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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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Proceedings ArticleDOI
18 Apr 2002
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 very high success rate. Application of the methods to breast cancer data seems to reveal significant local patterns.Our algorithm can be used to discover more than one OPSM within the same data set, even when these OPSMs overlap. It can also be adapted to handle relaxations and extensions of the OPSM condition. For example, we may allow the different rows of G x T to induce similar but not identical orderings of the columns, or we may allow the set T to include more than one representative of each stage of a biological process.

495 citations

Journal ArticleDOI
TL;DR: This work presents an elucidation of the electronic biosensing mechanisms with a newly developed microarray of nanotube "micromat" sensors and reveals that electronic effects occurring at the metal-nanotube contacts due to protein adsorption constitute a more significant contribution to the Electronic biosensing signal than adsorbed solely along the exposed lengths of the nanotubes.
Abstract: It has been reported that protein adsorption on single-walled carbon nanotube field effect transistors (FETs) leads to appreciable changes in the electrical conductance of the devices, a phenomenon that can be exploited for label-free detection of biomolecules with a high potential for miniaturization. This work presents an elucidation of the electronic biosensing mechanisms with a newly developed microarray of nanotube “micromat” sensors. Chemical functionalization schemes are devised to block selected components of the devices from protein adsorption, self-assembled monolayers (SAMs) of methoxy(poly(ethylene glycol))thiol (mPEG-SH) on the metal electrodes (Au, Pd) and PEG-containing surfactants on the nanotubes. Extensive characterization reveals that electronic effects occurring at the metal−nanotube contacts due to protein adsorption constitute a more significant contribution to the electronic biosensing signal than adsorption solely along the exposed lengths of the nanotubes.

490 citations

Proceedings ArticleDOI
02 Nov 2005
TL;DR: Cyclops as discussed by the authors is a small camera device 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.

489 citations

Journal ArticleDOI
TL;DR: This method is simple, rapid, and selective compared with conventional techniques and could be readily applied to the analysis of free amino acids in soy sauce.
Abstract: A method for the determination of underivatized amino acids based on capillary electrophoresis coupled to electrospray ionization mass spectrometry (CE-ESI-MS) is described. To analyze free amino acids simultaneously a low acidic pH condition was used to confer positive charge on whole amino acids. The choice of the electrolyte and its concentration influenced resolution and peak shape of the amino acids, and 1 M formic acid was selected as the optimal electrolyte. Meanwhile, the sheath liquid composition had a significant effect on sensitivity and the highest sensitivity was obtained when 5 mM ammonium acetate in 50% (v/v) methanol-water was used. Protonated amino acids were roughly separated by CE and selectively detected by a quadrupole mass spectrometer with a sheath flow electrospray ionization interface. Under the optimized conditions, 19 free amino acids normally found in proteins and several physiological amino acids were well determined in less than 17 min. The detection limits for basic amino acids were between 0.3 and 1.1 mumol/L and for acidic and low molecular weight amino acids were less than 6.0 mumol/L with pressure injection of 50 mbar for 3 s (3 nL) at a signal-to-noise ratio of 3. This method is simple, rapid, and selective compared with conventional techniques and could be readily applied to the analysis of free amino acids in soy sauce.

484 citations

Journal ArticleDOI
TL;DR: A method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters is devised and applied to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences.
Abstract: Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited. We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences. Our analyses reveal a clear relationship between expression and binding-site multiplicity, as well as dependencies of expression on the distance between transcription-factor binding sites and gene starts which are transcription-factor specific, including a striking ~10-bp periodic relationship between gene expression and binding-site location. We show how this approach can measure transcription-factor sequence specificities and the sensitivity of transcription-factor sites to the surrounding sequence context, and compare the activity of 75 yeast transcription factors. Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control.

483 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