Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine.

abstract：BACKGROUND:The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies. RESULTS:We propose an intuitive and efficient algorithm, titled extreme MApping of OligoNucleotide (xMAN), to rapidly map millions of oligonucleotide fragments to a...

journal_title：BMC genomics

authors： Li W,Carroll JS,Brown M,Liu xS

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental prog...

journal_title：BMC genomics

authors： Rosengarten RD,Santhanam B,Fuller D,Katoh-Kurasawa M,Loomis WF,Zupan B,Shaulsky G

更新日期：2015-04-13 00:00:00

abstract：BACKGROUND:Determination of genome-wide DNA methylation is significant for both basic research and drug development. As a key epigenetic modification, this biochemical process can modulate gene expression to influence the cell differentiation which can possibly lead to cancer. Due to the involuted biochemical mechanism...

journal_title：BMC genomics

authors： Tian Q,Zou J,Tang J,Fang Y,Yu Z,Fan S

更新日期：2019-04-04 00:00:00

abstract：BACKGROUND:The steroid hormone environment in healthy horses seems to have a significant impact on the efficiency of their uterine immune response. The objective of this study was to characterize the changes in gene expression in the equine endometrium in response to the introduction of bacterial pathogens and the infl...

journal_title：BMC genomics

authors： Marth CD,Young ND,Glenton LY,Noden DM,Browning GF,Krekeler N

更新日期：2015-11-14 00:00:00

abstract：BACKGROUND:The complex genome of rapeseed (Brassica napus) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence gen...

journal_title：BMC genomics

authors： Bus A,Hecht J,Huettel B,Reinhardt R,Stich B

更新日期：2012-06-24 00:00:00

abstract：BACKGROUND:Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding program...

journal_title：BMC genomics

authors： Houston RD,Taggart JB,Cézard T,Bekaert M,Lowe NR,Downing A,Talbot R,Bishop SC,Archibald AL,Bron JE,Penman DJ,Davassi A,Brew F,Tinch AE,Gharbi K,Hamilton A

更新日期：2014-02-06 00:00:00

abstract：BACKGROUND:Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have ana...

journal_title：BMC genomics

authors： Sczyrba A,Beckstette M,Brivanlou AH,Giegerich R,Altmann CR

更新日期：2005-09-14 00:00:00

abstract：UNLABELLED:Transcription-induced chimerism, a mechanism involving the transcription and intergenic splicing of two consecutive genes, has recently been estimated to account for approximately 5% of the human transcriptome. Despite this prevalence, the regulation and function of these fused transcripts remains largely un...

journal_title：BMC genomics

authors： Wang K,Ubriaco G,Sutherland LC

更新日期：2007-10-01 00:00:00

abstract：BACKGROUND:The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp191), which is the most highly conserved among the human-mouse SCAN family member orthologues pairs. ...

journal_title：BMC genomics

authors： Li J,Chen X,Gong X,Liu Y,Feng H,Qiu L,Hu Z,Zhang J

更新日期：2009-05-22 00:00:00

abstract：BACKGROUND:Very little is known about the immunological responses of amphibians to pathogens that are causing global population declines. We used a custom microarray gene chip to characterize gene expression responses of axolotls (Ambystoma mexicanum) to an emerging viral pathogen, Ambystoma tigrinum virus (ATV). RESU...

journal_title：BMC genomics

authors： Cotter JD,Storfer A,Page RB,Beachy CK,Voss SR

更新日期：2008-10-20 00:00:00

abstract：BACKGROUND:High throughput genotyping of single nucleotide polymorphisms (SNPs) for genome-wide association requires technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. In this work, we have developed a theoretical approach to estimate allele freque...

journal_title：BMC genomics

authors： Yin BC,Li H,Ye BC

更新日期：2008-12-16 00:00:00

abstract：BACKGROUND:Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. RESULTS:We describe a Web-...

journal_title：BMC genomics

authors： Tan TW,Xie C,De Silva M,Lim KS,Patro CP,Lim SJ,Govindarajan KR,Tong JC,Choo KH,Ranganathan S,Khan AM

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Understanding the genetic basis of adaptive evolution is one of the major goals in evolutionary biology. Recently, it has been revealed that gene copy number variations (GCNVs) constitute significant proportions of genomic diversities within natural populations. However, it has been unclear whether GCNVs are...

journal_title：BMC genomics

authors： Hirase S,Ozaki H,Iwasaki W

更新日期：2014-08-29 00:00:00

abstract：BACKGROUND:Genotype imputation can help reduce genotyping costs particularly for implementation of genomic selection. In applications entailing large populations, recovering the genotypes of untyped loci using information from reference individuals that were genotyped with a higher density panel is computationally chal...

journal_title：BMC genomics

authors： Sargolzaei M,Chesnais JP,Schenkel FS

更新日期：2014-06-17 00:00:00

abstract：BACKGROUND:Variation in gene expression between two Drosophila melanogaster strains, as revealed by transcriptional profiling, seldom corresponded to variation in proximal promoter sequence for 34 genes analyzed. Two sets of protein-coding genes were selected from pre-existing microarray data: (1) those whose expressio...

journal_title：BMC genomics

authors： Brown RP,Feder ME

更新日期：2005-08-17 00:00:00

abstract：BACKGROUND:Litchi (Litchi chinensis Sonn.) is an economically important evergreen fruit tree widely cultivated in subtropical areas. Low temperature is absolutely required for floral induction of litchi, but its molecular mechanism is not fully understood. Leaves of litchi played a key role during floral induction and ...

journal_title：BMC genomics

authors： Zhang H,Shen J,Wei Y,Chen H

更新日期：2017-05-10 00:00:00

abstract：BACKGROUND:The Pacific oyster Crassostrea gigas is an important fishery resource that is sensitive to temperature fluctuations. Thus, it has evolved a protection mechanism against heat stress by increasing the expression of the gene coding for heat shock protein (HSP) 70 under elevated temperatures. In other animals, h...

journal_title：BMC genomics

authors： Liu Y,Li L,Huang B,Wang W,Zhang G

更新日期：2019-08-08 00:00:00

abstract：BACKGROUND:Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of t...

journal_title：BMC genomics

authors： Huang X,Otecko NO,Peng M,Weng Z,Li W,Chen J,Zhong M,Zhong F,Jin S,Geng Z,Luo W,He D,Ma C,Han J,Ommeh SC,Zhang Y,Zhang X,Du B

更新日期：2020-04-20 00:00:00

abstract：BACKGROUND:Fitness epistasis, the interaction effect of genes at different loci on fitness, makes an important contribution to adaptive evolution. Although fitness interaction evidence has been observed in model organisms, it is more difficult to detect and remains poorly understood in human populations as a result of ...

journal_title：BMC genomics

authors： Ni X,Zhou M,Wang H,He KY,Broeckel U,Hanis C,Kardia S,Redline S,Cooper RS,Tang H,Zhu X

更新日期：2020-07-11 00:00:00

abstract：BACKGROUND:Ramie (Boehmeria nivea L.), popularly known as "China grass", is one of the oldest crops in China and the second most important fiber crop in terms of area sown. Ramie fiber, extracted from the plant bast, is important in the textile industry. However, the molecular mechanism of ramie fiber development remai...

journal_title：BMC genomics

authors： Chen J,Pei Z,Dai L,Wang B,Liu L,An X,Peng D

更新日期：2014-10-22 00:00:00

abstract：BACKGROUND:The spiral cleavage mode of early development is utilized in over one-third of all animal phyla and generates embryonic cells of different size, position, and fate through a conserved set of stereotypic and invariant asymmetric cell divisions. Despite the widespread use of spiral cleavage, regulatory and mol...

journal_title：BMC genomics

authors： Chou HC,Pruitt MM,Bastin BR,Schneider SQ

更新日期：2016-08-05 00:00:00

abstract：BACKGROUND:We use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant categories, and enables the identification of genes and pathways most significantly associated to each phenotypic group, while allowing for the partici...

journal_title：BMC genomics

authors： Lozano JJ,Soler M,Bermudo R,Abia D,Fernandez PL,Thomson TM,Ortiz AR

更新日期：2005-08-17 00:00:00

abstract：BACKGROUND:MECP2, the gene mutated in the majority of Rett syndrome cases, is a transcriptional regulator that can activate or repress transcription. Although the transcription regulatory function of MECP2 has been known for over a decade, it remains unclear how transcriptional dysregulation leads to the neurodevelopme...

journal_title：BMC genomics

authors： Lin P,Nicholls L,Assareh H,Fang Z,Amos TG,Edwards RJ,Assareh AA,Voineagu I

更新日期：2016-06-06 00:00:00

abstract：BACKGROUND:Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, perhaps the b...

journal_title：BMC genomics

authors： Pannebakker BA,Cook N,van den Heuvel J,van de Zande L,Shuker DM

更新日期：2020-07-20 00:00:00

abstract：BACKGROUND:Pitayas are currently attracting considerable interest as a tropical fruit with numerous health benefits. However, as a long-day plant, pitaya plants cannot flower in the winter season from November to April in Hainan, China. To harvest pitayas with high economic value in the winter season, it is necessary t...

journal_title：BMC genomics

authors： Xiong R,Liu C,Xu M,Wei SS,Huang JQ,Tang H

更新日期：2020-04-29 00:00:00

abstract：BACKGROUND:The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the geno...

journal_title：BMC genomics

authors： Prunier J,Pelgas B,Gagnon F,Desponts M,Isabel N,Beaulieu J,Bousquet J

更新日期：2013-06-01 00:00:00

abstract：BACKGROUND:The genomewide evaluation of genetic epistasis is a computationally demanding task, and a current challenge in Genetics. HFCC (Hypothesis-Free Clinical Cloning) is one of the methods that have been suggested for genomewide epistasis analysis. In order to perform an exhaustive search of epistasis, HFCC has im...

journal_title：BMC genomics

authors： Gayán J,González-Pérez A,Ruiz A

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we...

journal_title：BMC genomics

authors： Silva DG,Schönbach C,Brusic V,Socha LA,Nagashima T,Petrovsky N

更新日期：2004-04-29 00:00:00

abstract：BACKGROUND:Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. RESULTS:In this study, 48 CIPK genes (SsCIPKs) were identifi...

journal_title：BMC genomics

authors： Su W,Ren Y,Wang D,Huang L,Fu X,Ling H,Su Y,Huang N,Tang H,Xu L,Que Y

更新日期：2020-12-07 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