DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.

abstract：BACKGROUND:Calcium ion is tightly regulated in body fluids and for euryhaline fish, which are exposed to rapid changes in environmental [Ca2+], homeostasis is especially challenging. The gill is the main organ of active calcium uptake and therefore plays a crucial role in the maintenance of calcium ion homeostasis. To ...

journal_title：BMC genomics

authors： Pinto PI,Matsumura H,Thorne MA,Power DM,Terauchi R,Reinhardt R,Canário AV

更新日期：2010-08-17 00:00:00

abstract：BACKGROUND:Bovine papillomavirus (BPV) belongs to the Papillomaviridae family and infects epithelial cells of bovines and closely related animals, causing hyperproliferative lesions known as warts or papillomas, which may regress or progress to form benign or malignant tumors. The virus enters the host cell and interac...

journal_title：BMC genomics

authors： Barreto DM,Barros GS,Santos LABO,Soares RC,Batista MVA

更新日期：2018-12-19 00:00:00

abstract：BACKGROUND:Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease re...

journal_title：BMC genomics

authors： Tadmor-Levi R,Doron-Faigenboim A,Marcos-Hadad E,Petit J,Hulata G,Forlenza M,Wiegertjes GF,David L

更新日期：2019-12-26 00:00:00

abstract：BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...

journal_title：BMC genomics

authors： Lehnert EM,Burriesci MS,Pringle JR

更新日期：2012-06-22 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:Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clin...

journal_title：BMC genomics

authors： Samarasinghe SR,Samaranayake N,Kariyawasam UL,Siriwardana YD,Imamura H,Karunaweera ND

更新日期：2018-11-28 00:00:00

abstract：BACKGROUND:Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. I...

journal_title：BMC genomics

authors： Ruan Y,Shen L,Zou Y,Qi Z,Yin J,Jiang J,Guo L,He L,Chen Z,Tang Z,Qin S

更新日期：2015-02-25 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:Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infection with the destructive bacterial pathogen Xanthomonas oryzae pv. oryzae(Xoo) in both resistant and s...

journal_title：BMC genomics

authors： Narsai R,Wang C,Chen J,Wu J,Shou H,Whelan J

更新日期：2013-02-12 00:00:00

abstract：BACKGROUND:Alternative σ factors are important transcriptional regulators in bacteria. While σ(B) has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σ(H) has not yet been well defined in Listeria, even though σ(H) c...

journal_title：BMC genomics

authors： Liu Y,Orsi RH,Boor KJ,Wiedmann M,Guariglia-Oropeza V

更新日期：2016-02-16 00:00:00

abstract：BACKGROUND:Precise identification of three-dimensional genome organization, especially enhancer-promoter interactions (EPIs), is important to deciphering gene regulation, cell differentiation and disease mechanisms. Currently, it is a challenging task to distinguish true interactions from other nearby non-interacting o...

journal_title：BMC genomics

authors： Zeng W,Wu M,Jiang R

更新日期：2018-05-09 00:00:00

abstract：BACKGROUND:In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective val...

journal_title：BMC genomics

authors： van Hijum SA,de Jong A,Baerends RJ,Karsens HA,Kramer NE,Larsen R,den Hengst CD,Albers CJ,Kok J,Kuipers OP

更新日期：2005-05-20 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:Nuclear receptors are hormone-regulated transcription factors whose signaling controls numerous aspects of development and physiology. Many receptors recognize DNA hormone response elements formed by direct repeats of RGKTCA motifs separated by 1 to 5 bp (DR1-DR5). Although many known such response elements ...

journal_title：BMC genomics

authors： Laperriere D,Wang TT,White JH,Mader S

更新日期：2007-01-19 00:00:00

abstract：BACKGROUND:Matrix attachment regions (MAR) are the sites on genomic DNA that interact with the nuclear matrix. There is increasing evidence for the involvement of MAR in regulation of gene expression. The unsuitability of experimental detection of MAR for genome-wide analyses has led to the development of computational...

journal_title：BMC genomics

authors： Anthony A,Blaxter M

更新日期：2007-11-15 00:00:00

abstract：BACKGROUND:The pattern of point mutation is important for studying mutational mechanisms, genome evolution, and diseases. Previous studies of mutation direction were largely based on substitution data from a limited number of loci. To date, there is no genome-wide analysis of mutation direction or methylation-dependent...

journal_title：BMC genomics

authors： Jiang C,Zhao Z

更新日期：2006-12-13 00:00:00

abstract：BACKGROUND:Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of...

journal_title：BMC genomics

authors： Armstrong AF,Grosberg RK

更新日期：2018-05-18 00:00:00

abstract：BACKGROUND:Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression system...

journal_title：BMC genomics

authors： Moshonov S,Elfakess R,Golan-Mashiach M,Sinvani H,Dikstein R

更新日期：2008-02-25 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:Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transc...

journal_title：BMC genomics

authors： Zhu BH,Xiao J,Xue W,Xu GC,Sun MY,Li JT

更新日期：2018-03-02 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:Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections...

journal_title：BMC genomics

authors： Li H,Cui P,Fu X,Zhang L,Yan W,Zhai Y,Lei C,Wang H,Yang X

更新日期：2021-01-20 00:00:00

abstract：BACKGROUND:Protein phosphorylation is responsible for a large portion of the regulatory functions of eukaryotic cells. Although the list of sequenced genomes of filamentous fungi has grown rapidly, the kinomes of recently sequenced species have not yet been studied in detail. The objective of this study is to apply a c...

journal_title：BMC genomics

authors： Kosti I,Mandel-Gutfreund Y,Glaser F,Horwitz BA

更新日期：2010-02-24 00:00:00

abstract：BACKGROUND:Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodontitis. Individual clonal types of A. actinomycetemcomitans may exhibit variable virulence and di...

journal_title：BMC genomics

authors： Kittichotirat W,Bumgarner R,Chen C

更新日期：2010-09-08 00:00:00

abstract：BACKGROUND:Lack of power and reproducibility are caveats of genetic association studies of common complex diseases. Indeed, the heterogeneity of disease etiology demands that causal models consider the simultaneous involvement of multiple genes. Rothman's sufficient-cause model, which is well known in epidemiology, pro...

journal_title：BMC genomics

authors： Lynn KS,Lu CH,Yang HY,Hsu WL,Pan WH

更新日期：2013-07-23 00:00:00

abstract：BACKGROUND:Housekeeping (HK) genes are ubiquitously expressed in all tissue/cell types and constitute a basal transcriptome for the maintenance of basic cellular functions. Partitioning transcriptomes into HK and tissue-specific (TS) genes relatively is fundamental for studying gene expression and cellular differentiat...

journal_title：BMC genomics

authors： Zhu J,He F,Song S,Wang J,Yu J

更新日期：2008-04-16 00:00:00

abstract：BACKGROUND:Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown...

journal_title：BMC genomics

authors： Zhang L,Zuo K,Zhang F,Cao Y,Wang J,Zhang Y,Sun X,Tang K

更新日期：2006-12-25 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:MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes at the post-transcriptional level in spatiotemporal manner. Several miRNAs are identified as prognostic and diagnostic markers in many human cancers. Estimation of the temporal activities of the miRNAs is an important step in the way to underst...

journal_title：BMC genomics

authors： Jayavelu ND,Bar N

更新日期：2015-12-18 00:00:00

abstract：BACKGROUND:Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence T...

journal_title：BMC genomics

authors： Ponyared P,Ponsawat J,Tongsima S,Seresangtakul P,Akkasaeng C,Tantisuwichwong N

更新日期：2016-12-22 00:00:00