Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development.

abstract：BACKGROUND:Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age gro...

journal_title：BMC genomics

authors： Cowley LA,Beckett SJ,Chase-Topping M,Perry N,Dallman TJ,Gally DL,Jenkins C

更新日期：2015-04-08 00:00:00

abstract：BACKGROUND:Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This transcriptome analysis of pectoralis muscle tissue aimed to identify functional genes and biological...

journal_title：BMC genomics

authors： Liu L,Liu X,Cui H,Liu R,Zhao G,Wen J

更新日期：2019-11-15 00:00:00

abstract：BACKGROUND:Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while such sites in the host DNA are protected by methylation. Prokaryotic viruses have developed a number ...

journal_title：BMC genomics

authors： Rusinov IS,Ershova AS,Karyagina AS,Spirin SA,Alexeevski AV

更新日期：2018-12-07 00:00:00

abstract：BACKGROUND:Fish under intensive culture conditions are exposed to a variety of acute and chronic stressors, including high rearing densities, sub-optimal water quality, and severe thermal fluctuations. Such stressors are inherent in aquaculture production and can induce physiological responses with adverse effects on t...

journal_title：BMC genomics

authors： Sánchez CC,Weber GM,Gao G,Cleveland BM,Yao J,Rexroad CE 3rd

更新日期：2011-12-21 00:00:00

abstract：BACKGROUND:Cotton (Gossypium spp.) is the most important natural fiber crop worldwide, and cottonseed oil is its most important byproduct. Phospholipid: diacylglycerol acyltransferase (PDAT) is important in TAG biosynthesis, as it catalyzes the transfer of a fatty acyl moiety from the sn-2 position of a phospholipid to...

journal_title：BMC genomics

authors： Zang X,Geng X,Ma L,Wang N,Pei W,Wu M,Zhang J,Yu J

更新日期：2019-05-22 00:00:00

abstract：MOTIVATION:With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree estimation is difficult in the presence of gene tree discordance, which is often due to incomplete l...

journal_title：BMC genomics

authors： Bayzid MS,Hunt T,Warnow T

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and perfo...

journal_title：BMC genomics

authors： Northcutt AJ,Lett KM,Garcia VB,Diester CM,Lane BJ,Marder E,Schulz DJ

更新日期：2016-11-04 00:00:00

abstract：BACKGROUND:Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA...

journal_title：BMC genomics

authors： Seifert F,Thiemann A,Schrag TA,Rybka D,Melchinger AE,Frisch M,Scholten S

更新日期：2018-05-21 00:00:00

abstract：BACKGROUND:Expression profiling has been proposed as a means for screening non-model organisms in their natural environments to identify genes potentially important in adaptive diversification. Tag profiling using high throughput sequencing is a relatively low cost means of expression profiling with deep coverage. Howe...

journal_title：BMC genomics

authors： Voelckel C,Gruenheit N,Biggs P,Deusch O,Lockhart P

更新日期：2012-07-19 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:Protein phosphorylation by kinases plays crucial roles in various biological processes including signal transduction and tumorigenesis, thus a better understanding of protein phosphorylation events in cells is fundamental for studying protein functions and designing drugs to treat diseases caused by the malf...

journal_title：BMC genomics

authors： Ma H,Li G,Su Z

更新日期：2020-08-04 00:00:00

abstract：BACKGROUND:Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5-245 gigabases) and produce structurally unique and biologically active polyketide secondary metabolites. Although polyketide biosynthesis is well studied in terrestrial and freshwater organisms, only rec...

journal_title：BMC genomics

authors： Beedessee G,Hisata K,Roy MC,Satoh N,Shoguchi E

更新日期：2015-11-14 00:00:00

abstract：BACKGROUND:Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-B...

journal_title：BMC genomics

authors： Ebert G,Steininger A,Weißmann R,Boldt V,Lind-Thomsen A,Grune J,Badelt S,Heßler M,Peiser M,Hitzler M,Jensen LR,Müller I,Hu H,Arndt PF,Kuss AW,Tebel K,Ullmann R

更新日期：2014-06-29 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:Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromos...

journal_title：BMC genomics

authors： Norman JD,Robinson M,Glebe B,Ferguson MM,Danzmann RG

更新日期：2012-08-24 00:00:00

abstract：BACKGROUND:Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) w...

journal_title：BMC genomics

authors： Bera BC,Virmani N,Kumar N,Anand T,Pavulraj S,Rash A,Elton D,Rash N,Bhatia S,Sood R,Singh RK,Tripathi BN

更新日期：2017-08-23 00:00:00

abstract：BACKGROUND:Filarial nematodes cause debilitating human diseases. While treatable, recent evidence suggests drug resistance is developing, necessitating the development of novel targets and new treatment options. Although transcriptomic and proteomic studies around the nematode life cycle have greatly enhanced our knowl...

journal_title：BMC genomics

authors： Luck AN,Anderson KG,McClung CM,VerBerkmoes NC,Foster JM,Michalski ML,Slatko BE

更新日期：2015-11-11 00:00:00

abstract：BACKGROUND:Aquaculture is the quickest growing sector in agriculture. However, QTL for important traits have been only identified in a few aquaculture species. We conducted QTL mapping for growth traits in an Asian seabass F(2) family with 359 individuals using 123 microsatellites and 22 SNPs, and performed association...

journal_title：BMC genomics

authors： Xia JH,Lin G,He X,Liu P,Liu F,Sun F,Tu R,Yue GH

更新日期：2013-05-01 00:00:00

abstract：BACKGROUND:Mapping DNaseI hypersensitive sites is commonly used to identify regulatory regions in the genome. However, currently available methods are either time consuming and laborious, expensive or require large numbers of cells. We aimed to develop a quick and straightforward method for the analysis of DNaseI hyper...

journal_title：BMC genomics

authors： Ohnesorg T,Eggers S,Leonhard WN,Sinclair AH,White SJ

更新日期：2009-09-04 00:00:00

abstract：BACKGROUND:Due to the advancement in high throughput technology, single nucleotide polymorphism (SNP) is routinely being incorporated along with phenotypic information into genetic evaluation. However, this approach often cannot achieve high accuracy for some complex traits. It is possible that SNP markers are not suff...

journal_title：BMC genomics

authors： Hay EHA,Utsunomiya YT,Xu L,Zhou Y,Neves HHR,Carvalheiro R,Bickhart DM,Ma L,Garcia JF,Liu GE

更新日期：2018-06-05 00:00:00

abstract：BACKGROUND:In clinical and basic research custom panels for transcript profiling are gaining importance because only project specific informative genes are interrogated. This approach reduces costs and complexity of data analysis and allows multiplexing of samples. Polymerase-chain-reaction (PCR) based TaqMan assays ha...

journal_title：BMC genomics

authors： Zhang JD,Schindler T,Küng E,Ebeling M,Certa U

更新日期：2014-07-05 00:00:00

abstract：BACKGROUND:There are no commercially available vaccines against human protozoan parasitic diseases, despite the success of vaccination-induced long-term protection against infectious diseases. East Coast fever, caused by the protist Theileria parva, kills one million cattle each year in sub-Saharan Africa, and contribu...

journal_title：BMC genomics

authors： Norling M,Bishop RP,Pelle R,Qi W,Henson S,Drábek EF,Tretina K,Odongo D,Mwaura S,Njoroge T,Bongcam-Rudloff E,Daubenberger CA,Silva JC

更新日期：2015-09-24 00:00:00

abstract：BACKGROUND:Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. RESULTS:To enable functional analysis of human transposase-derived genes, we comb...

journal_title：BMC genomics

authors： Henssen AG,Jiang E,Zhuang J,Pinello L,Socci ND,Koche R,Gonen M,Villasante CM,Armstrong SA,Bauer DE,Weng Z,Kentsis A

更新日期：2016-08-04 00:00:00

abstract：BACKGROUND:Transporter proteins are one of an organism's primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. The functional annotation of most transporters is currently limited to general...

journal_title：BMC genomics

authors： Giuliani SE,Frank AM,Corgliano DM,Seifert C,Hauser L,Collart FR

更新日期：2011-06-15 00:00:00

abstract：BACKGROUND:Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of word embedding. RESULTS:From a pure data-driven fashion, we trained a 200-dimension vector represe...

journal_title：BMC genomics

authors： Du J,Jia P,Dai Y,Tao C,Zhao Z,Zhi D

更新日期：2019-02-04 00:00:00

abstract：BACKGROUND:Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new di...

journal_title：BMC genomics

authors： Rodríguez-Ramilo ST,Toro MA,Bouza C,Hermida M,Pardo BG,Cabaleiro S,Martínez P,Fernández J

更新日期：2011-11-02 00:00:00

abstract：BACKGROUND:The beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease), the role of multisite sequence va...

journal_title：BMC genomics

authors： Taudien S,Groth M,Huse K,Petzold A,Szafranski K,Hampe J,Rosenstiel P,Schreiber S,Platzer M

更新日期：2010-04-19 00:00:00

abstract：BACKGROUND:Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires cha...

journal_title：BMC genomics

authors： Valdes Franco JA,Wang Y,Huo N,Ponciano G,Colvin HA,McMahan CM,Gu YQ,Belknap WR

更新日期：2018-04-19 00:00:00

abstract：BACKGROUND:Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or Illumina short-read low-coverage ...

journal_title：BMC genomics

authors： Baeza JA

更新日期：2020-12-09 00:00:00

abstract：BACKGROUND:DNA methylation is associated with aberrant gene expression in cancer, and has been shown to correlate with therapeutic response and disease prognosis in some types of cancer. We sought to investigate the biological significance of DNA methylation in lung cancer. RESULTS:We integrated the gene expression pr...

journal_title：BMC genomics

authors： Lin SH,Wang J,Saintigny P,Wu CC,Giri U,Zhang J,Menju T,Diao L,Byers L,Weinstein JN,Coombes KR,Girard L,Komaki R,Wistuba II,Date H,Minna JD,Heymach JV

更新日期：2014-12-08 00:00:00