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Genomics Data
ISSN 2213-5960 · Elsevier · 712 artikel di indeks
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Artikel Jurnal
Complete genome sequence of Luteibacter rhizovicinus strain LJ96T, isolated from the rhizosphere of barley (Hordeum vulgare L.) in Denmark
We present the complete genome sequence of Luteibacter rhizovicinus type strain LJ96T, a yellow-pigmented gammaproteobacterium isolated from the rhizosphere of barley (Hordeum vulgare) Johansen et al. (2005) , a species with numerous potential applications. The genome sequence was deposited to NCBI…
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Artikel Jurnal
Cataloguing the bacterial community of the Great Salt Plains, Oklahoma using 16S rRNA based metagenomics pyrosequencing
The Great Salt Plains of Oklahoma (GSP) is an extreme region, a hypersaline environment from marine origin and a unique area of the Salt National Wild Refuge in the north-central region of Oklahoma. In this study we analyzed the diversity and distribution of bacteria in two habitats; vegetated…
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Artikel Jurnal
Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC)
Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC (n = 97). Six hub genes (CCNB2, CDC20, CEP55, KIF20A, TOP2A and…
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Artikel Jurnal
Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India
Mine tailings from copper mines are considered as one of the sources of highly hazardous acid mine drainage (AMD) due to bio-oxidation of its sulfidic constituents. This study was designed to understand microbial community composition and potential for acid generation using samples from mine…
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Artikel Jurnal
RNA-Seq analysis of human cell lines established from normal and neoplastic esophageal squamous epithelium
Esophageal cancer (EC) is the eighth most common cancer globally in 2012 and predominantly occurs in the man (Enzinger and Mayer, 2003; Conteduca et al., 2012). EC is classified mainly into two types, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma, accounting for 60–70% and…
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Artikel Jurnal
Genome-wide analysis of mouse cortical neurons lacking miR-27b
MicroRNAs (miRNAs), short non-coding RNAs that repress gene expression [1], have recently emerged as important regulators of synaptic transmission and plasticity in the central nervous system [2]. This suggests an important role of this gene silencing mechanism in brain function both in health and…
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Artikel Jurnal
Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA
Savannah River Site (SRS), an approximately 800-km2 former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistant to…
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Artikel Jurnal
A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam
Metagenomic approach was used to understand the structural and functional diversity present in arsenic contaminated groundwater of the Ganges Brahmaputra Delta aquifer system. A metagene dataset (coded as TTGW1) of 89,171 sequences (totaling 125,449,864 base pairs) with an average length of 1406…
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Artikel Jurnal
Transcriptome analysis of the Chinese giant salamander (Andrias davidianus) using RNA-sequencing
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total…
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Artikel Jurnal
Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s.
The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the…
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Artikel Jurnal
Cultivar-specific transcriptome prediction and annotation in Ficus carica L.
The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study…
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Artikel Jurnal
Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem
Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04 Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G + C content of 53%…
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Artikel Jurnal
Molecular characterization of endophytic fungi associated with the roots of Chenopodium quinoa inhabiting the Atacama Desert, Chile
Plant roots can be highly colonized by fungal endophytes. This seems to be of particular importance for the survival of plants inhabiting stressful habitats. This study focused on the Identification of the fungal endophytic community associated with the roots of quinoa plants (Chenopodium quinoa)…
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Artikel Jurnal
Novel quorum quenching enzymes identified from draft genome of Roseomonas sp. TAS13
Roseomonas sp. strain TAS13 isolated from an activated sludge sample degrades N-acylhomoserine lactones (AHLs) that are widely utilized as a signal in bacterial quorum sensing systems. The draft genome of Roseomonas sp. TAS13 contains 816 contigs (total 5,078,941 bp) which carries 4760…
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Artikel Jurnal
APMicroDB: A microsatellite database of Acyrthosiphon pisum
Pea aphids represent a complex genetic system that could be used for QTL analysis, genetic diversity and population genetics studies. Here, we described the development of first microsatellite repeat database of the pea aphid (APMicroDB), accessible at “http://deepaklab.com/aphidmicrodb”. We…
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Artikel Jurnal
Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus)
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we…
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Artikel Jurnal
Impact of aspirin on the transcriptome of Streptococcus pneumoniae D39
Aspirin or acetylsalicylic acid (ASA) is a medicine used to treat pain, fever, and inflammation. Here, we for the very first time reported the genome-wide transcriptional profiling of aspirin-regulated genes in Streptococcus pneumoniae in the presence of 5 mM aspirin in chemically-defined medium…
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Artikel Jurnal
Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat
Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample collected from the coastal region of Gujarat, India, from a surface water stream. Based on 16sRNA sequencing, the organism was identified as Salinicoccus sp. BAB 3246 (Genebank ID: KF889285). The present work…
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Artikel Jurnal
Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells
Constitutional biological processes involve the generation of DNA double-strand breaks (DSBs). The production of such breaks and their subsequent resolution are also highly relevant to neurodegenerative diseases and cancer, in which extensive DNA fragmentation has been described Stephens et al…