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Institution

Agilent Technologies

CompanySanta Clara, California, United States
About: Agilent Technologies is a company organization based out in Santa Clara, California, United States. It is known for research contribution in the topics: Signal & Mass spectrometry. The organization has 7398 authors who have published 11518 publications receiving 262410 citations. The organization is also known as: Agilent Technologies, Inc..


Papers
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Journal ArticleDOI
TL;DR: This review serves to summarize the available literature on the impacts of fermentation in coffee processing on coffee aroma as well as other unconventional avenues where fermentation is employed for coffee aroma modulation.

178 citations

Journal ArticleDOI
TL;DR: When the method was applied to two pairs of sibling human embryonic stem cell lines, the sibling lines were more similar in allele-specific expression than were the genetically unrelated lines, suggesting the presence of tissue-specific cis regulation.
Abstract: We developed a digital RNA allelotyping method for quantitatively interrogating allele-specific gene expression. This method involves ultra-deep sequencing of padlock captured SNPs from the transcriptome. We characterized four cell lines established from two human subjects in the Personal Genome Project. Approximately 11–22% of the heterozygous mRNA-associated SNPs show allele-specific expression in each cell line; and 4.3–8.5% are tissue-specific, suggesting the presence of tissue-specific cis-regulation. When applied to two pairs of sibling human embryonic stem cell lines, the sibling lines were more similar in allele-specific expression than were the genetically unrelated lines. We found that the variation of allelic ratios in gene expression among different cell lines is primarily explained by genetic variations, much more so than by specific tissue types or culturing conditions. Comparison of expressed SNPs on the sense and anti-sense transcripts suggested that allelic ratios are primarily determined by cis-regulatory mechanisms on the sense transcripts.

178 citations

Journal ArticleDOI
TL;DR: RNA titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples.
Abstract: We have assessed the utility of RNA titration samples for evaluating microarray platform performance and the impact of different normalization methods on the results obtained. As part of the MicroArray Quality Control project, we investigated the performance of five commercial microarray platforms using two independent RNA samples and two titration mixtures of these samples. Focusing on 12,091 genes common across all platforms, we determined the ability of each platform to detect the correct titration response across the samples. Global deviations from the response predicted by the titration ratios were observed. These differences could be explained by variations in relative amounts of messenger RNA as a fraction of total RNA between the two independent samples. Overall, both the qualitative and quantitative correspondence across platforms was high. In summary, titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples.

178 citations

Journal ArticleDOI
TL;DR: In this paper, the authors performed a comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen and found that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection.
Abstract: Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood. We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection. We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.

177 citations


Authors

Showing all 7402 results

NameH-indexPapersCitations
Hongjie Dai197570182579
Zhuang Liu14953587662
Jie Liu131153168891
Thomas Quertermous10340552437
John E. Bowers102176749290
Roy G. Gordon8944931058
Masaru Tomita7667740415
Stuart Lindsay7434722224
Ron Shamir7431923670
W. Richard McCombie7114464155
Tomoyoshi Soga7139221209
Michael R. Krames6532118448
Shabaz Mohammed6418817254
Geert Leus6260919492
Giuseppe Gigli6154115159
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
20231
20228
2021142
2020157
2019168
2018164