High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing.

abstract：BACKGROUND:Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcin...

journal_title：BMC genomics

authors： Brogaard L,Klitgaard K,Heegaard PM,Hansen MS,Jensen TK,Skovgaard K

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:The use of RNAseq to resolve the transcriptional organization of an organism was established in recent years and also showed the complexity and dynamics of bacterial transcriptomes. The aim of this study was to comprehensively investigate the transcriptome of the industrially relevant amino acid producer and...

journal_title：BMC genomics

authors： Pfeifer-Sancar K,Mentz A,Rückert C,Kalinowski J

更新日期：2013-12-17 00:00:00

abstract：BACKGROUND:Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but...

journal_title：BMC genomics

authors： Gavelis GS,White RA,Suttle CA,Keeling PJ,Leander BS

更新日期：2015-07-17 00:00:00

abstract：BACKGROUND:Candida albicans is an opportunistic pathogenic yeast, which could become pathogenic in various stressful environmental factors including the spaceflight environment. In this study, we aim to explore the phenotypic changes and possible mechanisms of C. albicans after exposure to spaceflight conditions. RESU...

journal_title：BMC genomics

authors： Wang J,Liu Y,Zhao G,Gao J,Liu J,Wu X,Xu C,Li Y

更新日期：2020-01-17 00:00:00

abstract：BACKGROUND:Although the study of gene regulation via the action of specific microRNAs (miRNAs) has experienced a boom in recent years, the analysis of genome-wide interaction networks among miRNAs and respective targeted mRNAs has lagged behind. MicroRNAs simultaneously target many transcripts and fine-tune the express...

journal_title：BMC genomics

authors： Nunez YO,Truitt JM,Gorini G,Ponomareva ON,Blednov YA,Harris RA,Mayfield RD

更新日期：2013-10-22 00:00:00

abstract：BACKGROUND:Hypoxia Inducible Factor (HIF) regulates a cascade of transcriptional events in response to decreased oxygenation, acting from the cellular to the physiological level. This response is evolutionarily conserved, allowing the use of zebrafish (Danio rerio) as a model for studying the hypoxic response. Activati...

journal_title：BMC genomics

authors： Greenald D,Jeyakani J,Pelster B,Sealy I,Mathavan S,van Eeden FJ

更新日期：2015-11-11 00:00:00

abstract：BACKGROUND:Increased focus surrounds identifying patients with advanced non-small cell lung cancer (NSCLC) who will benefit from treatment with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI). EGFR mutation, gene copy number, coexpression of ErbB proteins and ligands, and epithelial to mesenchy...

journal_title：BMC genomics

authors： Balko JM,Potti A,Saunders C,Stromberg A,Haura EB,Black EP

更新日期：2006-11-10 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) regulate the expression of target genes by mediating gene silencing in both plants and animals. The miRNA targets have been extensively investigated in Arabidopsis and rice using computational prediction, experimental validation by overexpression in transgenic plants, and by degradome or P...

journal_title：BMC genomics

authors： Shamimuzzaman M,Vodkin L

更新日期：2012-07-16 00:00:00

abstract：BACKGROUND:Various cancer cells, including those of colorectal cancer (CRC), release microvesicles (exosomes) into surrounding tissues and peripheral circulation. These microvesicles can mediate communication between cells and affect various tumor-related processes in their target cells. RESULTS:We present potential r...

journal_title：BMC genomics

authors： Hong BS,Cho JH,Kim H,Choi EJ,Rho S,Kim J,Kim JH,Choi DS,Kim YK,Hwang D,Gho YS

更新日期：2009-11-25 00:00:00

abstract：BACKGROUND:Xanthomonas citri pv. citri (Xcc) is a citrus canker causing Gram-negative bacteria. Currently, little is known about the biological and molecular responses of Xcc to low temperatures. RESULTS:Results depicted that low temperature significantly reduced growth and increased biofilm formation and unsaturated ...

journal_title：BMC genomics

authors： Liao JX,Li KH,Wang JP,Deng JR,Liu QG,Chang CQ

更新日期：2019-11-06 00:00:00

abstract：BACKGROUND:Oomycetes are a group of filamentous microorganisms that includes both animal and plant pathogens and causes major agricultural losses. Phytophthora species can infect most crops and plants from natural ecosystems. Despite their tremendous economic and ecologic importance, few effective methods exist for lim...

journal_title：BMC genomics

authors： Attard A,Evangelisti E,Kebdani-Minet N,Panabières F,Deleury E,Maggio C,Ponchet M,Gourgues M

更新日期：2014-06-29 00:00:00

abstract：BACKGROUND:Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. I...

journal_title：BMC genomics

authors： Ruan Y,Shen L,Zou Y,Qi Z,Yin J,Jiang J,Guo L,He L,Chen Z,Tang Z,Qin S

更新日期：2015-02-25 00:00:00

abstract：BACKGROUND:Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strateg...

journal_title：BMC genomics

authors： Anthon C,Tafer H,Havgaard JH,Thomsen B,Hedegaard J,Seemann SE,Pundhir S,Kehr S,Bartschat S,Nielsen M,Nielsen RO,Fredholm M,Stadler PF,Gorodkin J

更新日期：2014-06-10 00:00:00

abstract：BACKGROUND:Brucella abortus is an intracellular zoonotic pathogen which causes undulant fever, endocarditis, arthritis and osteomyelitis in human and abortion and infertility in cattle. This bacterium is able to invade and replicate in host macrophage instead of getting removed by this defense mechanism. Therefore, und...

journal_title：BMC genomics

authors： Cha SB,Lee WJ,Shin MK,Jung MH,Shin SW,Yoo AN,Kim JW,Yoo HS

更新日期：2013-06-27 00:00:00

abstract：BACKGROUND:RNA-seq has shown huge potential for phylogenomic inferences in non-model organisms. However, error, incompleteness, and redundant assembled transcripts for each gene in de novo assembly of short reads cause noise in analyses and a large amount of missing data in the aligned matrix. To address these problems...

journal_title：BMC genomics

authors： Yang Y,Smith SA

更新日期：2013-05-14 00:00:00

abstract：BACKGROUND:Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analysis, both haplotype alleles and blocks are tested. Haplotype alleles can be inferred with the same st...

journal_title：BMC genomics

authors： Chen H,Hao Z,Zhao Y,Yang R

更新日期：2020-02-11 00:00:00

abstract：BACKGROUND:Cryptocaryon irritans is an obligate parasitic ciliate protozoan that can infect various commercially important mariculture fish species and cause high lethality and economic loss. Current methods of controlling this parasite with chemicals or antibiotics are widely considered to be environmentally harmful. ...

journal_title：BMC genomics

authors： Chen R,Mao Y,Wang J,Liu M,Qiao Y,Zheng L,Su Y,Ke Q,Zheng W

更新日期：2018-03-12 00:00:00

abstract：BACKGROUND:Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of ...

journal_title：BMC genomics

authors： Van Zee JP,Schlueter JA,Schlueter S,Dixon P,Sierra CA,Hill CA

更新日期：2016-03-16 00:00:00

abstract：BACKGROUND:Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the div...

journal_title：BMC genomics

authors： Wang S,Yang C,Zhao X,Chen S,Qu GZ

更新日期：2018-12-20 00:00:00

abstract：BACKGROUND:Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study ...

journal_title：BMC genomics

authors： Li GH,Chen HC,Liu JL,Luo WL,Xie DS,Luo SB,Wu TQ,Akram W,Zhong YJ

更新日期：2019-05-07 00:00:00

abstract：BACKGROUND:Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs) play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern ...

journal_title：BMC genomics

authors： Haerty W,Artieri C,Khezri N,Singh RS,Gupta BP

更新日期：2008-08-27 00:00:00

abstract：BACKGROUND:The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AM...

journal_title：BMC genomics

authors： Gandemer V,Rio AG,de Tayrac M,Sibut V,Mottier S,Ly Sunnaram B,Henry C,Monnier A,Berthou C,Le Gall E,Le Treut A,Schmitt C,Le Gall JY,Mosser J,Galibert MD

更新日期：2007-10-23 00:00:00

abstract：BACKGROUND:Microarray gene expression (MAGE) signatures allow insights into the transcriptional processes of leukemias and may evolve as a molecular diagnostic test. Introduction of MAGE into clinical practice of leukemia diagnosis will require comprehensive assessment of variation due to the methodologies. Here we sys...

journal_title：BMC genomics

authors： Campo Dell'Orto M,Zangrando A,Trentin L,Li R,Liu WM,te Kronnie G,Basso G,Kohlmann A

更新日期：2007-06-22 00:00:00

abstract：BACKGROUND:Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections...

journal_title：BMC genomics

authors： Li H,Cui P,Fu X,Zhang L,Yan W,Zhai Y,Lei C,Wang H,Yang X

更新日期：2021-01-20 00:00:00

abstract：BACKGROUND:Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error. It has a negative impact on performance of downstream analysis. Technically, most existing approaches suffer from this prevalent problem. Imputation is one of the frequently used metho...

journal_title：BMC genomics

authors： Li H,Zhao C,Shao F,Li GZ,Wang X

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:The activity of the yeast activator protein 1 (Yap1p) increases under stress conditions, which leads to enhanced transcription of a number of genes encoding protective enzymes or other proteins. To obtain a global overview of changes in expression of Yap1p-targeted proteins, we compared a Yap1p-overexpressin...

journal_title：BMC genomics

authors： Jun H,Kieselbach T,Jönsson LJ

更新日期：2012-06-09 00:00:00

abstract：BACKGROUND:Microarray data analysts commonly filter out genes based on a number of ad hoc criteria prior to any high-level statistical analysis. Such ad hoc approaches could lead to conflicting conclusions with no clear guidance as to which method is most likely to be reproducible. Furthermore, the number of tests perf...

journal_title：BMC genomics

authors： Hu P,Beyene J,Greenwood CM

更新日期：2006-02-22 00:00:00

abstract：BACKGROUND:Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. RESULTS:Here,...

journal_title：BMC genomics

authors： Chow CN,Chiang-Hsieh YF,Chien CH,Zheng HQ,Lee TY,Wu NY,Tseng KC,Hou PF,Chang WC

更新日期：2018-05-09 00:00:00

abstract：BACKGROUND:Tea is one of the most popular non-alcoholic beverages worldwide. However, the tea plant, Camellia sinensis, is difficult to culture in vitro, to transform, and has a large genome, rendering little genomic information available. Recent advances in large-scale RNA sequencing (RNA-seq) provide a fast, cost-eff...

journal_title：BMC genomics

authors： Shi CY,Yang H,Wei CL,Yu O,Zhang ZZ,Jiang CJ,Sun J,Li YY,Chen Q,Xia T,Wan XC

更新日期：2011-02-28 00:00:00

abstract：BACKGROUND:The mitochondrial genomes of higher plants vary remarkably in size, structure and sequence content, as demonstrated by the accumulation and activity of repetitive DNA sequences. Incompatibility between mitochondrial genome and nuclear genome leads to non-functional male reproductive organs and results in cyt...

journal_title：BMC genomics

authors： Li S,Chen Z,Zhao N,Wang Y,Nie H,Hua J

更新日期：2018-10-26 00:00:00