Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data.

abstract：BACKGROUND:Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated...

journal_title：BMC genomics

authors： Luo P,Yun L,Li Y,Tian Y,Liu Q,Huang W,Hu C

更新日期：2018-10-11 00:00:00

abstract：BACKGROUND:The orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide nematode phylogenetic hypotheses have mainly been based on nuclear rDNA sequences, but more recently complete mitochondrial (m...

journal_title：BMC genomics

authors： Park JK,Sultana T,Lee SH,Kang S,Kim HK,Min GS,Eom KS,Nadler SA

更新日期：2011-08-03 00:00:00

abstract：BACKGROUND:The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome, we set-up an analysis pipeline based on a short read de novo seq...

journal_title：BMC genomics

authors： Kerstens HH,Crooijmans RP,Veenendaal A,Dibbits BW,Chin-A-Woeng TF,den Dunnen JT,Groenen MA

更新日期：2009-10-16 00:00:00

abstract：BACKGROUND:The accurate determination of the genomic coordinates for a given gene - its gene model - is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, frequentl...

journal_title：BMC genomics

authors： Dunne MP,Kelly S

更新日期：2018-04-27 00:00:00

abstract：BACKGROUND:In our previous study, Citrobacter werkmanii BF-6 was isolated from an industrial spoilage sample and demonstrated an excellent ability to form biofilms, which could be affected by various environmental factors. However, the genome sequence of this organism has not been reported so far. RESULTS:We report th...

journal_title：BMC genomics

authors： Zhou G,Peng H,Wang YS,Huang XM,Xie XB,Shi QS

更新日期：2017-10-10 00:00:00

abstract：BACKGROUND:A systems toxicology investigation comparing and integrating transcriptomic and proteomic results was conducted to develop holistic effects characterizations for the wildlife bird model, Northern bobwhite (Colinus virginianus) dosed with the explosives degradation product 2-amino-4,6-dinitrotoluene (2A-DNT)....

journal_title：BMC genomics

authors： Gust KA,Nanduri B,Rawat A,Wilbanks MS,Ang CY,Johnson DR,Pendarvis K,Chen X,Quinn MJ Jr,Johnson MS,Burgess SC,Perkins EJ

更新日期：2015-08-07 00:00:00

abstract：BACKGROUND:Azadirachtin A is a triterpenoid from neem tree exhibiting excellent activities against over 600 insect species in agriculture. The production of azadirachtin A depends on extraction from neem tissues, which is not an eco-friendly and sustainable process. The low yield and discontinuous supply of azadirachti...

journal_title：BMC genomics

authors： Wang H,Wang N,Huo Y

更新日期：2020-10-28 00:00:00

abstract：BACKGROUND:In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However,...

journal_title：BMC genomics

authors： Qiu H,Hildebrand F,Kuraku S,Meyer A

更新日期：2011-06-23 00:00:00

abstract：BACKGROUND:Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes der...

journal_title：BMC genomics

authors： Park KD,Park J,Ko J,Kim BC,Kim HS,Ahn K,Do KT,Choi H,Kim HM,Song S,Lee S,Jho S,Kong HS,Yang YM,Jhun BH,Kim C,Kim TH,Hwang S,Bhak J,Lee HK,Cho BW

更新日期：2012-09-12 00:00:00

abstract：BACKGROUND:Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular sys...

journal_title：BMC genomics

authors： Wang J,Hua L,Chen J,Zhang J,Bai X,Gao B,Li C,Shi Z,Sheng W,Gao Y,Xing B

更新日期：2017-07-19 00:00:00

abstract：BACKGROUND:Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental studies on the signaling cross-talks between bacteria and human host to date. METHODS:In this work, ta...

journal_title：BMC genomics

authors： Mei S,Flemington EK,Zhang K

更新日期：2018-06-28 00:00:00

abstract：BACKGROUND:DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid accumulation of muscle microarray data, it is of great interest to understand how to compare and co...

journal_title：BMC genomics

authors： Baron D,Dubois E,Bihouée A,Teusan R,Steenman M,Jourdon P,Magot A,Péréon Y,Veitia R,Savagner F,Ramstein G,Houlgatte R

更新日期：2011-02-16 00:00:00

abstract：BACKGROUND:The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's...

journal_title：BMC genomics

authors： Krishna A,Biryukov M,Trefois C,Antony PM,Hussong R,Lin J,Heinäniemi M,Glusman G,Köglsberger S,Boyd O,van den Berg BH,Linke D,Huang D,Wang K,Hood L,Tholey A,Schneider R,Galas DJ,Balling R,May P

更新日期：2014-12-20 00:00:00

abstract：BACKGROUND:To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consistin...

journal_title：BMC genomics

authors： Jones SI,Gonzalez DO,Vodkin LO

更新日期：2010-02-24 00:00:00

abstract：BACKGROUND:The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, wh...

journal_title：BMC genomics

authors： Cai H,Gu J,Wang Y

更新日期：2010-12-01 00:00:00

abstract：BACKGROUND:Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI), which could be re...

journal_title：BMC genomics

authors： Toussaint J,Sieuwerts AM,Haibe-Kains B,Desmedt C,Rouas G,Harris AL,Larsimont D,Piccart M,Foekens JA,Durbecq V,Sotiriou C

更新日期：2009-09-10 00:00:00

abstract：BACKGROUND:Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool. RESULTS:In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and ...

journal_title：BMC genomics

authors： Zhou F,Olman V,Xu Y

更新日期：2008-01-24 00:00:00

abstract：BACKGROUND:Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and ...

journal_title：BMC genomics

authors： Sánchez-Sevilla JF,Cruz-Rus E,Valpuesta V,Botella MA,Amaya I

更新日期：2014-04-17 00:00:00

abstract：BACKGROUND:Tumor angiogenesis is a highly regulated process involving intercellular communication as well as the interactions of multiple downstream signal transduction pathways. Disrupting one or even a few angiogenesis pathways is often insufficient to achieve sustained therapeutic benefits due to the complexity of a...

journal_title：BMC genomics

authors： Chen Y,Wei T,Yan L,Lawrence F,Qian HR,Burkholder TP,Starling JJ,Yingling JM,Shou J

更新日期：2008-06-02 00:00:00

abstract：BACKGROUND:Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity,...

journal_title：BMC genomics

authors： English AC,Salerno WJ,Hampton OA,Gonzaga-Jauregui C,Ambreth S,Ritter DI,Beck CR,Davis CF,Dahdouli M,Ma S,Carroll A,Veeraraghavan N,Bruestle J,Drees B,Hastie A,Lam ET,White S,Mishra P,Wang M,Han Y,Zhang F,Stankie

更新日期：2015-04-11 00:00:00

abstract：BACKGROUND:Infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) infection causes high mortality and huge economic losses in the poultry industry. To protect chickens against ILTV infection, chicken-embryo origin (CEO) and tissue-culture origin (TCO) vaccines have been used. However, the transmission of vacci...

journal_title：BMC genomics

authors： Lee J,Bottje WG,Kong BW

更新日期：2012-04-24 00:00:00

abstract：BACKGROUND:Although profiling of RNA in single cells has broadened our understanding of development, cancer biology and mechanisms of disease dissemination, it requires the development of reliable and flexible methods. Here we demonstrate that the EpiStem RNA-Amp™ methodology reproducibly generates microgram amounts of...

journal_title：BMC genomics

authors： Rothwell DG,Li Y,Ayub M,Tate C,Newton G,Hey Y,Carter L,Faulkner S,Moro M,Pepper S,Miller C,Blackhall F,Bertolini G,Roz L,Dive C,Brady G

更新日期：2014-12-17 00:00:00

abstract：BACKGROUND:Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize second...

journal_title：BMC genomics

authors： Bobek J,Strakova E,Zikova A,Vohradsky J

更新日期：2014-12-23 00:00:00

abstract：:The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catal...

journal_title：BMC genomics

authors： Blighe K,DeDionisio L,Christie KA,Chawes B,Shareef S,Kakouli-Duarte T,Chao-Shern C,Harding V,Kelly RS,Castellano L,Stebbing J,Lasky-Su JA,Nesbit MA,Moore CBT

更新日期：2018-08-08 00:00:00

abstract：BACKGROUND:The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptos...

journal_title：BMC genomics

authors： Zhu W,Wang J,Zhu Y,Tang B,Zhang Y,He P,Zhang Y,Liu B,Guo X,Zhao G,Qin J

更新日期：2015-02-15 00:00:00

abstract：BACKGROUND:The recently developed RNA interference (RNAi) technology has created an unprecedented opportunity which allows the function of individual genes in whole organisms or cell lines to be interrogated at genome-wide scale. However, multiple issues, such as off-target effects or low efficacies in knocking down ce...

journal_title：BMC genomics

authors： Wang L,Tu Z,Sun F

更新日期：2009-05-12 00:00:00

abstract：BACKGROUND:Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, plays a crucial role in protec...

journal_title：BMC genomics

authors： Liu J,Sharma A,Niewiara MJ,Singh R,Ming R,Yu Q

更新日期：2018-01-06 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in...

journal_title：BMC genomics

authors： Wang B,Ye N,Cao SJ,Wen XT,Huang Y,Yan QG

更新日期：2016-11-08 00:00:00

abstract：BACKGROUND:The environmental light-dark cycle is the dominant cue that maintains 24-h biological rhythms in multicellular organisms. In Drosophila, light entrainment is mediated by the photosensitive protein CRYPTOCHROME, but the role and extent of transcription regulation in light resetting of the dipteran clock is ye...

journal_title：BMC genomics

authors： Adewoye AB,Kyriacou CP,Tauber E

更新日期：2015-08-01 00:00:00

abstract：BACKGROUND:Reading disability (RD) is a common syndrome with a large genetic component. Chromosome 6 has been identified in several linkage studies as playing a significant role. A more recent study identified a peak of transmission disequilibrium to marker JA04 (G72384) on chromosome 6p22.3, suggesting that a gene is ...

journal_title：BMC genomics

authors： Londin ER,Meng H,Gruen JR

更新日期：2003-06-30 00:00:00