Consistent levels of A-to-I RNA editing across individuals in coding sequences and non-conserved Alu repeats.

abstract：BACKGROUND:Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. A...

journal_title：BMC genomics

authors： Ding Y,Chen M,Liu Z,Ding D,Ye Y,Zhang M,Kelly R,Guo L,Su Z,Harris SC,Qian F,Ge W,Fang H,Xu X,Tong W

更新日期：2012-07-20 00:00:00

abstract：BACKGROUND:Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent. RES...

journal_title：BMC genomics

authors： Lavoie H,Sellam A,Askew C,Nantel A,Whiteway M

更新日期：2008-12-02 00:00:00

abstract：BACKGROUND:Osteoporosis is a common and debilitating bone disease that is characterised by a low bone mineral density (BMD), a highly heritable trait. Genome-wide association studies (GWAS) have proven to be very successful in identifying common genetic variants associated with BMD adjusted for age, gender and weight, ...

journal_title：BMC genomics

authors： Mullin BH,Walsh JP,Zheng HF,Brown SJ,Surdulescu GL,Curtis C,Breen G,Dudbridge F,Richards JB,Spector TD,Wilson SG

更新日期：2016-02-25 00:00:00

abstract：BACKGROUND:Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant specie...

journal_title：BMC genomics

authors： De Paola D,Cattonaro F,Pignone D,Sonnante G

更新日期：2012-01-24 00:00:00

abstract：BACKGROUND:Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily spec...

journal_title：BMC genomics

authors： Yusuf D,Marz M,Stadler PF,Hofacker IL

更新日期：2010-07-13 00:00:00

abstract：BACKGROUND:5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway, and is the target of the herbicide glyphosate. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous cop...

journal_title：BMC genomics

authors： Aramrak A,Kidwell KK,Steber CM,Burke IC

更新日期：2015-10-23 00:00:00

abstract：BACKGROUND:Intergenic splicing resulting in the combination of mRNAs sequences from distinct genes is a newly identified mechanism likely to contribute to protein diversity. Few cases have been described, most of them involving neighboring genes and thus suggesting a cotranscription event presumably due to transcriptio...

journal_title：BMC genomics

authors： Roux M,Levéziel H,Amarger V

更新日期：2006-04-04 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNAs affecting the expression of target genes via translational repression or mRNA degradation mechanisms. With the increasing availability of mRNA and miRNA expression data, it might be possible to assess functional targets using the fact that a miRNA might down-regul...

journal_title：BMC genomics

authors： Wang YP,Li KB

更新日期：2009-05-12 00:00:00

abstract：BACKGROUND:Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are varia...

journal_title：BMC genomics

authors： Novoradovskaya N,Whitfield ML,Basehore LS,Novoradovsky A,Pesich R,Usary J,Karaca M,Wong WK,Aprelikova O,Fero M,Perou CM,Botstein D,Braman J

更新日期：2004-03-09 00:00:00

abstract：BACKGROUND:The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or very low temperatures. Being able to accurately predict this based on a genomic sequence, would thu...

journal_title：BMC genomics

authors： Jensen DB,Vesth TC,Hallin PF,Pedersen AG,Ussery DW

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an infl...

journal_title：BMC genomics

authors： Klepikova AV,Logacheva MD,Dmitriev SE,Penin AA

更新日期：2015-06-18 00:00:00

abstract：BACKGROUND:Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue predi...

journal_title：BMC genomics

authors： Rane RV,Oakeshott JG,Nguyen T,Hoffmann AA,Lee SF

更新日期：2017-08-31 00:00:00

abstract：BACKGROUND:Based on sequence similarity, the superfamily of G protein-coupled receptors (GPRs) can be subdivided into several subfamilies, the members of which often share similar ligands. The sequence data provided by the human genome project allows us to identify new GPRs by in silico homology screening, and to predi...

journal_title：BMC genomics

authors： Wittenberger T,Hellebrand S,Munck A,Kreienkamp HJ,Schaller HC,Hampe W

更新日期：2002-07-05 00:00:00

abstract：BACKGROUND:While DNA and RNA methods are routine to disrupt the expression of specific genes, complete understanding of developmental processes requires also protein methods, because: oocytes and early embryos accumulate proteins and these are not directly affected by DNA and RNA methods. When proteins in the oocyte en...

journal_title：BMC genomics

authors： Israel S,Casser E,Drexler HCA,Fuellen G,Boiani M

更新日期：2019-10-21 00:00:00

abstract：BACKGROUND:Dimethylsulfoniopropionate (DMSP) is a small sulphur compound which is produced in prodigious amounts in the oceans and plays a pivotal role in the marine sulfur cycle. Until recently, DMSP was believed to be synthesized exclusively by photosynthetic organisms; however we now know that corals and specific ba...

journal_title：BMC genomics

authors： Aguilar C,Raina JB,Motti CA,Fôret S,Hayward DC,Lapeyre B,Bourne DG,Miller DJ

更新日期：2017-08-14 00:00:00

abstract：BACKGROUND:Wood formation affects the chemical and physical properties of wood, and thus affects its utility as a building material or a feedstock for biofuels, pulp and paper. To obtain genome-wide insights on the transcriptome changes and regulatory networks in wood formation, we used high-throughput RNA sequencing t...

journal_title：BMC genomics

authors： Chen J,Chen B,Zhang D

更新日期：2015-03-10 00:00:00

abstract：BACKGROUND:Accurate de novo genome assembly has become reality with the advancements in sequencing technology. With the ever-increasing number of de novo genome assembly tools, assessing the quality of assemblies has become of great importance in genome research. Although many quality metrics have been proposed and sof...

journal_title：BMC genomics

authors： Yavas G,Hong H,Xiao W

更新日期：2019-09-11 00:00:00

abstract：BACKGROUND:The Lundehund is a highly specialized breed characterized by a unique flexibility of the joints and polydactyly in all four limbs. The extremely small population size and high inbreeding has promoted a high frequency of diseased dogs affected by the Lundehund syndrome (LS), a severe gastro-enteropathic disea...

journal_title：BMC genomics

authors： Metzger J,Pfahler S,Distl O

更新日期：2016-08-02 00:00:00

abstract：BACKGROUND:Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of ...

journal_title：BMC genomics

authors： Domingues DS,Cruz GM,Metcalfe CJ,Nogueira FT,Vicentini R,Alves Cde S,Van Sluys MA

更新日期：2012-04-16 00:00:00

abstract：BACKGROUND:Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report ...

journal_title：BMC genomics

authors： Merrill BD,Grose JH,Breakwell DP,Burnett SH

更新日期：2014-08-30 00:00:00

abstract：BACKGROUND:High throughput experiments resulted in many genomic datasets and hundreds of candidate disease genes. To discover the real disease genes from a set of candidate genes, computational methods have been proposed and worked on various types of genomic data sources. As a single source of genomic data is prone of...

journal_title：BMC genomics

authors： Li Y,Li J

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing factor binding sites. RESULTS:Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment)...

journal_title：BMC genomics

authors： Agostini F,Cirillo D,Ponti RD,Tartaglia GG

更新日期：2014-10-23 00:00:00

abstract：BACKGROUND:The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS:In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characteriz...

journal_title：BMC genomics

authors： Wang X,Zhong J,Gao Y,Ju Z,Huang J

更新日期：2014-07-28 00:00:00

abstract：BACKGROUND:As economically relevant traits, feeding behavior and food preference domestication determine production cost and profitability. Although there are intensive research efforts on feeding behavior and food intake, little is known about food preference. Mandarin fish accept only live prey fish and refuse dead p...

journal_title：BMC genomics

authors： He S,Liang XF,Sun J,Li L,Yu Y,Huang W,Qu CM,Cao L,Bai XL,Tao YX

更新日期：2013-09-05 00:00:00

abstract：BACKGROUND:The histone variant H2A.Z, which has been reported to have both activating and repressive effects on gene expression, is known to occupy nucleosomes at the 5' ends of protein-coding genes. RESULTS:We now find that H2A.Z is also significantly enriched in gene coding regions and at the 3' ends of genes in bud...

journal_title：BMC genomics

authors： Gu M,Naiyachit Y,Wood TJ,Millar CB

更新日期：2015-02-19 00:00:00

abstract：BACKGROUND:Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a n...

journal_title：BMC genomics

authors： Dang X,Xie Z,Liu W,Sun Y,Liu X,Zhu Y,Staehelin C

更新日期：2019-08-12 00:00:00

abstract：BACKGROUND:High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection. This was done using a rainbow trout (Oncorhynchus mykiss) model following infection with Aeromonas salmonicida, the causative agent of furunculosis. The vertebrate liver has multifaceted f...

journal_title：BMC genomics

authors： Causey DR,Pohl MAN,Stead DA,Martin SAM,Secombes CJ,Macqueen DJ

更新日期：2018-10-01 00:00:00

abstract：BACKGROUND:The use of dispersants can be an effective way to deal with acute oil spills to limit environmental damage, however very little is known about whether chemically dispersed oil have the same toxic effect on marine organisms as mechanically dispersed oil. We exposed Atlantic cod larvae to chemically and mechan...

journal_title：BMC genomics

authors： Olsvik PA,Lie KK,Nordtug T,Hansen BH

更新日期：2012-12-14 00:00:00

abstract：BACKGROUND:Genome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic variances, leaving a substantial portion of genetic heritability unexplained. As a result, searches for "m...

journal_title：BMC genomics

authors： Chen Q,Sun F

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:The recent advance of high-throughput sequencing makes it feasible to study entire transcriptomes through the application of de novo sequence assembly algorithms. While a popular strategy is to first construct an intermediate de Bruijn graph structure to represent the transcriptome, an additional step is nee...

journal_title：BMC genomics

authors： Sze SH,Tarone AM

更新日期：2014-01-01 00:00:00