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BMC Genomics
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#1Georgina Mansell (University of Exeter)H-Index: 2
#2Tyler J. Gorrie-Stone (University of Essex)H-Index: 3
Last.Eilis Hannon (University of Exeter)H-Index: 20
view all 7 authors...
Background There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study design and interpretation have been discussed in detail, however there are analytical concerns that are outstanding and require further exploration. In this study we seek to address three analytical issues. First, we quantify the multiple testing burden and propose a standard stati...
2 CitationsSource
#1Pritha Ghosh (NCBS: National Centre for Biological Sciences)H-Index: 7
#2Adwait G. Joshi (NCBS: National Centre for Biological Sciences)H-Index: 3
Last.Ramanathan Sowdhamini (NCBS: National Centre for Biological Sciences)H-Index: 28
view all 5 authors...
The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism into a comprehensive database named EcRBPome. It contains RBPs recorded from 614 complete E. coli proteomes available in the RefSeq database (as of O...
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#1Cihangir Yandim (IUE: İzmir University of Economics)H-Index: 4
#2Gökhan Karakülah (Dokuz Eylül University)H-Index: 6
The last decade witnessed a number of genome-wide studies on human pre-implantation, which mostly focused on genes and provided only limited information on repeats, excluding the satellites. Considering the fact that repeats constitute a large portion of our genome with reported links to human physiology and disease, a thorough understanding of their spatiotemporal regulation during human embryogenesis will give invaluable clues on chromatin dynamics across time and space. Therefore, we performe...
2 CitationsSource
#1Samiullah Khan (University of Adelaide)H-Index: 2
#2Shu-Biao Wu (UNE: University of New England (Australia))H-Index: 16
Last.J. R. Roberts (UNE: University of New England (Australia))H-Index: 15
view all 3 authors...
Eggshell formation takes place in the shell gland of the oviduct of laying hens. The eggshell is rich in calcium and various glycoproteins synthesised in the shell gland. Although studies have identified genes involved in eggshell formation, little is known about the regulation of genes in the shell gland particularly in a temporal manner. The current study investigated the global gene expression profile of the shell gland of laying hens at different time-points of eggshell formation using RNA-S...
2 CitationsSource
#1Christian P. Kubicek (TU Wien: Vienna University of Technology)H-Index: 68
#2Andrei Stecca Steindorff (UnB: University of Brasília)H-Index: 1
Last.Irina S. Druzhinina (NAU: Nanjing Agricultural University)H-Index: 44
view all 17 authors...
The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the inn...
1 CitationsSource
#1Weixi Li (NAU: Nanjing Agricultural University)H-Index: 2
#2Dayong Zhang (NAU: Nanjing Agricultural University)H-Index: 1
Last.GUOWangzhen (NAU: Nanjing Agricultural University)H-Index: 33
view all 5 authors...
Background Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. The availability of the whole-genome data of different cotton species allows us to study systematic evolution and function of cotton AQPs on a genome-wide level.
1 CitationsSource
#1Xing Wu (Yale University)
#2Christopher Heffelfinger (Yale University)H-Index: 11
Last.Stephen L. Dellaporta (Yale University)H-Index: 34
view all 4 authors...
The ability to accurately and comprehensively identify genomic variations is critical for plant studies utilizing high-throughput sequencing. Most bioinformatics tools for processing next-generation sequencing data were originally developed and tested in human studies, raising questions as to their efficacy for plant research. A detailed evaluation of the entire variant calling pipeline, including alignment, variant calling, variant filtering, and imputation was performed on different programs u...
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#1Hiroya Oka (Nagoya University)H-Index: 1
#2Takaaki Kojima (Nagoya University)H-Index: 11
Last.Hideo Nakano (Nagoya University)H-Index: 26
view all 5 authors...
Transcription factors (TFs) specifically bind to DNA sequences and control the expression of target genes. AoXlnR is a key TF involved in the expression of xylanolytic and cellulolytic enzymes in the filamentous fungi, Aspergillus oryzae. Genomic SELEX-Seq (gSELEX-Seq) can reveal the in vitro binding sites of a TF in a genome. To date, the gene expression network controlled by AoXlnR in A. oryzae is not fully explored. In this study, the data from gSELEX-Seq analysis and data mining were applied...
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#1Navneet Kaur (ARS: Agricultural Research Service)H-Index: 12
#2Wenbo Chen (Boyce Thompson Institute for Plant Research)H-Index: 7
Last.William M. Wintermantel (ARS: Agricultural Research Service)H-Index: 22
view all 4 authors...
Cucurbit yellow stunting disorder virus (CYSDV; genus Crinivirus, Closteroviridae) is transmitted in a semipersistent manner by the whitefly, Bemisia tabaci, and is efficiently transmitted by the widely prevalent B. tabaci cryptic species, MEAM1. In this study, we compared transcriptome profiles of B. tabaci MEAM1, after 24 h, 72 h and 7 days of acquisition feeding on melon plants infected with CYSDV (CYSDV-whiteflies) with those fed on virus-free melon, using RNA-Seq technology. We also compare...
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#1Carolina M. Rodrigues (American Physical Therapy Association)H-Index: 9
#2Marco A. Takita (American Physical Therapy Association)H-Index: 21
Last.Marcos Antonio Machado (American Physical Therapy Association)H-Index: 37
view all 5 authors...
Background Citrus are among the most important crops in the world. However, there are many diseases that affect Citrus caused by different pathogens. Citrus also hosts many symbiotic microorganisms in a relationship that may be advantageous for both organisms. The fungi Phyllosticta citricarpa, responsible for citrus black spot, and Phyllosticta capitalensis, an endophytic species, are examples of closely related species with different behavior in citrus. Both species are always biologically ass...
1 CitationsSource
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