The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate Monosiga brevicollis.

abstract：BACKGROUND:A sense-antisense gene pair (SAGP) is a gene pair where two oppositely transcribed genes share a common nucleotide sequence region. In eukaryotic genomes, SAGPs can be organized in complex sense-antisense architectures (CSAGAs) in which at least one sense gene shares loci with two or more antisense partners....

journal_title：BMC genomics

authors： Grinchuk OV,Motakis E,Kuznetsov VA

更新日期：2010-02-10 00:00:00

abstract：BACKGROUND:The desiccation-tolerant moss Bryum argenteum is an important component of the Biological Soil Crusts (BSCs) found in the Gurbantunggut desert. Desiccation tolerance is defined as the ability to revive from the air dried state. To elucidate the molecular mechanisms related to desiccation tolerance, we employ...

journal_title：BMC genomics

authors： Gao B,Zhang D,Li X,Yang H,Zhang Y,Wood AJ

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gall...

journal_title：BMC genomics

authors： Wu T,Zhang Z,Liu B,Hou D,Liang Y,Zhang J,Shi P

更新日期：2013-10-01 00:00:00

abstract：BACKGROUND:Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens ar...

journal_title：BMC genomics

authors： Kwenda S,Gorshkov V,Ramesh AM,Naidoo S,Rubagotti E,Birch PR,Moleleki LN

更新日期：2016-01-12 00:00:00

abstract：BACKGROUND:Two fifths of the world's population is at risk from dengue. The absence of effective drugs and vaccines leaves vector control as the primary intervention tool. Understanding dengue virus (DENV) host interactions is essential for the development of novel control strategies. The availability of genome sequenc...

journal_title：BMC genomics

authors： Guo X,Xu Y,Bian G,Pike AD,Xie Y,Xi Z

更新日期：2010-06-16 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 identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise...

journal_title：BMC genomics

authors： Zhang J,Haskins W

更新日期：2010-12-01 00:00:00

abstract：BACKGROUND:The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese jujube (Ziziphus jujuba Mill.) is the largest type of dried fruit tree in China in terms of production,...

journal_title：BMC genomics

authors： Xue C,Li H,Liu Z,Wang L,Zhao Y,Wei X,Fang H,Liu M,Zhao J

更新日期：2019-06-07 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:It is believed that the main factors of low prenatal growth in mammals are genetic and environmental. We used isogenic mice maintained in standard conditions to analyze how natural non-genetic microsomia (low birth weight) is produced in inbred mice and its long term effect on health. To better understand th...

journal_title：BMC genomics

authors： Miranda A,López-Cardona AP,Laguna-Barraza R,Calle A,López-Vidriero I,Pintado B,Gutiérrez-Adán A

更新日期：2014-05-01 00:00:00

abstract：BACKGROUND:Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Population-Specific Expression Analysis (PSEA), a statistical method that identifies individual cell types...

journal_title：BMC genomics

authors： Kuhn A,Kumar A,Beilina A,Dillman A,Cookson MR,Singleton AB

更新日期：2012-11-12 00:00:00

abstract：BACKGROUND:Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic al...

journal_title：BMC genomics

authors： Posey T,Weng T,Chen Z,Chintagari NR,Wang P,Jin N,Stricker H,Liu L

更新日期：2008-03-03 00:00:00

abstract：BACKGROUND:In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success ...

journal_title：BMC genomics

authors： Groenen MA,Megens HJ,Zare Y,Warren WC,Hillier LW,Crooijmans RP,Vereijken A,Okimoto R,Muir WM,Cheng HH

更新日期：2011-05-31 00:00:00

abstract：BACKGROUND:Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone m...

journal_title：BMC genomics

authors： Deng Y,Dai X,Xiang Q,Dai Z,He C,Wang J,Feng J

更新日期：2010-10-09 00:00:00

abstract：BACKGROUND:Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which ...

journal_title：BMC genomics

authors： Brown CW,Sridhara V,Boutz DR,Person MD,Marcotte EM,Barrick JE,Wilke CO

更新日期：2017-04-17 00:00:00

abstract：BACKGROUND:Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using thre...

journal_title：BMC genomics

authors： Huang X,Yuan T,Tschannen M,Sun Z,Jacob H,Du M,Liang M,Dittmar RL,Liu Y,Liang M,Kohli M,Thibodeau SN,Boardman L,Wang L

更新日期：2013-05-10 00:00:00

abstract：BACKGROUND:Defensins are important components of innate immunity to combat bacterial and viral infections, and can even elicit antitumor responses. Clusters of defensin (DEF) genes are located in a 2 Mb range of the human chromosome 8p23.1. This DEF locus, however, represents one of the regions in the euchromatic part ...

journal_title：BMC genomics

authors： Taudien S,Galgoczy P,Huse K,Reichwald K,Schilhabel M,Szafranski K,Shimizu A,Asakawa S,Frankish A,Loncarevic IF,Shimizu N,Siddiqui R,Platzer M

更新日期：2004-12-10 00:00:00

abstract：BACKGROUND:Theileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle. It does so by inducing cancer-like phenotypes in the host cells it infects, although the molecular and regulatory mechanisms involved remain poorly understood. RNAseq data, and the resulting updated genome annot...

journal_title：BMC genomics

authors： Tretina K,Pelle R,Silva JC

更新日期：2016-02-20 00:00:00

abstract：BACKGROUND:Although numerous investigations have compared gene expression microarray platforms, preprocessing methods and batch correction algorithms using constructed spike-in or dilution datasets, there remains a paucity of studies examining the properties of microarray data using diverse biological samples. Most mic...

journal_title：BMC genomics

authors： Richard AC,Lyons PA,Peters JE,Biasci D,Flint SM,Lee JC,McKinney EF,Siegel RM,Smith KG

更新日期：2014-08-04 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:Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying phy...

journal_title：BMC genomics

authors： Sun RX,Chong LC,Simmons TT,Houlahan KE,Prokopec SD,Watson JD,Moffat ID,Lensu S,Lindén J,P'ng C,Okey AB,Pohjanvirta R,Boutros PC

更新日期：2014-12-03 00:00:00

abstract：BACKGROUND:Cadmium (Cd) is a severe detrimental environmental pollutant. To adapt to Cd-induced deleterious effects, plants have evolved sophisticated defence mechanisms. In this study, a genome-wide transcriptome analysis was performed to identify the mechanisms of Cd tolerance using two barley genotypes with distinct...

journal_title：BMC genomics

authors： Cao F,Chen F,Sun H,Zhang G,Chen ZH,Wu F

更新日期：2014-07-19 00:00:00

abstract：BACKGROUND:Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS:To overcome these limitations, we developed a novel RoV capture and genome sequencing method combin...

journal_title：BMC genomics

authors： Dung TTN,Duy PT,Sessions OM,Sangumathi UK,Phat VV,Tam PTT,To NTN,Phuc TM,Hong Chau TT,Chau NNM,Minh NN,Thwaites GE,Rabaa MA,Baker S

更新日期：2017-04-24 00:00:00

abstract：BACKGROUND:The increasing numbers of 3D compounds and protein complexes stored in databases contribute greatly to current advances in biotechnology, being employed in several pharmaceutical and industrial applications. However, screening and retrieving appropriate candidates as well as handling false positives presents...

journal_title：BMC genomics

authors： Clinciu DL,Chen YF,Ko CN,Lo CC,Yang JM

更新日期：2010-12-02 00:00:00

abstract：BACKGROUND:In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can ...

journal_title：BMC genomics

authors： Teran Hidalgo SJ,Wu M,Ma S

更新日期：2017-08-16 00:00:00

abstract：BACKGROUND:Horseradish peroxidases (HRPs) from Armoracia rusticana have long been utilized as reporters in various diagnostic assays and histochemical stainings. Regardless of their increasing importance in the field of life sciences and suggested uses in medical applications, chemical synthesis and other industrial ap...

journal_title：BMC genomics

authors： Näätsaari L,Krainer FW,Schubert M,Glieder A,Thallinger GG

更新日期：2014-03-24 00:00:00

abstract：BACKGROUND:Retrogenes are processed copies of other genes. This duplication mechanism produces a copy of the parental gene that should not contain introns, and usually does not contain cis-regulatory regions. Here, we computationally address the evolutionary origin of promoter and other cis-regulatory regions in retrog...

journal_title：BMC genomics

authors： Bai Y,Casola C,Betrán E

更新日期：2008-05-22 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:Microarrays have revolutionized breast cancer (BC) research by enabling studies of gene expression on a transcriptome-wide scale. Recently, RNA-Sequencing (RNA-Seq) has emerged as an alternative for precise readouts of the transcriptome. To date, no study has compared the ability of the two technologies to q...

journal_title：BMC genomics

authors： Fumagalli D,Blanchet-Cohen A,Brown D,Desmedt C,Gacquer D,Michiels S,Rothé F,Majjaj S,Salgado R,Larsimont D,Ignatiadis M,Maetens M,Piccart M,Detours V,Sotiriou C,Haibe-Kains B

更新日期：2014-11-21 00:00:00

abstract：BACKGROUND:Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly b...

journal_title：BMC genomics

authors： Timko MP,Rushton PJ,Laudeman TW,Bokowiec MT,Chipumuro E,Cheung F,Town CD,Chen X

更新日期：2008-02-27 00:00:00