization of miRNAs in S. mansoni will facilitate novel approaches towards prevention and treatment of Schistosomiasis and suggests that the sma-mir-71 may be involved in female sexual maturation.

TL;DR: A robust RNA-seq strategy for multiplex analysis of RNA samples based on deep sequencing that preserves strand information, permits rapid identification of potentially new polyadenylation sites, and profiles gene expression in a highly cost effective manner is described.

TL;DR: The findings address several technical issues associated with the Illumina 27k microarray that, once considered, will enhance the analysis and interpretation of data generated from this platform.

TL;DR: A Support Vector Machine (SVM) classifier trained on a set of 3163 cancer-causing variants and an equal number of neutral polymorphisms is presented, which results in higher prediction accuracy and correlation coefficient in identifying cancer- Causing variants.

TL;DR: Insight is provided into miRNA-controlled processes in Sorghum and the foundation for manipulating miRNAs or their targets for improving biomass production and stress tolerance in sorghum is laid.

TL;DR: DNA methylation in two colon cancer cell lines was measured using MSDS and many differentially methylated regions (DMRs) were identified in CpG island shore regions, gene body regions and intergenic regions.

TL;DR: An optimized feature subset including 13 features using a hybrid of genetic algorithm and support vector machine (GA-SVM) is generated and miR-SF is effective for identifying pre-miRNAs.

TL;DR: It is concluded that CF and non-CF nasal and bronchial epithelium are transcriptionally distinct and CF nasal epithelio is not a good surrogate for the lung respiratory epithelia.

TL;DR: A transcriptome sequence of a Planaria subspecies Dugesia japonica derived by high-throughput sequencing is reported, providing a fairly comprehensive molecular biology background to the research on planarian development, particularly with regard to its regeneration progress.

TL;DR: A rigorous performance assessment of 32 computational methods/variants for de-novo reverse-engineering of genome-scale regulatory networks by benchmarking these methods in 15 high-quality datasets and gold-standards of experimentally verified mechanistic knowledge shows that some methods need to be substantially improved upon, while others should be used routinely.

TL;DR: This study discovered that co-expressed microRNA target genes are often co-regulated, and different groups of target genes of the same microRNA are often regulated differently, and observed that transcription factors regulating a microRNA gene often regulate its target genes.

TL;DR: An analysis of global microsatellite variation on the two kindreds sequenced at high depth in the 1000 Genomes Project pilot studies using a more stringent approach in computing robust allelotypes resulting in 94.4% of the 1095 informative repeats conforming to traditional inheritance.

TL;DR: It is determined that acquisition of DNA methylation at the paternal allele of the Gtl2-DMR is initiated after the blastocyst stage and completed by embryonic day 6.5, and that Gtl1 (approved symbol: Meg3) is monoallelically expressed from the maternal allele as early as the Blastocyst.

TL;DR: The PDI family is larger in mammals than in land plants (around 10 members) and Saccharomyces cerevisiae (5 members), however, PDIs from photosynthetic organisms display an important structural and functional diversity considering their association to specific protein domains.

TL;DR: Genomic sequence analysis indicates that cassette I of S LC4A4 is conserved in all NCBT genes except for SLC4A5, which presumably lost cassette I during its evolution.

TL;DR: In contrast to previous studies, interstitial telomere-like repeats were identified in the pericentromeres of Brassica chromosomes, and these repeats may be associated with genomic stability and provide insight into genome evolution during polyploidization in Brassica and divergence within the Brassicaceae.

TL;DR: The good performance of the hybrid promoters and the experimental data indicate that the hybrid multi-feature approach for predicting the two types of promoters has the ability to locate the promoter region of the plant genome.