The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression.

abstract：BACKGROUND:Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the...

journal_title：BMC genomics

authors： Su Y,Xu L,Wang Z,Peng Q,Yang Y,Chen Y,Que Y

更新日期：2016-10-12 00:00:00

abstract：BACKGROUND:Cardiorespiratory fitness (VO2max) is an excellent predictor of chronic disease morbidity and mortality risk. Guidelines recommend individuals undertake exercise training to improve VO2max for chronic disease reduction. However, there are large inter-individual differences between exercise training responses...

journal_title：BMC genomics

authors： Williams CJ,Williams MG,Eynon N,Ashton KJ,Little JP,Wisloff U,Coombes JS

更新日期：2017-11-14 00:00:00

abstract：BACKGROUND:Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for pro...

journal_title：BMC genomics

authors： Baksa I,Nagy T,Barta E,Havelda Z,Várallyay É,Silhavy D,Burgyán J,Szittya G

更新日期：2015-12-01 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:Higher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Ma...

journal_title：BMC genomics

authors： Koyama T,Asakawa S,Katagiri T,Shimizu A,Fagutao FF,Mavichak R,Santos MD,Fuji K,Sakamoto T,Kitakado T,Kondo H,Shimizu N,Aoki T,Hirono I

更新日期：2010-02-26 00:00:00

abstract：BACKGROUND:Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androstenone is a steroid produced in the testis in parallel with biosynthesis of other sex steroids like tes...

journal_title：BMC genomics

authors： Grindflek E,Lien S,Hamland H,Hansen MH,Kent M,van Son M,Meuwissen TH

更新日期：2011-07-13 00:00:00

abstract：BACKGROUND:The MHC and KIR loci are clinically relevant regions of the genome. Typing the sequence of these loci has a wide range of applications including organ transplantation, drug discovery, pharmacogenomics and furthering fundamental research in immune genetics. Rapid advances in biochemical and next-generation se...

journal_title：BMC genomics

authors： Selvaraj S,Schmitt AD,Dixon JR,Ren B

更新日期：2015-11-05 00:00:00

abstract：BACKGROUND:Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and...

journal_title：BMC genomics

authors： Xu F,Bao J,He Q,Park YJ

更新日期：2016-08-20 00:00:00

abstract：BACKGROUND:While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus performed full genome analyses on four Listeria monocytogenes, including human and food isolates from both a 1988 case of sporadic...

journal_title：BMC genomics

authors： Orsi RH,Borowsky ML,Lauer P,Young SK,Nusbaum C,Galagan JE,Birren BW,Ivy RA,Sun Q,Graves LM,Swaminathan B,Wiedmann M

更新日期：2008-11-13 00:00:00

abstract：BACKGROUND:Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induce...

journal_title：BMC genomics

authors： Cohen D,Bogeat-Triboulot MB,Tisserant E,Balzergue S,Martin-Magniette ML,Lelandais G,Ningre N,Renou JP,Tamby JP,Le Thiec D,Hummel I

更新日期：2010-11-12 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:Mitochondrial genomes comprise a small but critical component of the total DNA in eukaryotic organisms. They encode several key proteins for the cell's major energy producing apparatus, the mitochondrial respiratory chain. Additionally, their nucleotide and amino acid sequences are of great utility as marker...

journal_title：BMC genomics

authors： Lloyd RE,Foster PG,Guille M,Littlewood DT

更新日期：2012-09-19 00:00:00

abstract：BACKGROUND:Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant s...

journal_title：BMC genomics

authors： Li L,Briskine R,Schaefer R,Schnable PS,Myers CL,Flagel LE,Springer NM,Muehlbauer GJ

更新日期：2016-11-04 00:00:00

abstract：BACKGROUND:The establishment of C4 photosynthesis in maize is associated with differential accumulation of gene transcripts and proteins between bundle sheath and mesophyll photosynthetic cell types. We have physically separated photosynthetic cell types in the leaf blade to characterize differences in gene expression ...

journal_title：BMC genomics

authors： Sawers RJ,Liu P,Anufrikova K,Hwang JT,Brutnell TP

更新日期：2007-01-09 00:00:00

abstract：BACKGROUND:Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data from various conditions generated by 3' end sequencing provides a valuable data source for the study o...

journal_title：BMC genomics

authors： Ye W,Long Y,Ji G,Su Y,Ye P,Fu H,Wu X

更新日期：2019-01-22 00:00:00

abstract：BACKGROUND:Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. This aflatoxigenic species is capable of secreting both B and G aflatoxins, similar to A. parasit...

journal_title：BMC genomics

authors： Moore GG,Mack BM,Beltz SB,Puel O

更新日期：2018-03-09 00:00:00

abstract：BACKGROUND:Host-specific environmental factors induce changes in Bacillus anthracis gene transcription during infection. A global transcription regulator, CodY, plays a pivotal role in regulating central metabolism, biosynthesis, and virulence in B. anthracis. In this study, we utilized RNA-sequencing to assess changes...

journal_title：BMC genomics

authors： Kim SK,Jung KH,Chai YG

更新日期：2016-08-17 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:Major changes in gene expression occur in the fetal brain to modulate the function of this organ postnatally. Thus, factors can alter the genomics of the fetal brain, predisposing to neurological disorders later in life. We hypothesized that the physiological dynamics of the immune system transcriptome of th...

journal_title：BMC genomics

authors： Rabaglino MB,Keller-Wood M,Wood CE

更新日期：2014-11-19 00:00:00

abstract：BACKGROUND:The eyes and skin are obvious retinoid target organs. Vitamin A deficiency causes night blindness and retinoids are widely used to treat acne and psoriasis. However, more than 90% of total body retinol is stored in liver stellate cells. In addition, hepatocytes produce the largest amount of retinol binding p...

journal_title：BMC genomics

authors： He Y,Gong L,Fang Y,Zhan Q,Liu HX,Lu Y,Guo GL,Lehman-McKeeman L,Fang J,Wan YJ

更新日期：2013-08-28 00:00:00

abstract：BACKGROUND:Although primarily known as the site of ribosome subunit production, the nucleolus is involved in numerous and diverse cellular processes. Recent large-scale proteomics projects have identified thousands of human proteins that associate with the nucleolus. However, in most cases, we know neither the fraction...

journal_title：BMC genomics

authors： Scott MS,Boisvert FM,Lamond AI,Barton GJ

更新日期：2011-01-27 00:00:00

abstract：:An amendment to this paper has been published and can be accessed via the original article. ...

journal_title：BMC genomics

authors： Onizuka S,Yamazaki Y,Park SJ,Sugimoto T,Sone Y,Sjöqvist S,Usui M,Takeda A,Nakai K,Nakashima K,Iwata T

更新日期：2020-08-11 00:00:00

abstract：BACKGROUND:After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about...

journal_title：BMC genomics

authors： Zhang JZ,Ai XY,Sun LM,Zhang DL,Guo WW,Deng XX,Hu CG

更新日期：2011-01-26 00:00:00

abstract：BACKGROUND:In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical,...

journal_title：BMC genomics

authors： Ciric M,Moon CD,Leahy SC,Creevey CJ,Altermann E,Attwood GT,Rakonjac J,Gagic D

更新日期：2014-05-12 00:00:00

abstract：BACKGROUND:Lychas mucronatus is one scorpion species widely distributed in Southeast Asia and southern China. Anything is hardly known about its venom components, despite the fact that it can often cause human accidents. In this work, we performed a venomous gland transcriptome analysis by constructing and screening th...

journal_title：BMC genomics

authors： Ruiming Z,Yibao M,Yawen H,Zhiyong D,Yingliang W,Zhijian C,Wenxin L

更新日期：2010-07-28 00:00:00

abstract：BACKGROUND:Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transc...

journal_title：BMC genomics

authors： Zhu BH,Xiao J,Xue W,Xu GC,Sun MY,Li JT

更新日期：2018-03-02 00:00:00

abstract：BACKGROUND:RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Illumina 2000 RNA-seq for the analysis of patient samples - normal lung epithelium tissue and squamous...

journal_title：BMC genomics

authors： Nazarov PV,Muller A,Kaoma T,Nicot N,Maximo C,Birembaut P,Tran NL,Dittmar G,Vallar L

更新日期：2017-06-06 00:00:00

abstract：BACKGROUND:NGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads. The other k-mers are called weak k-mers. A solid k-mer does not likely contain errors, while a weak k-...

journal_title：BMC genomics

authors： Zhao L,Xie J,Bai L,Chen W,Wang M,Zhang Z,Wang Y,Zhao Z,Li J

更新日期：2018-12-31 00:00:00

abstract：BACKGROUND:Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-...

journal_title：BMC genomics

authors： Catalán A,Hutter S,Parsch J

更新日期：2012-11-21 00:00:00

abstract：BACKGROUND:Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-chara...

journal_title：BMC genomics

authors： Olender T,Keydar I,Pinto JM,Tatarskyy P,Alkelai A,Chien MS,Fishilevich S,Restrepo D,Matsunami H,Gilad Y,Lancet D

更新日期：2016-08-11 00:00:00