Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate.

abstract：BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...

journal_title：BMC genomics

authors： Zhang X,Liu X,Li L,Wei G,Zhang D,Liang Y,Miao B

更新日期：2019-05-30 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) regulate the expression of target genes by mediating gene silencing in both plants and animals. The miRNA targets have been extensively investigated in Arabidopsis and rice using computational prediction, experimental validation by overexpression in transgenic plants, and by degradome or P...

journal_title：BMC genomics

authors： Shamimuzzaman M,Vodkin L

更新日期：2012-07-16 00:00:00

abstract：BACKGROUND:Sweet sorghum is an annual C4 crop considered to be one of the most promising bio-energy crops due to its high sugar content in stem, yet it is poorly understood how this plant increases its sugar content in response to salt stress. In response to high NaCl, many of its major processes, such as photosynthesi...

journal_title：BMC genomics

authors： Sui N,Yang Z,Liu M,Wang B

更新日期：2015-07-19 00:00:00

abstract：BACKGROUND:Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geog...

journal_title：BMC genomics

authors： Gamboa M,Watanabe K

更新日期：2019-01-24 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are short non-coding RNAs that are emerging as important post-transcriptional regulators of neuronal and synaptic development. The precise impact of miRNAs on presynaptic function and neurotransmission remains, however, poorly understood. RESULTS:Here, we identify miR-27b-an abundant neur...

journal_title：BMC genomics

authors： Poon VY,Gu M,Ji F,VanDongen AM,Fivaz M

更新日期：2016-10-04 00:00:00

abstract：BACKGROUND:An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmen...

journal_title：BMC genomics

authors： Sinha A,Sommer RJ,Dieterich C

更新日期：2012-06-19 00:00:00

abstract：BACKGROUND:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was...

journal_title：BMC genomics

authors： Miao Y,Liu D,Li G,Li P,Xu Y,Shen Q,Zhang R

更新日期：2015-06-16 00:00:00

abstract：BACKGROUND:Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analysis, both haplotype alleles and blocks are tested. Haplotype alleles can be inferred with the same st...

journal_title：BMC genomics

authors： Chen H,Hao Z,Zhao Y,Yang R

更新日期：2020-02-11 00:00:00

abstract：BACKGROUND:Streptococcus uberis, a Gram positive bacterial pathogen responsible for a significant proportion of bovine mastitis in commercial dairy herds, colonises multiple body sites of the cow including the gut, genital tract and mammary gland. Comparative analysis of the complete genome sequence of S. uberis strain...

journal_title：BMC genomics

authors： Ward PN,Holden MT,Leigh JA,Lennard N,Bignell A,Barron A,Clark L,Quail MA,Woodward J,Barrell BG,Egan SA,Field TR,Maskell D,Kehoe M,Dowson CG,Chanter N,Whatmore AM,Bentley SD,Parkhill J

更新日期：2009-01-28 00:00:00

abstract：BACKGROUND:The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a ...

journal_title：BMC genomics

authors： Ishii K,Washio T,Uechi T,Yoshihama M,Kenmochi N,Tomita M

更新日期：2006-02-28 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:The endothelial PAS domain protein 1 (EPAS1) activates genes that are involved in erythropoiesis and angiogenesis, thus favoring a better delivery of oxygen to the tissues and is a plausible candidate to influence athletic performance. Using innovative statistical methods we compared genotype distributions a...

journal_title：BMC genomics

authors： Voisin S,Cieszczyk P,Pushkarev VP,Dyatlov DA,Vashlyayev BF,Shumaylov VA,Maciejewska-Karlowska A,Sawczuk M,Skuza L,Jastrzebski Z,Bishop DJ,Eynon N

更新日期：2014-05-18 00:00:00

abstract：BACKGROUND:In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be d...

journal_title：BMC genomics

authors： Xiang H,Li X,Dai F,Xu X,Tan A,Chen L,Zhang G,Ding Y,Li Q,Lian J,Willden A,Guo Q,Xia Q,Wang J,Wang W

更新日期：2013-09-23 00:00:00

abstract：BACKGROUND:The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential roles in contributing to their overall health and production performance. In the present study, RNA se...

journal_title：BMC genomics

authors： Wang WW,Wang J,Zhang HJ,Wu SG,Qi GH

更新日期：2019-12-12 00:00:00

abstract：BACKGROUND:Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been ...

journal_title：BMC genomics

authors： Feng C,Xu CJ,Wang Y,Liu WL,Yin XR,Li X,Chen M,Chen KS

更新日期：2013-10-25 00:00:00

abstract：BACKGROUND:Current ChIP-seq studies are interested in comparing multiple epigenetic profiles across several cell types and tissues simultaneously for studying constitutive and differential regulation. Simultaneous analysis of multiple epigenetic features in many samples can gain substantial power and specificity than a...

journal_title：BMC genomics

authors： Chen KB,Hardison R,Zhang Y

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the protein secretory pathway of this biotechnologically relevant fungus, we undertook genome-wide analyse...

journal_title：BMC genomics

authors： Aguiar TQ,Ribeiro O,Arvas M,Wiebe MG,Penttilä M,Domingues L

更新日期：2014-12-18 00:00:00

abstract：BACKGROUND:Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of pe...

journal_title：BMC genomics

authors： Zhang Q,Ma B,Li H,Chang Y,Han Y,Li J,Wei G,Zhao S,Khan MA,Zhou Y,Gu C,Zhang X,Han Z,Korban SS,Li S,Han Y

更新日期：2012-10-07 00:00:00

abstract：BACKGROUND:Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strateg...

journal_title：BMC genomics

authors： Anthon C,Tafer H,Havgaard JH,Thomsen B,Hedegaard J,Seemann SE,Pundhir S,Kehr S,Bartschat S,Nielsen M,Nielsen RO,Fredholm M,Stadler PF,Gorodkin J

更新日期：2014-06-10 00:00:00

abstract：BACKGROUND:Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not been identified. A transcriptomic approach was used to search for such genes in the intestine of eur...

journal_title：BMC genomics

authors： Wong MK,Ozaki H,Suzuki Y,Iwasaki W,Takei Y

更新日期：2014-12-18 00:00:00

abstract：BACKGROUND:Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily spec...

journal_title：BMC genomics

authors： Yusuf D,Marz M,Stadler PF,Hofacker IL

更新日期：2010-07-13 00:00:00

abstract：BACKGROUND:Crustacean moulting is a complex process involving many regulatory pathways. A holistic approach to examine differential gene expression profiles of transcripts relevant to the moulting process, across all moult cycle stages, was used in this study. Custom cDNA microarrays were constructed for Portunus pelag...

journal_title：BMC genomics

authors： Kuballa AV,Holton TA,Paterson B,Elizur A

更新日期：2011-03-12 00:00:00

abstract：BACKGROUND:BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specif...

journal_title：BMC genomics

authors： Feltus FA,Saski CA,Mockaitis K,Haiminen N,Parida L,Smith Z,Ford J,Staton ME,Ficklin SP,Blackmon BP,Cheng CH,Schnell RJ,Kuhn DN,Motamayor JC

更新日期：2011-07-27 00:00:00

abstract：BACKGROUND:The disease caused by Haemonchus contortus, a blood-feeding nematode of small ruminants, is of major economic importance worldwide. The infective third-stage larva (L3) of this gastric nematode is enclosed in a cuticle (sheath) and, once ingested with herbage by the host, undergoes an exsheathment process th...

journal_title：BMC genomics

authors： Cantacessi C,Campbell BE,Young ND,Jex AR,Hall RS,Presidente PJ,Zawadzki JL,Zhong W,Aleman-Meza B,Loukas A,Sternberg PW,Gasser RB

更新日期：2010-04-27 00:00:00

abstract：BACKGROUND:After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidization, after which the originally doubled chromosome numbers reduced to different chromosome numbers amo...

journal_title：BMC genomics

authors： Wang Z,Wang J,Pan Y,Lei T,Ge W,Wang L,Zhang L,Li Y,Zhao K,Liu T,Song X,Zhang J,Yu J,Hu J,Wang X

更新日期：2019-03-07 00:00:00

abstract：BACKGROUND:Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the most important oilseed crops. However, little is known on genes coding for LPAATs involved in oil biosy...

journal_title：BMC genomics

authors： Wang N,Ma J,Pei W,Wu M,Li H,Li X,Yu S,Zhang J,Yu J

更新日期：2017-03-01 00:00:00

abstract：BACKGROUND:Many computational methods are available for assembly and annotation of newly sequenced microbial genomes. However, when new genomes are reported in the literature, there is frequently very little critical analysis of choices made during the sequence assembly and gene annotation stages. These choices have a ...

journal_title：BMC genomics

authors： Morrison SS,Pyzh R,Jeon MS,Amaro C,Roig FJ,Baker-Austin C,Oliver JD,Gibas CJ

更新日期：2014-01-01 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:Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Singl...

journal_title：BMC genomics

authors： Childs LH,Witucka-Wall H,Günther T,Sulpice R,Korff MV,Stitt M,Walther D,Schmid KJ,Altmann T

更新日期：2010-03-20 00:00:00

abstract：BACKGROUND:Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepatocellular carcinoma (HCC) recurrence for application in clinical purposes. To overcome the limitati...

journal_title：BMC genomics

authors： Kim BY,Choi DW,Woo SR,Park ER,Lee JG,Kim SH,Koo I,Park SH,Han CJ,Kim SB,Yeom YI,Yang SJ,Yu A,Lee JW,Jang JJ,Cho MH,Jeon WK,Park YN,Suh KS,Lee KH

更新日期：2015-04-10 00:00:00