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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: The results indicate that each method for analysis of microRNA expression has its strengths and weaknesses, which help to guide informed selection of a quantitative microRNA gene expression platform for particular study goals.
Abstract: MicroRNAs are important negative regulators of protein-coding gene expression and have been studied intensively over the past years. Several measurement platforms have been developed to determine relative miRNA abundance in biological samples using different technologies such as small RNA sequencing, reverse transcription-quantitative PCR (RT-qPCR) and (microarray) hybridization. In this study, we systematically compared 12 commercially available platforms for analysis of microRNA expression. We measured an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples and synthetic spikes from microRNA family members with varying homology. We developed robust quality metrics to objectively assess platform performance in terms of reproducibility, sensitivity, accuracy, specificity and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which help to guide informed selection of a quantitative microRNA gene expression platform for particular study goals.

515 citations

Journal Article
TL;DR: A small camera device called Cyclops is developed that bridges the gap between the computationally constrained wireless sensor nodes such as Motes, and CMOS imagers which, while low power and inexpensive, are nevertheless designed to mate with resource-rich hosts.
Abstract: Despite their increasing sophistication, wireless sensor networks still do not exploit the most powerful of the human senses: vision. Indeed, vision provides humans with unmatched capabilities to distinguish objects and identify their importance. Our work seeks to provide sensor networks with similar capabilities by exploiting emerging, cheap, low-power and small form factor CMOS imaging technology. In fact, we can go beyond the stereo capabilities of human vision, and exploit the large scale of sensor networks to provide multiple, widely different perspectives of the physical phenomena. To this end, we have developed a small camera device called Cyclops that bridges the gap between the computationally constrained wireless sensor nodes such as Motes, and CMOS imagers which, while low power and inexpensive, are nevertheless designed to mate with resource-rich hosts. Cyclops enables development of new class of vision applications that span across wireless sensor network. We describe our hardware and software architecture, its temporal and power characteristics and present some representative applications.

514 citations

Journal ArticleDOI
TL;DR: It is shown that targeting oligonucleotides released from programmable microarrays can be used to capture and amplify ∼10,000 human exons in a single multiplex reaction, and it is anticipated that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing ofhuman exons at a fraction of the cost of whole-genome resequenced.
Abstract: A new generation of technologies is poised to reduce DNA sequencing costs by several orders of magnitude. But our ability to fully leverage the power of these technologies is crippled by the absence of suitable 'front-end' methods for isolating complex subsets of a mammalian genome at a scale that matches the throughput at which these platforms will routinely operate. We show that targeting oligonucleotides released from programmable microarrays can be used to capture and amplify approximately 10,000 human exons in a single multiplex reaction. Additionally, we show integration of this protocol with ultra-high-throughput sequencing for targeted variation discovery. Although the multiplex capture reaction is highly specific, we found that nonuniform capture is a key issue that will need to be resolved by additional optimization. We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing.

509 citations

Journal ArticleDOI
TL;DR: Cumulatively, these comparisons indicate that data quality is essentially equivalent between the one- and two-color approaches and strongly suggest that this variable need not be a primary factor in decisions regarding experimental microarray design.
Abstract: Microarray-based expression profiling experiments typically use either a one-color or a two-color design to measure mRNA abundance. The validity of each approach has been amply demonstrated. Here we provide a simultaneous comparison of results from one- and two-color labeling designs, using two independent RNA samples from the Microarray Quality Control (MAQC) project, tested on each of three different microarray platforms. The data were evaluated in terms of reproducibility, specificity, sensitivity and accuracy to determine if the two approaches provide comparable results. For each of the three microarray platforms tested, the results show good agreement with high correlation coefficients and high concordance of differentially expressed gene lists within each platform. Cumulatively, these comparisons indicate that data quality is essentially equivalent between the one- and two-color approaches and strongly suggest that this variable need not be a primary factor in decisions regarding experimental microarray design.

505 citations

Journal ArticleDOI
TL;DR: A probabilistic model in which an OPSM is hidden within an otherwise random matrix is defined, and an efficient algorithm is developed for finding the hidden OPSM in the random matrix.
Abstract: This paper concerns the discovery of patterns in gene expression matrices, in which each element gives the expression level of a given gene in a given experiment. Most existing methods for pattern discovery in such matrices are based on clustering genes by comparing their expression levels in all experiments, or clustering experiments by comparing their expression levels for all genes. Our work goes beyond such global approaches by looking for local patterns that manifest themselves when we focus simultaneously on a subset G of the genes and a subset T of the experiments. Specifically, we look for order-preserving submatrices (OPSMs), in which the expression levels of all genes induce the same linear ordering of the experiments (we show that the OPSM search problem is NP-hard in the worst case). Such a pattern might arise, for example, if the experiments in T represent distinct stages in the progress of a disease or in a cellular process and the expression levels of all genes in G vary across the stages in the same way. We define a probabilistic model in which an OPSM is hidden within an otherwise random matrix. Guided by this model, we develop an efficient algorithm for finding the hidden OPSM in the random matrix. In data generated according to the model, the algorithm recovers the hidden OPSM with a very high success rate. Application of the methods to breast cancer data seem to reveal significant local patterns.

503 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