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- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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| 2. |
- Edwards, N.V., et al.
(författare)
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Optical characterization of wide bandgap semiconductors
- 2000
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Ingår i: Thin Solid Films. - 0040-6090 .- 1879-2731. ; 364:1, s. 98-106
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Tidskriftsartikel (refereegranskat)abstract
- Our work primarily concerns the characterization of wide-gap III-V nitride semiconductors, nondestructively and at variable temperature, with spectroscopic ellipsometry (SE) and reflectometry in the spectral range from 1.5 to 6 eV. In the case of GaN, there are three main concerns associated with such data: (a) the quantification of the dispersion of the index of refraction with energy, (b) the removal of surface overlayers in real-time, and (c) the determination of the variation of valence bands with biaxial stress and the quantification of residual stress in thin films. The SE and reflectance capabilities provide (1) broadband spectra from 1.5 to 6 eV, which yield information about (a) below the bandgap and (b) above it, and (2) high resolution spectra (less than 1 meV at 3.4 eV) in the vicinity of the gap (3.3-3.6 eV), which enables (c). Here we will discuss issues concerning the relation of (c) to GaN material and growth parameters, though similar data for other wide bandgap materials will be discussed where relevant. Specifically, optimal heterostructure design for potential valence band engineering applications will be discussed in the context of trends in residual stress as a function of film thickness, growth temperature and substrate orientation for GaN/AlN/6H-SiC heterostructures. Standard heterostructures are mostly compressive for samples less than about 0.7 µm thick, are tensile up to about 2 µm and then abruptly become less tensile with stress values near 1 kbar thereafter. Additionally, these trends can be circumvented for moderately thick (approximately 2 µm) GaN layers (normally>2 kbar, tensile) by the introduction of a `buried interface' approach, namely, a strain mediating layer (SML) above the standard high-temperature AlN buffer layer designed to yield a range of compressive stresses from 0 to 2 kbar. The strain characteristics but also the growth rates of subsequently deposited nitride layers can be modulated by changing the growth parameters of the SML. This is achieved by in situ techniques during crystal growth without degrading the optical and structural properties of the deposited layer, as confirmed by XRD, SEM, PL, and AFM data taken on the overlying GaN layers. These results are interpreted in terms of coefficient of thermal expansion data for the layers and data concerning the planarization of GaN layers and growth behavior in non-(0001) directions.
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