Sat, 26 Jul 2008 04:37:08 BST CiteULike: Tag array http://www.citeulike.org/tag/array CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/zeroisland/article/1898498 <i>Journal of Applied Physics, Vol. 87, No. 1. (2000), pp. 345-352.</i><br /><br />Email Address: Temperature behavior of multiple tunnel junction devices based on disordered dot arrays AS Cordan Y Leroy A Goltzené A Pépin C Vieu M Mejias H Launois Journal of Applied Physics, Vol. 87, No. 1. (2000), pp. 345-352. 2007-11-11T12:08:32-00:00 2000 Journal of Applied Physics 87 1 345 352 AIP array current nc transport http://www.citeulike.org/user/yoanjacquemin/article/2394654 <i>Bioinformatics, Vol. 17, No. 11. (November 2001), pp. 1067-1076.</i><br /><br />MOTIVATION: High density DNA oligo microarrays are widely used in biomedical research. Selection of optimal DNA oligos that are deposited on the microarrays is critical. Based on sequence information and hybridization free energy, we developed a new algorithm to select optimal short (20-25 bases) or long (50 or 70 bases) oligos from genes or open reading frames (ORFs) and predict their hybridization behavior. Having optimized probes for each gene is valuable for two reasons. By minimizing background hybridization they provide more accurate determinations of true expression levels. Having optimum probes minimizes the number of probes needed per gene, thereby decreasing the cost of each microarray, raising the number of genes on each chip and increasing its usage. RESULTS: In this paper we describe algorithms to optimize the selection of specific probes for each gene in an entire genome. The criteria for truly optimum probes are easily stated but they are not computable at all levels currently. We have developed an heuristic approach that is efficiently computable at all levels and should provide a good approximation to the true optimum set. We have run the program on the complete genomes for several model organisms and deposited the results in a database that is available on-line (http://ural.wustl.edu/~lif/probe.pl). AVAILABILITY: The program is available upon request. Selection of optimal DNA oligos for gene expression arrays. F Li GD Stormo Bioinformatics, Vol. 17, No. 11. (November 2001), pp. 1067-1076. 2008-02-18T14:58:37-00:00 2001 Bioinformatics 1367-4803 17 11 1067 1076 array probe http://www.citeulike.org/user/yoanjacquemin/article/100059 <i>Biochemistry, Vol. 35, No. 11. (19 March 1996), pp. 3555-3562.</i><br /><br />Thermodynamic data were determined from UV absorbance vs temperature profiles of 23 oligonucleotides. These data were combined with data from the literature for 21 sequences to derive improved parameters for the 10 Watson-Crick nearest neighbors. The observed trend in nearest-neighbor stabilities at 37 degrees C is GC > CG > GG > GA approximately GT approximately CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. On average, the improved parameters predict deltaG degrees(37), deltaH degrees, deltaS degrees, and T(m) within 4%, 7%, 8%, and 2 degrees C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaC1. Improved nearest-neighbor parameters for predicting DNA duplex stability. J SantaLucia HT Allawi PA Seneviratne doi:10.1021/bi951907q Biochemistry, Vol. 35, No. 11. (19 March 1996), pp. 3555-3562. 2005-02-21T16:22:36-00:00 1996 Biochemistry 0006-2960 35 11 3555 3562 array probe http://www.citeulike.org/user/yoanjacquemin/article/586192 <i>Nucl. Acids Res., Vol. 31, No. 12. (15 June 2003), pp. 3057-3062.</i><br /><br />There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic DNA fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally specific to their respective targets to avoid any cross-hybridization and should not form stable secondary structures that may interfere with the labeled probes during hybridization. We have developed OligoArray 2.0, a program that designs specific oligonucleotides at the genomic scale. It uses a thermodynamic approach to predict secondary structures and to calculate the specificity of targets on chips for a unique probe in a mixture of labeled probes. Furthermore, OligoArray 2.0 can adjust the oligonucleotide length, according to user input, to fit a narrow Tm range compatible with hybridization requirements. Combined with on chip oligonucleotide synthesis, this program makes it feasible to perform expression analysis on a genomic scale for any organism for which the genome sequence is known. This is without relying on cDNA or oligonucleotide libraries. OligoArray 2.0 was used to design 75 764 oligonucleotides representing 26 140 transcripts from Arabidopsis thaliana. Among this set, we provide at least one specific oligonucleotide for 93% of these transcripts. 10.1093/nar/gkg426 OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach Jean-Marie Rouillard Michael Zuker Erdogan Gulari doi:10.1093/nar/gkg426 Nucl. Acids Res., Vol. 31, No. 12. (15 June 2003), pp. 3057-3062. 2006-04-14T06:08:46-00:00 2003 Nucl. Acids Res. 31 12 3057 3062 array probe http://www.citeulike.org/user/yanjiang/article/532057 <i>Science, Vol. 295, No. 5559. (22 February 2002), pp. 1503-1506.</i><br /><br />A DNA array detection method is reported in which the binding of oligonucleotides functionalized with gold nanoparticles leads to conductivity changes associated with target-probe binding events. The binding events localize gold nanoparticles in an electrode gap; silver deposition facilitated by these nanoparticles bridges the gap and leads to readily measurable conductivity changes. An unusual salt concentration-dependent hybridization behavior associated with these nanoparticle probes was exploited to achieve selectivity without a thermal-stringency wash. Using this method, we have detected target DNA at concentrations as low as 500 femtomolar with a point mutation selectivity factor of approximately 100,000:1. Array-based electrical detection of DNA with nanoparticle probes. SJ Park TA Taton CA Mirkin doi:10.1126/science.1067003 Science, Vol. 295, No. 5559. (22 February 2002), pp. 1503-1506. 2006-03-07T00:10:05-00:00 2002 Science 1095-9203 295 5559 1503 1506 array dna nanoparticle http://www.citeulike.org/user/vikasraykar/article/436423 <i>Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP '04). IEEE International Conference on, Vol. 4 (2004), pp. iv-69-iv-72 vol.4.</i><br /><br />We describe a method to determine automatically the relative three dimensional positions of multiple microphones using at least five loudspeakers in unknown positions. The only assumption we make is that there is a microphone which is very close to a loudspeaker. In our experimental setup, we attach one microphone to each loudspeaker. We derive the maximum likelihood estimator and the solution turns out to be a non-linear least squares problem. A closed form solution which can be used as the initial guess for the minimization routine is derived. We also derive an approximate expression for the covariance of the estimator using the implicit function theorem. Using this, we analyze the performance of the estimator with respect to the positions of the loudspeakers. The algorithm is validated using both Monte-Carlo simulations and a real-time experimental setup. Automatic position calibration of multiple microphones VC Raykar R Duraiswami Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP '04). IEEE International Conference on, Vol. 4 (2004), pp. iv-69-iv-72 vol.4. 2005-12-13T01:08:00-00:00 2004 Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP '04). IEEE International Conference on 4 iv-69 iv-72 vol.4 array calibration microphone http://www.citeulike.org/user/uz_labu_laimi/article/1139297 <i>Annu Rev Genomics Hum Genet, Vol. 6 (2005), pp. 331-354.</i><br /><br />Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results. Comparative genomic hybridization. D Pinkel DG Albertson doi:10.1146/annurev.genom.6.080604.162140 Annu Rev Genomics Hum Genet, Vol. 6 (2005), pp. 331-354. 2007-03-04T05:33:16-00:00 2005 Annu Rev Genomics Hum Genet 1527-8204 6 331 354 array cgh review http://www.citeulike.org/user/stajich/article/2341756 <i>BMC Bioinformatics, Vol. 9, No. 1. (2008)</i><br /><br />BACKGROUND:Illumina bead-based arrays are becoming increasingly popular due to their high degree of replication and reported high data quality. However, little attention has been paid to the pre-processing of Illumina data. In this paper, we present our experience of analysing the raw data from an Illumina spike-in experiment and offer guidelines for those wishing to analyse expression data or develop new methodologies for this technology.RESULTS:We find that the local background estimated by Illumina is consistently low, and subtracting this background is beneficial for detecting differential expression (DE). Illumina's summary method performs well at removing outliers; producing estimates which are less biased and are less variable than other robust summary methods. However, quality assessment on summarised data may miss spatial artefacts present in the raw data. Also, we find that the background normalisation method used in Illumina's proprietary software (BeadStudio) can cause problems with a standard DE analysis. We demonstrate that variances calculated from the raw data can be used as inverse weights in the DE analysis to improve power. Finally, variability in both expression levels and DE statistics can be attributed to differences in probe composition. These differences are not accounted for by current analysis methods and require further investigation.CONCLUSIONS:Analysing Illumina expression data using BeadStudio is reasonable because of the conservative estimates of summary values produced by the software. Improvements can however be made by not using background normalisation. Access to the raw data allows for a more detailed quality assessment and flexible analyses. In the case of a gene expression study, data can be analysed on an appropriate scale using established tools. Similar improvements can be expected for other Illumina assays. Statistical issues in the analysis of Illumina data Mark Dunning Nuno Morais Andy Lynch Simon Tavare Matthew Ritchie doi:10.1186/1471-2105-9-85 BMC Bioinformatics, Vol. 9, No. 1. (2008) 2008-02-06T14:10:49-00:00 2008 BMC Bioinformatics 9 1 array illumina methods shortread statistics http://www.citeulike.org/user/skirnir/article/2506629 <i>Advanced Materials, Vol. 18, No. 18. (2006), pp. 2444-2447.</i><br /><br />No abstract. Reversible Formation of Molecular Junctions in 2D Nanoparticle Arrays J Liao L Bernard M Langer C Schönenberger M Calame doi:10.1002/adma.200601001 Advanced Materials, Vol. 18, No. 18. (2006), pp. 2444-2447. 2008-03-11T09:49:43-00:00 2006 Advanced Materials 18 18 2444 2447 array colloids fabrication gold microcontact nanoparticles sam synthesis http://www.citeulike.org/user/shanewanick/article/2618052 <i>Anal Chem, Vol. 79, No. 15. (1 August 2007), pp. 5567-5573.</i><br /><br />This paper describes the design, modeling, and experimental characterization of an electrochemical sensor array for on-line monitoring of fermentor conditions in both miniaturized cell assays and in industrial scale fermentations. The viable biomass concentration is determined from impedance spectroscopy. As a miniaturized electrode configuration with high cell constant is applied, the spectral conductivity variation is monitored instead of the permittivity variation. The dissolved oxygen concentration is monitored amperometrically using an ultramicroelectrode array, which is shown to have negligible flow dependence. pH is monitored using an ion-sensitive field effect transistor (ISFET), and a platinum thermistor is included for temperature measurements. All sensors were shown to be sufficiently accurate within the range relevant to yeast fermentations. The sensor array is shown to be very stable and durable and withstands steam-sterilization. Integrated electrochemical sensor array for on-line monitoring of yeast fermentations. EE Krommenhoek JG Gardeniers JG Bomer X Li M Ottens GW van Dedem M Van Leeuwen WM van Gulik LA van der Wielen JJ Heijnen AA van den Berg doi:10.1021/ac0623078 Anal Chem, Vol. 79, No. 15. (1 August 2007), pp. 5567-5573. 2008-04-01T00:40:29-00:00 2007 Anal Chem 0003-2700 79 15 5567 5573 array fermentation http://www.citeulike.org/user/shanewanick/article/2621229 <i>Biotechnol. Prog., Vol. 15, No. 4. (6 August 1999), pp. 617-621.</i><br /><br />Abstract: The fermentability of lignocellulose hydrolyzates have been predicted from the responses of a combination of chemical gas sensors. The hydrolyzates were prepared by dilute-acid hydrolysis of wood from pine, aspen, birch, and spruce. The volatile emission from the hydrolyzates before fermentation was measured, and the sensor array response pattern was compared with the observed fermentability of the hydrolyzates, i.e. with the final ethanol concentration after fermentation and the maximum specific ethanol production rate. Two concentration parameters in the hydrolyzates, furfural and the sum of furfural and 5-(hydroxymethyl)furfural (HMF), were also predicted from the responses. The sensors used were metal oxide semiconductor field effect transistors (MOSFET), tin oxide semiconductor devices, and conductive polymer sensors configured in two sensor arrays. The sensor array response pattern was analyzed by principal component analysis and artificial neural networks. Predictions from artificial neural networks deviated from measured values with less than 15%. Predicting Fermentability of Wood Hydrolyzates with Responses from Electronic Noses CF Mandenius H Liden T Eklov MJ Taherzadeh G Liden doi:10.1021/bp990059d Biotechnol. Prog., Vol. 15, No. 4. (6 August 1999), pp. 617-621. 2008-04-01T23:32:41-00:00 1999 Biotechnol. Prog. 15 4 617 621 array fermentation http://www.citeulike.org/user/shanewanick/article/2621173 <i>Biotechnology and Bioengineering, Vol. 93, No. 5. (2006), pp. 880-886.</i><br /><br />Current attempts to produce ethanol from lignocellulosic biomass are focused on the optimization of pretreatment to reduce substrate recalcitrance and the improvement of enzymes for hydrolysis of the cellulose and hemicellulose components to produce fermentable sugars. Research aimed at optimizing both aspects of the bioconversion process involves assessment of the effects of multiple variables on enzyme efficiency, resulting in large factorial experiments with intensive assay requirements. A rapid assay for lignocellulose hydrolysis has been developed to address this need. Pretreated lignocellulose is formed into handsheets, which are then used to prepare small disks that are easily dispensed into microtiter plates. The hydrolysis of cellulose to glucose is estimated using an enzyme-coupled spectrophotometric assay. Using disks prepared from ethanol organosolv pretreated yellow poplar, it is shown that the assay generates data comparable with those produced by hydrolysis of pretreated yellow poplar pulp in Erlenmeyer flasks, followed by HPLC analysis of glucose. The assay shows considerable time and cost benefits over the standard assay protocol and is applicable to a broad range of lignocellulosic substrates. © 2005 Wiley Periodicals, Inc. A rapid microassay to evaluate enzymatic hydrolysis of lignocellulosic substrates Alex Berlin Vera Maximenko Renata Bura Kyu-Young Kang Neil Gilkes Jack Saddler doi:10.1002/bit.20783 Biotechnology and Bioengineering, Vol. 93, No. 5. (2006), pp. 880-886. 2008-04-01T23:02:06-00:00 2006 Biotechnology and Bioengineering 93 5 880 886 array hydrolysis http://www.citeulike.org/user/setar/article/151946 <i>Nat Genet, Vol. 29, No. 4. (December 2001), pp. 365-371.</i><br /><br />Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. A Brazma P Hingamp J Quackenbush G Sherlock P Spellman C Stoeckert J Aach W Ansorge CA Ball HC Causton T Gaasterland P Glenisson FC Holstege IF Kim V Markowitz JC Matese H Parkinson A Robinson U Sarkans S Schulze-Kremer J Stewart R Taylor J Vilo M Vingron doi:10.1038/ng1201-365 Nat Genet, Vol. 29, No. 4. (December 2001), pp. 365-371. 2005-04-07T11:33:49-00:00 2001 Nat Genet 1061-4036 29 4 365 371 array gene_expression ontology http://www.citeulike.org/user/setar/article/94827 <i>Nature Biotechnology, Vol. 23, No. 2. (16 January 2005), pp. 238-243.</i> Functional annotation and network reconstruction through cross-platform integration of microarray data Xianghong Zhou Ming-Chih Kao Haiyan Huang Angela Wong Juan Nunez-Iglesias Michael Primig Oscar Aparicio Caleb Finch Todd Morgan Wing Wong doi:10.1038/nbt1058 Nature Biotechnology, Vol. 23, No. 2. (16 January 2005), pp. 238-243. 2005-02-15T07:20:33-00:00 2005 Nature Biotechnology 1087-0156 23 2 238 243 Nature Publishing Group array cross_platform gene_expression http://www.citeulike.org/user/scblackman/article/92031 <i>Neoplasia, Vol. 7, No. 1. (January 2005), pp. 7-16.</i> Gene Expression Profile of Glioblastoma Multiforme Invasive Phenotype Points to New Therapeutic Targets Dominique Hoelzinger Luigi Mariani Joachim Weis Tanja Woyke Theresa Berens Wendy Mcdonough Andrew Sloan Stephen Coons Michael Berens doi:10.1593/neo.04535 Neoplasia, Vol. 7, No. 1. (January 2005), pp. 7-16. 2005-02-10T03:19:31-00:00 2005 Neoplasia 1522-8002 7 1 7 16 Neoplasia Press array gbm invasion http://www.citeulike.org/user/samal/article/482101 <i>PNAS, Vol. 103, No. 4. (24 January 2006), pp. 867-872.</i><br /><br />Determining the sequence-recognition properties of DNA-binding proteins and small molecules remains a major challenge. To address this need, we have developed a high-throughput approach that provides a comprehensive profile of the binding properties of DNA-binding molecules. The approach is based on displaying every permutation of a duplex DNA sequence (up to 10 positional variants) on a microfabricated array. The entire sequence space is interrogated simultaneously, and the affinity of a DNA-binding molecule for every sequence is obtained in a rapid, unbiased, and unsupervised manner. Using this platform, we have determined the full molecular recognition profile of an engineered small molecule and a eukaryotic transcription factor. The approach also yielded unique insights into the altered sequence-recognition landscapes as a result of cooperative assembly of DNA-binding molecules in a ternary complex. Solution studies strongly corroborated the sequence preferences identified by the array analysis. Defining the sequence-recognition profile of DNA-binding molecules Christopher Warren Natasha Kratochvil Karl Hauschild Shane Foister Mary Brezinski Peter Dervan George Phillips Aseem Ansari doi:10.1073/pnas.0509843102 PNAS, Vol. 103, No. 4. (24 January 2006), pp. 867-872. 2006-01-26T22:16:34-00:00 2006 PNAS 103 4 867 872 array binding factor selex transcription http://www.citeulike.org/user/samal/article/710941 <i>Proc Natl Acad Sci U S A (19 June 2006)</i><br /><br />Analyses of whole-genome sequences and experimental data sets have revealed a large number of DNA sequence motifs that are conserved in many species and may be functional. However, methods of sufficient scale to explore the roles of these elements are lacking. We describe the use of protein arrays to identify proteins that bind to DNA sequences of interest. A microarray of 282 known and potential yeast transcription factors was produced and probed with oligonucleotides of evolutionarily conserved sequences that are potentially functional. Transcription factors that bound to specific DNA sequences were identified. One previously uncharacterized DNA-binding protein, Yjl103, was characterized in detail. We defined the binding site for this protein and identified a number of its target genes, many of which are involved in stress response and oxidative phosphorylation. Protein microarrays offer a high-throughput method for determining DNA-protein interactions. Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Su-Wen Ho Ghil Jona Christina T L Chen Mark Johnston Michael Snyder doi:10.1073/pnas.0509185103 Proc Natl Acad Sci U S A (19 June 2006) 2006-06-26T11:14:05-00:00 2006 Proc Natl Acad Sci U S A 0027-8424 array protein transcription http://www.citeulike.org/user/rodney/article/1621514 <i>Journal of Vacuum Science \amp Technology B: Microelectronics and Nanometer Structures, Volume 14, Issue 3, May 1996, pp.2005-2007, Vol. 14 (May 1996), pp. 2005-2007.</i><br /><br />Not Available Fabrication of sub-0.5 micron diameter cobalt dots on silicon substrates and photoresist pedestals on 50 cm × 50 cm glass substrates using laser interference lithograph JP Spallas RD Boyd JA Britten A Fernandez AM Hawryluk MD Perry DR Kania Journal of Vacuum Science \amp Technology B: Microelectronics and Nanometer Structures, Volume 14, Issue 3, May 1996, pp.2005-2007, Vol. 14 (May 1996), pp. 2005-2007. 2007-09-04T22:59:07-00:00 1996 Journal of Vacuum Science \amp Technology B: Microelectronics and Nanometer Structures, Volume 14, Issue 3, May 1996, pp.2005-2007 14 2005 2007 array cobalt dots fabrication glass holography interference large-field lithography pedestals photolithography photoresist resist silicon submicron substrates http://www.citeulike.org/user/rodney/article/1621511 <i>Journal of Vacuum Science \amp Technology B: Microelectronics and Nanometer Structures, Volume 13, Issue 5, September 1995, pp.1973-1978, Vol. 13 (September 1995), pp. 1973-1978.</i><br /><br />Not Available Field emitter array mask patterning using laser interference lithography JP Spallas AM Hawryluk DR Kania Journal of Vacuum Science \amp Technology B: Microelectronics and Nanometer Structures, Volume 13, Issue 5, September 1995, pp.1973-1978, Vol. 13 (September 1995), pp. 1973-1978. 2007-09-04T22:54:34-00:00 1995 Journal of Vacuum Science \amp Technology B: Microelectronics and Nanometer Structures, Volume 13, Issue 5, September 1995, pp.1973-1978 13 1973 1978 array emitter field holography interference lithography mask pattern photolithography http://www.citeulike.org/user/rodney/article/1826135 <i>Nat Mater, Vol. 3, No. 1. (January 2004), pp. 9-10.</i> Microfluidics: Sorting particles with light Jesper Gluckstad doi:10.1038/nmat1041 Nat Mater, Vol. 3, No. 1. (January 2004), pp. 9-10. 2007-10-26T18:16:22-00:00 2004 Nat Mater 3 1 9 10 array microfluidics microparticles optical sorting tweezers http://www.citeulike.org/user/rodney/article/1826130 <i>Nat Mater, Vol. 4, No. 8. (2005), pp. 579-580.</i> Micromanipulation: Optoelectronic tweezers Kishan Dholakia doi:10.1038/nmat1436 Nat Mater, Vol. 4, No. 8. (2005), pp. 579-580. 2007-10-26T18:12:59-00:00 2005 Nat Mater 4 8 579 580 array large-field manipulation optical optoelectronic tweezers http://www.citeulike.org/user/rodney/article/260532 <i>Nature, Vol. 436, No. 7049., pp. 370-372.</i> Massively parallel manipulation of single cells and microparticles using optical images Pei Chiou Aaron Ohta Ming Wu doi:10.1038/nature03831 Nature, Vol. 436, No. 7049., pp. 370-372. 2005-07-21T05:11:07-00:00 Nature 0028-0836 436 7049 370 372 Nature Publishing Group array microparticles optical optoelectronic parallel tweezers http://www.citeulike.org/user/rodney/article/1606150 <i>The Journal of Chemical Physics, Vol. 111, No. 10. (1999), pp. 4817-4826.</i><br /><br />The calculation of hydrodynamic properties of macromolecules in terms of bead models requires an adequate description of the hydrodynamic interaction between the spherical elements. For this purpose, the original or modified Oseen tensor are customarily used, although it has been shown that this simple description may lead to erroneous results, particularly for rotational coefficients. In this paper we study several more elaborate theories for multisphere systems. We apply those treatments to our problem of rigid bead models, implementing them in computer programs, and making calculations for various test structures. The comparison of the results from the various theories, and from other, presumably very accurate procedures, allow us to give some guidelines to improve the treatment of hydrodynamic interactions in macromolecular bead models. These advances are introduced in new versions of our public-domain computer software. ©1999 American Institute of Physics. Improved hydrodynamic interaction in macromolecular bead models B Carrasco Garc\ia doi:10.1063/1.479743 The Journal of Chemical Physics, Vol. 111, No. 10. (1999), pp. 4817-4826. 2007-08-29T20:49:24-00:00 1999 The Journal of Chemical Physics 111 10 4817 4826 AIP array beads chain diffusion dimer doublet hydrodynamic linear microparticles rotation simulation translation http://www.citeulike.org/user/rodney/article/942299 <i>Science, Vol. 251, No. 4995. (15 February 1991), pp. 767-773.</i><br /><br />Solid-phase chemistry, photolabile protecting groups, and photolithography have been combined to achieve light-directed, spatially addressable parallel chemical synthesis to yield a highly diverse set of chemical products. Binary masking, one of many possible combinatorial synthesis strategies, yields 2n compounds in n chemical steps. An array of 1024 peptides was synthesized in ten steps, and its interaction with a monoclonal antibody was assayed by epifluorescence microscopy. High-density arrays formed by light-directed synthesis are potentially rich sources of chemical diversity for discovering new ligands that bind to biological receptors and for elucidating principles governing molecular interactions. The generality of this approach is illustrated by the light-directed synthesis of a dinucleotide. Spatially directed synthesis of complex compounds could also be used for microfabrication of devices. Light-directed, spatially addressable parallel chemical synthesis. SP Fodor JL Read MC Pirrung L Stryer AT Lu D Solas Science, Vol. 251, No. 4995. (15 February 1991), pp. 767-773. 2006-11-14T00:56:52-00:00 1991 Science 0036-8075 251 4995 767 773 array chemical light membranes parallel spatial synthesis http://www.citeulike.org/user/rodney/article/1151428 <i>The Journal of Chemical Physics, Vol. 122, No. 9. (2005)</i><br /><br />In this Comment I discuss two incorrect statements which were made in the paper "Silver nanoparticle array structures that produce remarkably narrow plasmon line shapes" [J. Chem. Phys.130, 10871 (2004)] by Zou, Janel, and Schatz (ZJS). The first statement is about the use of quasistatic approximation in my earlier work on the similar subject, and the second statement concerns the possibility of exact cancellation of radiative relaxation in periodical chains of nanoparticles. The relationship between the quasistatic approximation, the dipole approximation, and the approximation due to Doyle [Phys. Rev. B39, 9852 (1989)] which was used by ZJS is clarified. It is shown that the exact cancellation of radiative relaxation cannot take place in the particular geometry considered by ZJS. ©2005 American Institute of Physics Comment on “Silver nanoparticle array structures that produce remarkably narrow plasmon line shapes” [J. Chem. Phys. [bold 120], 10871 (2004)] Vadim Markel doi:10.1063/1.1859281 The Journal of Chemical Physics, Vol. 122, No. 9. (2005) 2007-03-09T15:13:03-00:00 2005 The Journal of Chemical Physics 122 9 AIP array comment nanoparticles plasmons silver http://www.citeulike.org/user/rodney/article/1151392 <i>Physical Review B (Condensed Matter and Materials Physics), Vol. 74, No. 21. (2006)</i><br /><br />I have recalculated the extinction spectra of aggregates of two silver nanospheres shown in Figs. 2 and 3 of the paper by J. J. Xiao, J. P. Huang, and K. W. Yu [Phys. Rev. B 71, 045404 (2005)]. I have used the approximate method of images according to the formulas published in that reference and an exact numerical technique. I have found that the three sets of data (those I have obtained by the method of images, the numerical results, and the results published in the reference in question) do not coincide. In this Comment, I discuss the reasons for these discrepancies and the general applicability of the method of images to the quasistatic electromagnetic problem of two interacting nanospheres. Comment on “Optical response of strongly coupled metal nanoparticles in dimer arrays” Vadim Markel doi:10.1103/PhysRevB.74.216401 Physical Review B (Condensed Matter and Materials Physics), Vol. 74, No. 21. (2006) 2007-03-09T15:01:22-00:00 2006 Physical Review B (Condensed Matter and Materials Physics) 74 21 APS array comment dimer metal nanoparticles optical http://www.citeulike.org/user/rodney/article/2223891 <i>Physical Review Letters, Vol. 89, No. 12. (2002), 128301.</i><br /><br />We describe measurements of colloidal transport through arrays of micrometer-scale potential wells created with holographic optical tweezers. Varying the orientation of the trap array relative to the external driving force results in a hierarchy of lock-in transitions analogous to symmetry-selecting processes in a wide variety of systems. Focusing on colloid as a model system provides the first opportunity to observe the microscopic mechanisms of kinetic lock-in transitions and reveals a new class of statistically locked-in states. This particular realization also has immediate applications for continuously fractionating particles; biological cells; and macromolecules. Kinetically Locked-In Colloidal Transport in an Array of Optical Tweezers Pamela Korda Michael Taylor David Grier doi:10.1103/PhysRevLett.89.128301 Physical Review Letters, Vol. 89, No. 12. (2002), 128301. 2008-01-13T01:01:42-00:00 2002 Physical Review Letters 89 12 128301 American Physical Society array colloidal locked optical transport trap tweezers http://www.citeulike.org/user/rodney/article/1771337 <i>Applied Physics Letters, Vol. 84, No. 26. (2004), pp. 5440-5442.</i><br /><br />We investigate the creation and the rotation of the array of microparticles trapped by circularly polarized light. We find that a smooth rotation requires two-dimensional structure having a rotational symmetry along the light beam axis. We show that it is possible to control smoothly both the rate and the sense of rotation not only by varying the handedness and the power of the incident beam but also by varying the position of the beam focus. ©2004 American Institute of Physics Rotation of two-dimensional arrays of microparticles trapped by circularly polarized light Kenji Miyakawa Hiroto Adachi Yoshinori Inoue doi:10.1063/1.1767953 Applied Physics Letters, Vol. 84, No. 26. (2004), pp. 5440-5442. 2007-10-15T21:06:29-00:00 2004 Applied Physics Letters 84 26 5440 5442 AIP 2-d array circular laser microspheres optical polarization rotation torque trap tweezers http://www.citeulike.org/user/rdiaz/article/938007 <i>Nat Biotech, Vol. 22, No. 8. (2004), pp. 1017-1019.</i> In silico simulation of biological network dynamics Lukasz Salwinski David Eisenberg doi:10.1038/nbt991 Nat Biotech, Vol. 22, No. 8. (2004), pp. 1017-1019. 2006-11-09T16:57:36-00:00 2004 Nat Biotech 22 8 1017 1019 array computing field fpga gate parallelization programmable http://www.citeulike.org/user/rbmoura/article/2637229 <i>Nuclear Science, IEEE Transactions on, Vol. 49, No. 3. (2002), pp. 649-654.</i><br /><br />We are developing a compact positron emission tomography (PET) detector module with a depth of interaction capability (DOI) based on a lutetium oxyorthosilicate (LSO) scintillator array coupled at both ends by avalanche photodiode (APD) arrays. This leads to a detector with high sensitivity that can provide high and uniform image resolution. We report studies on improving the DOI resolution by optimizing the crystal surface treatment. Six 2/spl times/2/spl times/20 mm LSO crystals were treated with different surface finishes along their length: raw saw-cut, polished optical finish, and chemically etched by hot anhydrous phosphoric acid (H/sub 3/PO/sub 4/) with etching times varying from 1 to 5 min. The ratio of the signals from the two APD arrays was used to measure DOI, and the sum of the signals to measure the total light output. Crystals finished by chemical etching for 2-3 min gave the best overall detector performance, with DOI resolutions ranging from 3.1 to 3.9 mm for events above a 150-keV threshold and uniform light output for different DOI positions. The energy resolution ranged between 14% and 18%. This detector design appears promising for PET applications requiring very high resolution and high sensitivity, for example, in small animal imaging and human breast imaging. Dual APD array readout of LSO crystals: optimization of crystal surface treatment Y Shao K Meadors RW Silverman R Farrell L Cirignano R Grazioso KS Shah SR Cherry doi:10.1109/TNS.2002.1039544 Nuclear Science, IEEE Transactions on, Vol. 49, No. 3. (2002), pp. 649-654. 2008-04-07T11:45:38-00:00 2002 Nuclear Science, IEEE Transactions on 49 3 649 654 apd array crystal crystals lso optical roughness surface http://www.citeulike.org/user/rbmoura/article/2616172 <i>Nuclear Science Symposium Conference Record, 2006. IEEE, Vol. 2 (2006), pp. 918-922.</i><br /><br />An approach to detect the light from scintillation materials using an array of small photon counting detectors, referred to as a "solid-state photomultiplier" (SSPM), detects light from a scintillation material to provide a sensitive radiation monitor. Each pixel acts as a binary photon detector, but the summed output is an analog representation of the total photon intensity, which is proportional to the energy of the gamma ray. We have successfully fabricated arrays of GPD pixels in a CMOS environment, which makes possible the production of miniaturized arrays integrated with the detector electronics in a small silicon chip. This detector technology allows for a substantial cost reduction while preserving the energy resolution needed for radiological measurements. In this work, we demonstrate the operation of a 100-pixel array in reading an LSO scintillation crystal. In addition, we present the energy spectra corrected for saturation effects and examine the effects of cross talk on the performance of the SSPM. Characterization of CMOS Solid-State Photomultiplier for a Digital Radiation Rate Meter CJ Stapels FL Augustine MR Squillante JF Christian doi:10.1109/NSSMIC.2006.355996 Nuclear Science Symposium Conference Record, 2006. IEEE, Vol. 2 (2006), pp. 918-922. 2008-03-31T13:22:07-00:00 2006 Nuclear Science Symposium Conference Record, 2006. IEEE 2 918 922 apd array sipm http://www.citeulike.org/user/rbmoura/article/2533137 <i>Nuclear Science Symposium Conference Record, 2001 IEEE, Vol. 2 (2001), pp. 879-883 vol.2.</i><br /><br />Thin, highly reflective, opaque separators are required to assemble compact arrays of small discrete scintillation crystals used in conjunction with photodiode array readouts in high-resolution imaging applications. Mechanical stability, individual detector performance, and ease of handling for wrapping crystals are the main factors to be considered in the choice of a suitable separator. Three different types of reflective materials were tested with 4/spl times/4 arrays of LSO, BGO and GSO: Tyvek 1058D paper, Toray Lumirror E60L Polyester Film, and 3M VM2000 Radiant Light Film. The light output and intrinsic energy resolution of individual crystals were measured as a function of their position in the arrays and the results were compared to simulation of light collection efficiency obtained with DETECT97. Optical crosstalk between adjacent and diagonal pixels was evaluated. The Lumirror film consistently yielded superior results with BGO. With LSO and GSO, the 3M reflector was found to provide slightly better light output and energy resolution. Despite the sharp cutoff in spectral reflectivity at 400 nm with this reflector, the crosstalk between adjacent LSO crystals was not found to be significant. Assessment of reflective separator films for small crystal arrays CM Pepin P Berard R Lecomte Nuclear Science Symposium Conference Record, 2001 IEEE, Vol. 2 (2001), pp. 879-883 vol.2. 2008-03-14T15:45:20-00:00 2001 Nuclear Science Symposium Conference Record, 2001 IEEE 2 879 883 vol.2 array crystal optical pixel reflector http://www.citeulike.org/user/rbmoura/article/2637133 <i>Nuclear Science, IEEE Transactions on, Vol. 48, No. 3. (2001), pp. 684-688.</i><br /><br />Presents construction methods and performance results for a production scintillator array of 64 optically isolated, 3 mm×3 mm×30 mm sized LSO crystals. This scintillator array has been developed for a PET detector module consisting of the 8×8 LSO array coupled on one end to a single photomultiplier tube (PMT) and on the opposite end to a 64 pixel array of silicon photodiodes (PD). The PMT provides an accurate timing pulse and initial energy discrimination, the PD identifies the crystal of interaction, the sum provides a total energy signal, and the PD/(PD+PMT) ratio determines the depth of interaction (DOI). Unlike the previous LSO array prototypes, the authors now glue Lumirror reflector material directly onto 4 sides of each crystal to obtain an easily manufactured, mechanically rugged array with the authors' desired depth dependence. With 511 keV excitation, the authors' obtain a total energy signal of 3600 electrons, pulse-height resolution of 25% FWHM, and 6-15 mm FWHM DOI resolution An LSO scintillator array for a PET detector module with depth of interaction measurement JS Huber WW Moses MS Andreaco O Petterson doi:10.1109/23.940147 Nuclear Science, IEEE Transactions on, Vol. 48, No. 3. (2001), pp. 684-688. 2008-04-07T11:14:25-00:00 2001 Nuclear Science, IEEE Transactions on 48 3 684 688 array detector doi lso measurement module pet scintillator http://www.citeulike.org/user/rbmoura/article/2646329 <i>Nuclear Science, IEEE Transactions on, Vol. 51, No. 5. (2004), pp. 2654-2661.</i><br /><br />The performance and in-beam imaging capabilities of two position-sensitive /spl gamma/-ray detectors consisting of Hamamatsu avalanche photodiode arrays (S8550) individually coupled to crystals of cerium-doped lutetium oxyorthosilicate (LSO) are presented. The two detectors were operated in coincidence at the medical beam line of the Gesellschaft fu/spl uml/r Schwerionenforschung, in Darmstadt, Germany. In a first set of experiments, their imaging performance was tested before, during, and after the irradiation of phantoms of polymethylmethacrylate with carbon ion beams with fluences equivalent to 1000 typical daily therapeutic fractions. Only minor energy, time, and spatial resolution deterioration was observed, with the initial values being recovered after stopping the irradiation. A second set of experiments successfully imaged the depth distribution of positron emitter radionuclides created in a phantom that stopped the high-energy carbon ion beam. The particular details for the in-beam PET acquisition are shortly outlined. The obtained results show that LSO is a suitable material for in-beam PET and that its coupling with avalanche photodiode arrays is feasible for a PET system dedicated to in-beam monitoring of ion therapy. First in-beam PET imaging with LSO/APD array detectors P Crespo M Kapusta J Pawelke M Moszynski W Enghardt doi:10.1109/TNS.2004.835780 Nuclear Science, IEEE Transactions on, Vol. 51, No. 5. (2004), pp. 2654-2661. 2008-04-09T16:02:25-00:00 2004 Nuclear Science, IEEE Transactions on 51 5 2654 2661 apd array detector in-beam lso pet http://www.citeulike.org/user/rbmoura/article/2637967 <i>Nuclear Science Symposium Conference Record, 2001 IEEE, Vol. 4 (2001), pp. 1988-1992.</i><br /><br />An ASIC-based readout electronics scheme is under development for high resolution, compact PET imagers based on independent readout of all channels of LSO scintillator and avalanche photodiode (APD) arrays. Depth of interaction is obtained by readout of both ends of the LSO crystals. A low power, highly integrated design is critical. We report here on a discrete electronics prototype, running at 22 mW per channel for the preamplifier and discriminator. The measured timing resolution is 3.6 ns FWHM, 9.2 ns full width at one tenth maximum, relative to an LSO/PMT detector, energy resolution is 13.3% FWHM at 511 keV, and depth of interaction position resolution is 2.5 mm FWHM throughout the full length of the crystal. Work is in progress towards an ASIC and a full scale prototype detector module suitable for a high resolution compact PET instrument Development of low power high speed readout electronics for high resolution PET with LSO and APD arrays G Visser S Cherry M Clajus Yiping Shao TO Tumer doi:10.1109/NSSMIC.2001.1009214 Nuclear Science Symposium Conference Record, 2001 IEEE, Vol. 4 (2001), pp. 1988-1992. 2008-04-07T15:19:34-00:00 2001 Nuclear Science Symposium Conference Record, 2001 IEEE 4 1988 1992 apd array electronics high lso pet resolution speed http://www.citeulike.org/user/rbmoura/article/1465502 <i>Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 555, No. 1-2. (15 December 2005), pp. 403-410.</i><br /><br />Development of dedicated metabolic breast imaging systems promise to improve the early detection of cancers in women with radio-dense and/or cystic breasts. Our group is constructing an imager based on discrete detector arrays that will acquire multi-angle data to produce tomographic images of the breast. The goal of this investigation was to utilize Monte-Carlo simulations to determine the effect of detector element dimensions on breast lesion detectability. Specifically, the Geant4 Application for Tomography Emission (GATE) software package was used to simulate the performance of the new system. Scanners configured with detector arrays having square elements with widths of 1.5, 2 and 3 mm, and thicknesses of 10, 15 and 20 mm were tested. An ellipsoid filled with 18F containing four spheres with diameters of 5, 4, 3 and 2 mm also filled with 18F (target-to-background ratio=8.5:1) was used to simulate a breast with tracer-avid tumors. Images were created with an iterative maximum likelihood expectation maximization (MLEM) image reconstruction algorithm. Lesion detectability was assessed by calculating the peak signal-to-noise ratio for each sphere. Since the GATE software does not model optical effects in the scintillator, a simulation study investigating photon transport in the detector elements using DETECT97 was performed. Results from these studies indicated that narrow (1.5 or 2.0 mm wide) elements 10 or 15 mm in length should produce an imager that would detect breast lesions [less-than-or-equals, slant]3 mm in diameter. A Monte-Carlo simulation study of detector array design for dedicated breast metabolic imaging systems Raymond Raylman Mark Smith Peter Menge Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 555, No. 1-2. (15 December 2005), pp. 403-410. 2007-07-18T18:30:26-00:00 2005 Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 555 1-2 403 410 array breast design detector monte-carlo pem pet simulation http://www.citeulike.org/user/rbmoura/article/1465477 <i>Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 504, No. 1-3. (21 May 2003), pp. 139-142.</i><br /><br />The performance of Hamamatsu S8550 avalanche photodiode (APD) arrays for scintillator matrices readout has been evaluated. The S8550 device is a monolithic 8x4 pixels structure with an active area of 2.56 mm2 for each pixel. The device allows stable operation at gains up to 74, with a detection efficiency of about 60% for photons of 420 nm wavelength. It is characterized by a low noise equal to 27 electrons equivalent noise charge at room temperature. The energy resolution of 14.6%, for the 511 keV peak from a 22Na source has been recorded with a 2x2x10 mm3 LSO crystal coupled to one pixel. The number of electron-hole pairs produced by the 511 keV photopeak absorbed in LSO is equal to 4830+/-240 e-h/MeV. Coupling LSO scintillator crystals to individual pixels of the APD array a coincidence timing resolution of 3.0+/-0.2 ns FWHM has been measured for the 511 keV [gamma]-rays from a 22Na source. Finally, we compared the characteristics and readout performance of the Hamamatsu array with the results measured earlier under the same conditions for the quadrant large area avalanche photodiodes of Advanced Photonics Inc. Hamamatsu S8550 APD arrays for high-resolution scintillator matrices readout M Kapusta P Crespo D Wolski M Moszynski W Enghardt doi:10.1016/S0168-9002(03)00809-X Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 504, No. 1-3. (21 May 2003), pp. 139-142. 2007-07-18T18:05:09-00:00 2003 Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 504 1-3 139 142 apd array avalanche detector hamamatsu lso scintillator http://www.citeulike.org/user/rbmoura/article/2616531 <i>Nuclear Science, IEEE Transactions on, Vol. 47, No. 3. (2000), pp. 1051-1057.</i><br /><br />The authors evaluated a compact, high resolution PET detector module using avalanche photodiode (APD) arrays to replace bulky position sensitive PMTs. The newly developed APD array is a planar processed 4×4 array which has a 2×2 mm² pixel size with 0.4 mm gaps between pixels, about 60% quantum efficiency at 420 nm wavelength, and uniform high gain (>1000) across all channels. A 4×4 array of 2×2×10 mm³ LSO crystals was coupled to an APD array. Different readout electronics and signal multiplexing schemes were explored. All crystals in the detector array were clearly identified in the flood source histogram, with average peak-to-valley ratios of about 12:1 using a charge sharing resistor network. The energy resolution was measured to be ~14% at 511 keV in the detector array. The measured timing resolution was 2.6 ns in coincidence with a LSO/PMT detector. By optimizing the readout electronics currently being used, it is likely that detector performance can be further improved. The authors have also determined depth-of-interaction (DOI) by reading out two APD arrays connected to the ends of a 2×2×22 mm³ LSO crystal. Preliminary measurements show good DOI measurement capability with DOI positioning uncertainty between 4 and 6.5 mm Design studies of a high resolution PET detector using APD arrays Y Shao RW Silverman R Farrell L Cirignano R Grazioso KS Shah G Vissel M Clajus TO Tumer TO Tumer SR Cherry A10 doi:10.1109/23.856546 Nuclear Science, IEEE Transactions on, Vol. 47, No. 3. (2000), pp. 1051-1057. 2008-03-31T15:10:15-00:00 2000 Nuclear Science, IEEE Transactions on 47 3 1051 1057 apd array design detector doi energy pet rmd scintillator time http://www.citeulike.org/user/rbmoura/article/1467276 <i>pp. 139-142.</i><br /><br />The performance of Hamamatsu S8550 avalanche photodiode (APD) arrays for scintillator matrices readout has been evaluated. The S8550 device is a monolithic 8x4 pixels structure with an active area of 2.56mm2 for each pixel. The device allows stable operation at gains up to 74, with a detection efficiency of about 60% for photons of 420nm wavelength. It is characterized by a low noise equal to 27 electrons equivalent noise charge at room temperature. The energy resolution of 14.6%, for the 511keV peak from a 22Na source has been recorded with a 2x2x10mm3 LSO crystal coupled to one pixel. The number of electron-hole pairs produced by the 511keV photopeak absorbed in LSO is equal to 4830+/-240e-h/MeV. Coupling LSO scintillator crystals to individual pixels of the APD array a coincidence timing resolution of 3.0+/-0.2ns FWHM has been measured for the 511keV -rays from a 22Na source. Finally, we compared the characteristics and readout performance of the Hamamatsu array with the results measured earlier under the same conditions for the quadrant large area avalanche photodiodes of Advanced Photonics Inc. Hamamatsu S8550 APD arrays for high-resolution scintillator matrices readout M Kapusta pp. 139-142. 2007-07-19T13:12:12-00:00 139 142 apd array avalanche crosstalk energy hamamatsu matrix resolution scintillator time http://www.citeulike.org/user/raiyar/article/307584 <i>Science, Vol. 278, No. 5338. (24 October 1997), pp. 680-686.</i><br /><br />DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration. The expression profiles observed for genes with known metabolic functions pointed to features of the metabolic reprogramming that occur during the diauxic shift, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions. The same DNA microarrays were also used to identify genes whose expression was affected by deletion of the transcriptional co-repressor TUP1 or overexpression of the transcriptional activator YAP1. These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns. Exploring the metabolic and genetic control of gene expression on a genomic scale. JL DeRisi VR Iyer PO Brown doi:10.1126/science.278.5338.680 Science, Vol. 278, No. 5338. (24 October 1997), pp. 680-686. 2005-08-30T22:20:01-00:00 1997 Science 0036-8075 278 5338 680 686 analysis array basis expression genomics ht methodspaper mitochondria yeast http://www.citeulike.org/user/raiyar/article/307585 <i>Mol Biol Cell, Vol. 11, No. 12. (December 2000), pp. 4241-4257.</i><br /><br />We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (approximately 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the genomic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell. Genomic expression programs in the response of yeast cells to environmental changes. AP Gasch PT Spellman CM Kao O Carmel-Harel MB Eisen G Storz D Botstein PO Brown Mol Biol Cell, Vol. 11, No. 12. (December 2000), pp. 4241-4257. 2005-08-30T22:21:15-00:00 2000 Mol Biol Cell 1059-1524 11 12 4241 4257 array condition expression genomics yeast http://www.citeulike.org/user/raiyar/article/1914380 <i>Mol. Cell. Biol., Vol. 27, No. 21. (1 November 2007), pp. 7414-7424.</i><br /><br />Changes in oxygen levels cause widespread changes in gene expression in organisms ranging from bacteria to humans. In Saccharomyces cerevisiae, this response is mediated in part by Hap1, originally identified as a heme-dependent transcriptional activator that functions during aerobic growth. We show here that Hap1 also plays a significant and direct role under hypoxic conditions, not as an activator, but as a repressor. The repressive activity of Hap1 controls several genes, including three ERG genes required for ergosterol biosynthesis. Chromatin immunoprecipitation experiments showed that Hap1 binds to the ERG gene promoters, while additional experiments showed that the corepressor Tup1/Ssn6 is recruited by Hap1 and is also required for repression. Furthermore, mutational analysis demonstrated that conserved Hap1 binding sites in the ERG5 5' regulatory region are required for repression. The switch of Hap1 from acting as a hypoxic repressor to an aerobic activator is determined by heme, which is synthesized only in the presence of oxygen. The ability of Hap1 to function as a ligand-dependent repressor and activator is a property shared with mammalian nuclear hormone receptors and likely allows greater transcriptional control by Hap1 in response to changing oxygen levels. 10.1128/MCB.00887-07 Heme Levels Switch the Function of Hap1 of Saccharomyces cerevisiae between Transcriptional Activator and Transcriptional Repressor Mark Hickman Fred Winston doi:10.1128/MCB.00887-07 Mol. Cell. Biol., Vol. 27, No. 21. (1 November 2007), pp. 7414-7424. 2007-11-14T14:47:43-00:00 2007 Mol. Cell. Biol. 27 21 7414 7424 array condition hap1 mutant regulation transcription yeast http://www.citeulike.org/user/raiyar/article/2100 <i>Science, Vol. 292, No. 5518. (4 May 2001), pp. 929-934.</i><br /><br />We demonstrate an integrated approach to build, test, and refine a model of a cellular pathway, in which perturbations to critical pathway components are analyzed using DNA microarrays, quantitative proteomics, and databases of known physical interactions. Using this approach, we identify 997 messenger RNAs responding to 20 systematic perturbations of the yeast galactose-utilization pathway, provide evidence that approximately 15 of 289 detected proteins are regulated posttranscriptionally, and identify explicit physical interactions governing the cellular response to each perturbation. We refine the model through further iterations of perturbation and global measurements, suggesting hypotheses about the regulation of galactose utilization and physical interactions between this and a variety of other metabolic pathways. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. T Ideker V Thorsson JA Ranish R Christmas J Buhler JK Eng R Bumgarner DR Goodlett R Aebersold L Hood doi:10.1126/science.292.5518.929 Science, Vol. 292, No. 5518. (4 May 2001), pp. 929-934. 2004-12-06T13:33:08-00:00 2001 Science 0036-8075 292 5518 929 934 analysis array bioinformatics deletion expression genomics integration methodspaper model network proteomics systems yeast http://www.citeulike.org/user/raiyar/article/1044754 <i>(2004)</i><br /><br />A large number of clustering approaches have been proposed for the analysis of gene expression data obtained from microarray experiments. However, the results of the application of standard clustering methods to genes are limited. These limited results are imposed by the existence of a number of experimental conditions where the activity of genes is uncorrelated. A similar limitation exists when clustering of conditions is performed. For this reason, a number of algorithms that perform simultaneous clustering on the row and column dimensions of the gene expression matrix has been proposed to date. This simultaneous clustering, usually designated by biclustering, seeks to find sub-matrices, that is subgroups of genes and subgroups of columns, where the genes exhibit highly correlated activities for every condition. This type of algorithms has also been proposed and used in other fields, such as information retrieval and data mining. In this comprehensive survey, we analyze a large number of existing approaches to biclustering, and classify them in accordance with the type of biclusters they can find, the patterns of biclusters that are discovered, the methods used to perform the search and the target applications. Biclustering algorithms for biological data analysis: a survey S Madeira A Oliveira (2004) 2007-01-16T18:41:13-00:00 2004 analysis array expression genes review http://www.citeulike.org/user/raiyar/article/1051885 <i>PLoS Biol, Vol. 2, No. 6. (June 2004)</i><br /><br />In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans. Integrative analysis of the mitochondrial proteome in yeast. H Prokisch C Scharfe DG Camp W Xiao L David C Andreoli ME Monroe RJ Moore MA Gritsenko C Kozany KK Hixson HM Mottaz H Zischka M Ueffing ZS Herman RW Davis T Meitinger PJ Oefner RD Smith LM Steinmetz doi:10.1371/journal.pbio.0020160 PLoS Biol, Vol. 2, No. 6. (June 2004) 2007-01-19T13:26:08-00:00 2004 PLoS Biol 1545-7885 2 6 array deletion expression genomics integration methodspaper mitochondria ms parts-list sgtcnih yeast http://www.citeulike.org/user/raiyar/article/695529 <i>PNAS, Vol. 103, No. 14. (4 April 2006), pp. 5320-5325.</i><br /><br />There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3' and 5' UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation. 10.1073/pnas.0601091103 A high-resolution map of transcription in the yeast genome Lior David Wolfgang Huber Marina Granovskaia Joern Toedling Curtis Palm Lee Bofkin Ted Jones Ronald Davis Lars Steinmetz doi:10.1073/pnas.0601091103 PNAS, Vol. 103, No. 14. (4 April 2006), pp. 5320-5325. 2006-06-14T09:34:50-00:00 2006 PNAS 103 14 5320 5325 array genomics sgtcnih tiling transcription yeast http://www.citeulike.org/user/raiyar/article/1051395 <i>Nature Genetics, Vol. 21, No. 3. (March 1999), pp. 278-283.</i><br /><br />Lowering the dosage of a single gene from two copies to one copy in diploid yeast results in a heterozygote that is sensitized to any drug that acts on the product of this gene. This haploinsufficient phenotype thereby identifies the gene product of the heterozygous locus as the likely drug target. We exploited this finding in a genomic approach to drug-target identification. Genome sequence information was used to generate molecularly tagged heterozygous yeast strains that were pooled, grown competitively in drug and analysed for drug sensitivity using high-density oligonucleotide arrays. Individual heterozygous strain analysis verified six known drug targets. Parallel analysis identified the known target and two hypersensitive loci in a mixed culture of 233 strains in the presence of the drug tunicamycin. Our discovery that both drug target and hypersensitive loci exhibit drug-induced haploinsufficiency may have important consequences in pharmacogenomics and variable drug toxicity observed in human populations. [Journal Article; In English; United States; MEDLINE] Genomic profiling of drug sensitivities via induced haploinsufficiency G Giaever DD Shoemaker TW Jones H Liang EA Winzeler A Astromoff RW Davis Nature Genetics, Vol. 21, No. 3. (March 1999), pp. 278-283. 2007-01-19T11:30:54-00:00 1999 Nature Genetics 21 3 278 283 array compound deletion genomics ht target yeast http://www.citeulike.org/user/raiyar/article/1051367 <i>Cell, Vol. 116, No. 1. (9 January 2004), pp. 121-137.</i><br /><br />Modern medicine faces the challenge of developing safer and more effective therapies to treat human diseases. Many drugs currently in use were discovered without knowledge of their underlying molecular mechanisms. Understanding their biological targets and modes of action will be essential to design improved second-generation compounds. Here, we describe the use of a genome-wide pool of tagged heterozygotes to assess the cellular effects of 78 compounds in Saccharomyces cerevisiae. Specifically, lanosterol synthase in the sterol biosynthetic pathway was identified as a target of the antianginal drug molsidomine, which may explain its cholesterol-lowering effects. Further, the rRNA processing exosome was identified as a potential target of the cell growth inhibitor 5-fluorouracil. This genome-wide screen validated previously characterized targets or helped identify potentially new modes of action for over half of the compounds tested, providing proof of this principle for analyzing the modes of action of clinically relevant compounds. Discovering Modes of Action for Therapeutic Compounds Using a Genome-Wide Screen of Yeast Heterozygotes Pek Lum Christopher Armour Sergey Stepaniants Guy Cavet Maria Wolf Scott Butler Jerald Hinshaw Philippe Garnier Glenn Prestwich Amy Leonardson doi:10.1016/S0092-8674(03)01035-3 Cell, Vol. 116, No. 1. (9 January 2004), pp. 121-137. 2007-01-19T11:25:03-00:00 2004 Cell 116 1 121 137 array barcode compound deletion genomics ht target yeast http://www.citeulike.org/user/rahulthadani/article/1375672 <i>Cell, Vol. 128, No. 2. (26 January 2007), pp. 357-368.</i><br /><br />Microtubule (MT) nucleation not only occurs from centrosomes, but also in large part from dispersed nucleation sites. The subsequent sorting of short MTs into networks like the mitotic spindle requires molecular motors that laterally slide overlapping MTs and bundling proteins that statically connect MTs. How bundling proteins interfere with MT sliding is unclear. In bipolar MT bundles in fission yeast, we found that the bundler ase1p localized all along the length of antiparallel MTs, whereas the motor klp2p (kinesin-14) accumulated only at MT plus ends. Consequently, sliding forces could only overcome resistant bundling forces for short, newly nucleated MTs, which were transported to their correct position within bundles. Ase1p thus regulated sliding forces based on polarity and overlap length, and computer simulations showed these mechanisms to be sufficient to generate stable bipolar bundles. By combining motor and bundling proteins, cells can thus dynamically organize stable regions of overlap between cytoskeletal filaments. Crosslinkers and motors organize dynamic microtubules to form stable bipolar arrays in fission yeast. ME Janson R Loughlin I Loïodice C Fu D Brunner FJ Nédélec PT Tran doi:10.1016/j.cell.2006.12.030 Cell, Vol. 128, No. 2. (26 January 2007), pp. 357-368. 2007-06-10T09:45:22-00:00 2007 Cell 0092-8674 128 2 357 368 array bipolar crosslinkers dynamics microtubule motors pombe http://www.citeulike.org/user/qwerty/article/2968720 <i>Physical Review A (Atomic, Molecular, and Optical Physics), Vol. 78, No. 1. (2008)</i><br /><br />We report the experimental observation of an enhancement in the yield of high-order harmonics using an array of gas jets as the source medium. By comparing the experimental outcome for jet arrays of different spacings with the predicted harmonic intensity in the case of slit sources of equivalent lengths, we clearly show how the periodic modulation of the gas density can improve the harmonic yield. This behavior may be attributed to a quasi-phase-matching effect which increases the length of coherent harmonic buildup during propagation by partially counteracting the dephasing induced by free electrons. Enhancing the yield of high-order harmonics with an array of gas jets Angela Pirri Chiara Corsi Marco Bellini doi:10.1103/PhysRevA.78.011801 Physical Review A (Atomic, Molecular, and Optical Physics), Vol. 78, No. 1. (2008) 2008-07-07T09:06:24-00:00 2008 Physical Review A (Atomic, Molecular, and Optical Physics) 78 1 APS array gas_jet hhg