jfr's affy [82 articles] Export

Recent papers added to jfr's library classified by the tag affy. You can also see everyone's affy.

	Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips [My Copy] Brief Bioinform, Vol. 10, No. 3. (1 May 2009), pp. 259-277. by William B. Langdon, Graham J. G. Upton, Andrew P. Harrison posted to low_level affy by jfr on 2009-11-04 11:09:53 as along with 2 people bertelsen zufar
	Inverse Langmuir method for oligonucleotide microarray analysis. [My Copy] BMC bioinformatics, Vol. 10 (20 February 2009), 64. by G. C. Mulders, G. T. Barkema, E. Carlon posted to affy low_level by jfr on 2009-07-09 13:03:12 as along with 1 group Bioinformatics
	Assessing the quality of hybridized RNA in Affymetrix GeneChips using linear regression. [My Copy] Journal of biomolecular techniques : JBT, Vol. 19, No. 2. (April 2008), pp. 122-128. by Meijuan Li, Cavan Reilly posted to affy quality_control rna_quality by jfr on 2009-04-14 11:29:44 as along with 1 person shikin
	Meta-analysis of gene expression profiles related to relapse-free survival in 1,079 breast cancer patients [My Copy] Breast Cancer Research and Treatment by Balazs Györffy, Reinhold Schäfer posted to affy breast_cancer meta-analysis survival_analysis by jfr on 2009-03-16 16:45:04 as along with 1 person daforerog
	Determining gene expression on a single pair of microarrays [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Robert Reid, Anthony Fodor posted to affy by jfr on 2009-03-16 10:25:21 as along with 6 people dswan guhjy lptolik rschulz barriot nuin
	Use of hidden correlations in short oligonucleotide array data are insufficient for accurate quantification of nucleic acid targets in complex target mixtures. [My Copy] Journal of microbiological methods, Vol. 76, No. 2. (February 2009), pp. 188-195. by R. A. Rule, A. E. Pozhitkov, P. A. Noble posted to affy low_level by jfr on 2009-03-12 11:20:12 as
	Power enhancement via multivariate outlier testing with gene expression arrays. [My Copy] Bioinformatics (Oxford, England) (16 November 2008) by Adam Asare, Zhong Gao, Vincent J J. Carey, Richard Wang, Vicki Seyfert-Margolis posted to affy bioconductor quality_control by jfr on 2009-03-12 11:00:08 as along with 3 people rschulz lptolik guhjy
	Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays [My Copy] Bioinformatics, Vol. 25, No. 1. (1 January 2009), pp. 36-41. by Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Tomoharu Agata, Hiroshi Shimizu, Tetsuya Yomo posted to affy low_level by jfr on 2009-03-11 11:05:44 as along with 2 people renatomilani guhjy
	Effect of single nucleotide polymorphisms on Affymetrix(R) match-mismatch probe pairs. [My Copy] Bioinformation, Vol. 2, No. 9. (2008), pp. 405-411. by E. C. Rouchka, A. W. Phatak, A. V. Singh posted to affy low_level snp by jfr on 2009-01-09 11:31:45 as
	Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. [My Copy] Genome biology, Vol. 9, No. 9. (2008) by Sami Kilpinen, Reija Autio, Kalle Ojala, et al.Kristiina Iljin, Elmar Bucher, Henri Sara, Tommi Pisto, Matti Saarela, Rolf I. Skotheim, Mari Björkman, John-Patrick P. Mpindi, Saija Haapa-Paananen, Paula Vainio, Henrik Edgren, Maija Wolf, Jaakko Astola, Matthias Nees, Sampsa Hautaniemi, Olli Kallioniemi posted to affy database gene_expression meta-analysis by jfr on 2008-11-26 17:47:45 as along with 10 people and 1 group zufar daforerog shikin grahamc pengchy imina guhjy klo fpattyn dolchan GeneGo
	"Hook"-calibration of GeneChip-microarrays: Theory and algorithm [My Copy] Algorithms for Molecular Biology, Vol. 3, No. 1. (2008) by Hans Binder, Stephan Preibisch posted to affy low_level quality_control by jfr on 2008-11-06 11:40:47 as along with 3 people zufar bertelsen talponer
	"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures [My Copy] Algorithms for Molecular Biology, Vol. 3, No. 1. (2008) by Hans Binder, Knut Krohn, Stephan Preibisch posted to affy low_level quality_control by jfr on 2008-11-06 11:40:02 as along with 2 people bertelsen talponer
	A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data [My Copy] BMC Genomics, Vol. 9 (24 April 2008), 188. by Hua Li, Dongxiao Zhu, Malcolm Cook posted to affy by jfr on 2008-09-24 14:15:13 as along with 2 people daforerog malcook
	I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2897-2902. by Willem Talloen, Djork-Arne Clevert, Sepp Hochreiter, et al.Dhammika Amaratunga, Luc Bijnens, Stefan Kass, Hinrich W. Gohlmann posted to affy low_level by jfr on 2008-09-19 15:34:15 as along with 2 people cassj aviad_work
	Methods for evaluating gene expression from Affymetrix microarray datasets. [My Copy] BMC bioinformatics, Vol. 9 (17 June 2008), 284. by Ning Jiang, Lindsey J. Leach, Xiaohua Hu, et al.Elena Potokina, Tianye Jia, Arnis Druka, Robbie Waugh, Michael J. Kearsey, Zewei W. Luo posted to affy low_level by jfr on 2008-09-16 18:57:54 as along with 7 people daforerog GeeSharpMinor heliopais caseybrown tonia_schwartz guhjy winterschlaefer
	A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (14 April 2008), 194. by Huanying Ge, Chao Cheng, Lei Li posted to affy low_level normalization by jfr on 2008-06-17 17:25:42 as along with 1 person VGreiff
	Empirical Bayes models for multiple probe type microarrays at the probe level. [My Copy] BMC bioinformatics, Vol. 9 (20 March 2008), 156. by Magnus Astrand, Petter Mostad, Mats Rudemo posted to affy feature_selection microarray_analysis by jfr on 2008-06-17 17:00:07 as along with 7 people daforerog bertelsen GeeSharpMinor heliopais ptrobajo guhjy Osorio
	A comparison of Affymetrix gene expression arrays [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Mark Robinson, Terence Speed posted to affy exon_arrays by jfr on 2008-06-17 16:52:18 as along with 3 people sebastien_vigneau hpaces waszak
	affyGG: computational protocols for genetical genomics with Affymetrix arrays. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 3. (1 February 2008), pp. 433-434. by R. Alberts, G. Vera, R. C. Jansen posted to affy qtl software by jfr on 2008-06-13 16:44:49 as along with 3 people guhjy djkt giovanni
	Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata [My Copy] Nucl. Acids Res. (11 October 2007), gkm815. by Jeremiah J. Faith, Michael E. Driscoll, Vincent A. Fusaro, et al.Elissa J. Cosgrove, Boris Hayete, Frank S. Juhn, Stephen J. Schneider, Timothy S. Gardner posted to affy bioinformatics database gene_expression by jfr on 2008-06-13 14:42:32 as along with 2 people bertelsen tvdbulck
	Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours [My Copy] British Journal of Cancer, Vol. aop, No. current. (01 April 2008) by K. M. Linton, Y. Hey, E. Saunders, et al.M. Jeziorska, J. Denton, C. L. Wilson, R. Swindell, S. Dibben, C. J. Miller, S. D. Pepper, J. A. Radford, A. J. Freemont posted to affy ffpe by jfr on 2008-05-21 13:24:50 as along with 1 person kmegq
	Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed. [My Copy] Physical biology, Vol. 5, No. 1. (2008) by C. J. Burden posted to affy low_level by jfr on 2008-05-16 10:27:30 as
	Normalization of oligonucleotide arrays based on the least-variant set of genes [My Copy] BMC Bioinformatics, Vol. 9 (05 March 2008), 140. by Stefano Calza, Davide Valentini, Yudi Pawitan posted to affy gene_expression low_level normalization software by jfr on 2008-05-05 10:58:52 as along with 5 people bertelsen waszak guhjy giovenko GeeSharpMinor
	EzArray: a web-based highly automated Affymetrix expression array data management and analysis system. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by Yuerong Zhu, Yuelin Zhu, Wei Xu posted to affy database software by jfr on 2008-04-28 15:32:03 as along with 8 people and 1 group daforerog songpku rdiaz Zephyrus guhjy cannin heliopais zhouyu Roswell Cancer Crosstalk
	Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis? [My Copy] Biology Direct, Vol. 2 (07 November 2007), 28. by Lev Klebanov, Linlin Chen, Andrei Yakovlev posted to affy by jfr on 2008-03-17 16:11:29 as
	Novel definition files for human GeneChips based on GeneAnnot [My Copy] BMC Bioinformatics, Vol. 8 (15 November 2007), 446. by Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, et al.Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian A. Danieli, Silvio Bicciato posted to affy annotation software by jfr on 2008-03-17 15:20:14 as along with 3 people daforerog giovenko ghattem
	BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips [My Copy] BMC Bioinformatics, Vol. 8 (12 November 2007), 439. by Ernest Turro, Natalia Bochkina, Anne-Mette K. Hein, Sylvia Richardson posted to affy bioconductor software by jfr on 2008-03-17 15:18:56 as along with 3 people guhjy shigepong waszak
	A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. [My Copy] Bioinformatics (25 April 2007) by Yuanyuan Xiao, Mark R R. Segal, Y H H. Yang, Ru-Fang F. Yeh posted to affy genotyping methodology snp-arrays by jfr on 2008-02-29 11:55:01 as along with 2 people guhjy shigepong
	A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences [My Copy] BMC Genomics, Vol. 8 (20 August 2007), 284. by Joseph C. Lee, David Stiles, Jun Lu, Margaret C. Cam posted to affy alternative_splicing annotation by jfr on 2008-02-19 16:28:14 as along with 2 people daforerog heliopais
	High correspondence between Affymetrix exon and standard expression arrays. [My Copy] Biotechniques, Vol. 42, No. 2. (February 2007), pp. 181-185. by M. J. Okoniewski, Y. Hey, S. D. Pepper, C. J. Miller posted to affy exon_arrays gene_expression by jfr on 2008-02-15 16:01:31 as
	AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip(TM) expression arrays with respect to SNPs [My Copy] BMC Bioinformatics, Vol. 8 (30 July 2007), 276. by Sunita Kumari, Lalit K. Verma, Jennifer W. Weller posted to affy low_level methodology software by jfr on 2008-02-13 13:45:39 as along with 1 person guhjy
	Allele-specific amplification in cancer revealed by SNP array analysis. [My Copy] PLoS Comput Biol, Vol. 1, No. 6. (November 2005) by T. LaFramboise, B. A. Weir, X. Zhao, et al.R. Beroukhim, C. Li, D. Harrington, W. R. Sellers, M. Meyerson posted to affy genoty snp-arrays by jfr on 2008-02-12 11:30:59 as along with 2 people and 1 group rebeccastojak jackjackjjj G4ID
	Genotyping and annotation of Affymetrix SNP arrays. [My Copy] Nucleic Acids Res, Vol. 34, No. 14. (2006) by P. Lamy, C. L. Andersen, F. P. Wikman, C. Wiuf posted to affy genotyping snp-arrays by jfr on 2008-02-12 11:21:14 as
	SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays [My Copy] Bioinformatics, Vol. 23, No. 1. (1 January 2007), pp. 57-63. by Jianping Hua, David W. Craig, Marcel Brun, et al.Jennifer Webster, Victoria Zismann, Waibhav Tembe, Keta Joshipura, Matthew J. Huentelman, Edward R. Dougherty, Dietrich A. Stephan posted to affy genotyping software snp-arrays by jfr on 2008-02-12 10:57:43 as along with 2 people GeeSharpMinor Ayest
	Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays. [My Copy] Cancer Res, Vol. 67, No. 6. (15 March 2007), pp. 2544-2551. by S. Jacobs, E. R. Thompson, Y. Nannya, et al.G. Yamamoto, R. Pillai, S. Ogawa, D. K. Bailey, I. G. Campbell posted to affy ffpe snp-arrays by jfr on 2008-02-11 16:54:39 as
	An overview of image-processing methods for Affymetrix GeneChips. [My Copy] Brief Bioinform (5 December 2007) by Jose M M. Arteaga-Salas, Harry Zuzan, William B B. Langdon, Graham J G J. Upton, Andrew P P. Harrison posted to affy image_analysis review by jfr on 2008-02-06 11:35:19 as along with 6 people and 1 group bertelsen lwaldron neils guhjy aswin yevishere Bioinformatics
	AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 18. (15 September 2007), pp. 2385-2390. by Hongfang Liu, Barry R. Zeeberg, Gang Qu, et al.A. Gunes Koru, Alessandro Ferrucci, Ari Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, John N. Weinstein posted to affy annotation by jfr on 2008-02-04 11:58:07 as along with 8 people VGreiff giovenko guhjy ghattem ryanraaum heliopais Montrachet bertelsen
	Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays [My Copy] Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2566-2572. by Chunlei Wu, Haitao Zhao, Keith Baggerly, Roberto Carta, Li Zhang posted to affy low_level by jfr on 2008-02-04 11:50:29 as along with 1 person niallhaslam
	Analysis of probe level patterns in Affymetrix microarray data [My Copy] BMC Bioinformatics, Vol. 8 (04 May 2007), 146. by Alexander C. Cambon, Abdelnaby Khalyfa, Nigel G. F. Cooper, Caryn M. Thompson posted to affy annotation low_level by jfr on 2008-01-24 17:16:35 as along with 4 people ghattem niallhaslam bertelsen ptrobajo
	Estimation and correction of non-specific binding in a large-scale spike-in experiment [My Copy] Genome Biology, Vol. 8 (26 June 2007), R126. by Eugene F. Schuster, Eric Blanc, Linda Partridge, Janet Thornton posted to affy low_level by jfr on 2007-12-05 10:24:09 as along with 1 person bertelsen
	Correcting for sequence biases in present/absent calls [My Copy] Genome Biology, Vol. 8 (26 June 2007), R125. by Eugene F. Schuster, Eric Blanc, Linda Partridge, Janet Thornton posted to affy low_level by jfr on 2007-12-05 10:21:45 as
	The utility of MAS5 expression summary and detection call algorithms [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Stuart Pepper, Emma Saunders, Laura Edwards, Claire Wilson, Crispin Miller posted to affy low_level normalization by jfr on 2007-12-04 15:22:25 as along with 7 people dswan lwaldron frohike heliopais ryanraaum wirawan waszak
	A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array [My Copy] Nucleic Acids Research, Vol. 33, No. 3. (2005), pp. e31-e31. by Jeremy Harbig, Robert Sprinkle, Steven A. Enkemann posted to affy annotation by jfr on 2007-12-03 11:04:09 as along with 3 people incovoma heliopais bertelsen
	Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips [My Copy] BMC Bioinformatics, Vol. 8 (11 June 2007), 195. by Andrew P. Harrison, Caroline E. Johnston, Christine A. Orengo posted to affy low_level by jfr on 2007-11-28 13:21:17 as along with 1 person heliopais
	Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data [My Copy] BMC Bioinformatics, Vol. 8 (11 June 2007), 194. by Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li, Yi-Xue Li posted to affy annotation by jfr on 2007-11-28 13:13:39 as along with 3 people guhjy heliopais bertelsen
	The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by R. G. Verhaak, F. J. Staal, P. J. Valk, B. Lowenberg, M. J. Reinders, D. de Ridder posted to affy evaluation low_level by jfr on 2007-11-23 15:31:50 as along with 3 people RMGraze ghattem frohike
	chip artifact CORRECTion (caCORRECT): a bioinformatics system for quality assurance of genomics and proteomics array data. [My Copy] Ann Biomed Eng, Vol. 35, No. 6. (June 2007), pp. 1068-1080. by T. H. Stokes, R. A. Moffitt, J. H. Phan, M. D. Wang posted to affy low_level quality_control by jfr on 2007-09-13 14:46:42 as
	Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays [My Copy] BMC Bioinformatics, Vol. 8 (29 March 2007), 108. by Jun Lu, Joseph C. Lee, Marc L. Salit, Margaret C. Cam posted to affy annotation by jfr on 2007-09-12 17:54:41 as along with 5 people and 1 group heliopais guhjy frohike ghattem bertelsen Bioinformatics
	Exploratory methods for checking quality of microarray data. [My Copy] Bioinformation, Vol. 1, No. 10. (2007), pp. 423-428. by E. K. Lee, T. Park posted to affy quality_control by jfr on 2007-09-05 11:43:20 as
	An application for assessing quality of RNA hybridized to Affymetrix GeneChips. [My Copy] Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2699-2701. by K. J. Archer, T. Guennel posted to affy microarray_technology quality_control by jfr on 2007-09-04 17:05:33 as along with 3 people bertelsen ghattem waszak

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breast_cancer	455
review	327
mirna	322
classification	261
software	254
colon_cancer	224
methodology	168
gene_expression	157
copy-number	150
network	145
microarray_technology	131
integration	130
bioinformatics	121
clustering	116
feature_selection	104
meta-analysis	89
affy	82
database	79
therapy	78
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crc_bib	69
array-cgh	68
gene_set_analysis	65
low_level	64
regulation	63
systems_biology	61
pathway_analysis	59
genomics	58
snp-arrays	56
annotation	53
subtypes	53
rt-pcr	52
comment	49
quality_control	47
mutations	43
normalization	41
prognosis	41
estrogen	40
metastasis	40
ffpe	38
cancer	37
microarray_analysis	36
alternative_splicing	35
progression	35
protein_interaction	35
statistics	35
markers	34
deep_sequencing	33
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proteomics	33
bioconductor	32
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r	25
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protocol	11
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loh	10
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msi	9
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pten	9
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go	4
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sage	3
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guidelines	2
in-situ	2
letter	2
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mage	2
meeting_report	2
mir20a	2
mir215	2
mutual_information	2
oncomine	2
ontologies	2
priors	2
projection	2
protein_microarray	2
protein_networks	2
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sweave	2
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stageiii	1
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study_design	1
translocation	1
ucs	1
web_server	1
wiki	1

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