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talponer's library [184 articles]

Recent papers added to talponer's library.
  • Analysis of gene regulatory networks in the Mammalian circadian rhythm.
    PLoS computational biology, Vol. 4, No. 10. (October 2008)
    by J Yan, H Wang, Y Liu, C Shao
    posted to network microarray meta-analysis by talponer on 2008-10-13 11:02:24 as **
  • Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana.
    PLoS ONE, Vol. 3, No. 8. (2008)
    by A Adamo, JW Pinney, A Kunova, DR Westhead, P Meyer
    posted to microarray atgenexpress by talponer on 2008-10-13 10:36:42 as **
  • A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments.
    Bioinformatics (18 January 2008)
    by Fangxin Hong, Rainer Breitling
    posted to microarray meta-analysis by talponer on 2008-09-30 17:11:38 as ** along with 5 people jyuh cannin jfr shigepong jdiezperezj
  • MAID : An effect size based model for microarray data integration across laboratories and platforms
    BMC Bioinformatics, Vol. 9 (10 July 2008), 305.
    by Ivan Borozan, Limin Chen, Bryan Paeper, Jenny E Heathcote, Aled M Edwards, Michael Katze, Zhaolei Zhang, Ian D Mcgilvray
    posted to microarray meta-analysis by talponer on 2008-09-30 17:09:41 as ** along with 3 people jfr jyuh GeeSharpMinor
  • Similarities of ordered gene lists.
    Journal of bioinformatics and computational biology, Vol. 4, No. 3. (June 2006), pp. 693-708.
    by X Yang, S Bentink, S Scheid, R Spang
    posted to microarray meta-analysis by talponer on 2008-09-30 17:05:28 as **
  • Combining Affymetrix microarray results.
    BMC Bioinformatics, Vol. 6 (2005)
    by JR Stevens, RW Doerge
    posted to microarray meta-analysis by talponer on 2008-09-30 16:43:24 as ** along with 1 person jfr
  • Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease
    BMC Bioinformatics, Vol. 9 (24 June 2008), 291.
    by Rob Jelier, Peter, Ellen Sterrenburg, Johan T den Dunnen, Gert-Jan B van Ommen, Jan A Kors, Barend Mons
    posted to microarray meta-analysis by talponer on 2008-09-30 16:42:24 as ** along with 2 people jfr GeeSharpMinor
  • A fast Bayesian change point analysis for the segmentation of microarray data
    Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2143-2148.
    by Chandra Erdman, John W Emerson
    posted to tiling normalisation microarray by talponer on 2008-09-29 14:50:25 as ** along with 2 people rdiaz jyuh
  • mlegp: statistical analysis for computer models of biological systems using R.
    Bioinformatics (Oxford, England) (17 July 2008)
    by Garrett M M Dancik, Karin S S Dorman
    posted to simulation by talponer on 2008-09-24 11:00:15 as ** along with 2 people jyuh rabio
  • Comparison of different melting temperature calculation methods for short DNA sequences
    Bioinformatics, Vol. 21, No. 6. (15 March 2005), pp. 711-722.
    by Alejandro Panjkovich, Francisco Melo
    posted to microarray by talponer on 2008-09-23 10:35:12 as ** along with 1 person wisdom_love
  • Combining multiple microarray studies and modeling interstudy variation
    Bioinformatics, Vol. 19 (2003), pp. i84-i90.
    by Jung K Choi, Ungsik Yu, Sangsoo Kim, Ook J Yoo
    posted to microarray by talponer on 2008-09-18 15:03:32 as **
  • Which is better for cDNA-microarray-based classification: ratios or direct intensities.
    Bioinformatics (Oxford, England), Vol. 20, No. 16. (1 November 2004), pp. 2513-2520.
    by S Attoor, ER Dougherty, Y Chen, ML Bittner, JM Trent
    posted to simulation microarray by talponer on 2008-09-01 13:57:44 as ** along with 1 person ptrobajo
  • Theory and Limitations of Genetic Network Inference from Microarray Data
    Annals of the New York Academy of Sciences, Vol. 1115, No. 1. (December 2007), pp. 51-72.
    by Adam A Margolin, Andrea Califano
    posted to network microarray by talponer on 2008-09-01 13:37:55 as ** along with 1 person roys
  • A Probe-Density Based Analysis Method for Array CGH data: Simulation, Normalization and Centralization.
    Bioinformatics (Oxford, England) (4 July 2008)
    by Hung-I Harry I Chen, Fang-Han H Hsu, Yuan Jiang, Mong-Hsun H Tsai, Pan-Chyr C Yang, Paul S S Meltzer, Eric Y Y Chuang, Yidong Chen
    posted to tiling simulation microarray by talponer on 2008-09-01 13:34:25 as ** along with 3 people jfr nuin ellakat
  • Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
    Stat Appl Genet Mol Biol, Vol. 3, No. 1. (2004)
    by GK Smyth
    posted to microarray by talponer on 2008-08-27 14:23:14 as ** along with 8 people giovenko RMGraze maryee mayercd justescaped ugengma heliopais jyuh
  • Combining Results of Microarray Experiments: A Rank Aggregation Approach
    Statistical Applications in Genetics and Molecular Biology, Vol. 5, No. 1. (2006), 15.
    by Robert P Deconde, Sarah Hawley, Seth Falcon, Nigel Clegg, Beatrice Knudsen, Ruth Etzioni
    edited by The
    posted to microarray by talponer on 2008-08-26 10:28:09 as **
  • A fast and flexible method for the segmentation of aCGH data.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by E Ben-Yaacov, YC Eldar
    posted to microarray tiling by talponer on 2008-08-26 09:33:52 as ** along with 3 people rdiaz nuin aviad_work
  • MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data.
    Genome Biol, Vol. 4, No. 1. (2003)
    by SW Doniger, N Salomonis, KD Dahlquist, K Vranizan, SC Lawlor, BR Conklin
    posted to microarray by talponer on 2008-08-18 14:18:12 as ** along with 3 people and 1 group dragonrez heliopais AlexanderPico ConklinLab
  • A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 13. (30 March 2004), pp. 4701-4705.
    by RM Mitra, CA Gleason, A Edwards, J Hadfield, JA Downie, GE Oldroyd, SR Long
    posted to tiling by talponer on 2008-08-08 14:35:49 as **
  • Analysis of fast neutron-generated mutants at the Arabidopsis thaliana HY4 locus
    The Plant Journal, Vol. 10, No. 4. (1996), pp. 755-760.
    by Edward Bruggemann, Korie Handwerger, Carrie Essex, Gisela Storz
    posted to mutagenesis neutron plant tiling by talponer on 2008-08-08 11:31:44 as **
  • Utilizing tiling microarrays for whole-genome analysis in plants
    The Plant Journal, Vol. 53, No. 4. (February 2008), pp. 636-644.
    by Gregory, D Brian, Yazaki, Junshi, Ecker, R Joseph
    posted to tiling by talponer on 2008-08-08 09:58:36 as **
  • Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
    Trends Genet, Vol. 21, No. 2. (February 2005), pp. 93-102.
    by JM Johnson, S Edwards, D Shoemaker, EE Schadt
    posted to tiling by talponer on 2008-08-08 09:56:42 as ** along with 7 people and 3 groups greg briann cassj eoghanharr imouthesmp xico adepace spliceml EisenLab WetBiology
  • Limma: linear models for microarray data
    (2005), pp. 397-420.
    by GK Smyth
    edited by R Gentleman, V Carey, S Dudoit, R Irizarry, W Huber
    posted to no-tag by talponer on 2008-07-04 11:15:40 as **
  • Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets.
    Proc Natl Acad Sci U S A, Vol. 102, No. 24. (14 June 2005), pp. 8633-8638.
    by S Persson, H Wei, J Milne, GP Page, CR Somerville
    posted to microarray statistics tiling by talponer on 2008-05-12 15:44:27 as ** along with 1 person kengg
  • CressExpress: A tool for large-scale mining of expression data from Arabidopsis thaliana.
    Plant physiology (8 May 2008)
    by Vinodh Srinivasasainagendra, Grier Page, Tapan Mehta, Issa Coulibaly, Ann E E Loraine
    posted to microarray statistics by talponer on 2008-05-12 11:22:32 as ** along with 2 people imtechnology kengg
  • BLAT--the BLAST-like alignment tool.
    Genome Res, Vol. 12, No. 4. (April 2002), pp. 656-664.
    by WJ Kent
    posted to sequences tiling by talponer on 2008-05-01 11:35:37 as ** along with 22 people and 1 group pwais umit mmartin paszkows operon miguel pcahan1 Ayest indigoviolet mtagaya treangen michC djkt timflutre olympos cjeans wenhan natstreet antonkratz yoanjacquemin bozdagd gpappas EisenLab
  • A model of molecular interactions on short oligonucleotide microarrays.
    Nat Biotechnol, Vol. 21, No. 7. (July 2003), pp. 818-821.
    by L Zhang, MF Miles, KD Aldape
    posted to tiling by talponer on 2008-04-30 10:03:06 as ** along with 3 people caseybrown nicholso bertelsen
  • Assessing the need for sequence-based normalization in tiling microarray experiments
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 988-997.
    by Royce, E Thomas, Rozowsky, S Joel, Gerstein, B Mark
    posted to microarray tiling by talponer on 2008-04-25 16:19:08 as ** along with 1 person magusina
  • Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray
    Nucl. Acids Res., Vol. 32, No. 2. (2 February 2004), pp. 681-690.
    by Inhan Lee, Alan A Dombkowski, Brian D Athey
    posted to statistics tiling by talponer on 2008-04-21 18:43:02 as **
  • Modeling of DNA microarray data by using physical properties of hybridization
    Proceedings of the National Academy of Sciences, Vol. 100, No. 13. (24 June 2003), pp. 7575-7580.
    by GA Held, G Grinstein, Y Tu
    posted to statistics tiling by talponer on 2008-04-17 16:30:34 as ** along with 1 person waszak
  • Relationship between gene expression and observed intensities in DNA microarraysa modeling study
    Nucleic Acids Research, Vol. 34, No. 9. (2006), pp. e70-e70.
    by Held, , Grinstein, , Tu,
    posted to statistics tiling by talponer on 2008-04-17 16:09:18 as ** along with 1 person bertelsen
  • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
    Proc Natl Acad Sci U S A, Vol. 95, No. 4. (17 February 1998), pp. 1460-1465.
    by J SantaLucia
    posted to statistics tiling by talponer on 2008-04-17 14:28:24 as ** along with 2 people davidng stsaft
  • Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 2928-2933.
    by Sven Rahmann, Christine Grafe
    posted to statistics tiling by talponer on 2008-04-17 14:17:15 as **
  • Improving comparability between microarray probe signals by thermodynamic intensity correction.
    Nucleic Acids Res (2 March 2007)
    by Georg M M Bruun, Rasmus Wernersson, Agnieszka S S Juncker, Hanni Willenbrock, Henrik Bjørn B Nielsen
    posted to microarray statistics tiling by talponer on 2008-04-17 10:29:53 as ** along with 5 people jyuh ghattem GeeSharpMinor niallhaslam waszak
  • Sterol biosynthesis via cycloartenol and other biochemical features related to photosynthetic phyla in the amoeba Naegleria lovaniensis and Naegleria gruberi.
    European journal of biochemistry / FEBS, Vol. 164, No. 2. (15 April 1987), pp. 427-434.
    by D Raederstorff, M Rohmer
    posted to no-tag by talponer on 2008-04-16 11:56:36 as **
  • The role of elastic stresses on leaf venation morphogenesis.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by MF Laguna, S Bohn, EA Jagla
    posted to no-tag by talponer on 2008-04-15 16:44:39 as ** along with 1 person cwr
  • Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 12. (22 March 2005), pp. 4453-4458.
    by V Stolc, MP Samanta, W Tongprasit, H Sethi, S Liang, DC Nelson, A Hegeman, C Nelson, D Rancour, S Bednarek, EL Ulrich, Q Zhao, RL Wrobel, CS Newman, BG Fox, GN Phillips, JL Markley, MR Sussman
    posted to microarray tiling by talponer on 2008-04-03 09:54:33 as **
  • Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays.
    PLoS Genet, Vol. 4, No. 3. (March 2008)
    by X Zhang, S Shiu, A Cal, JO Borevitz
    posted to microarray tiling by talponer on 2008-04-03 09:51:24 as ** along with 1 person rschulz
  • Regulators and Regulation of Legume Root Nodule Development
    Plant Physiol., Vol. 124, No. 2. (1 October 2000), pp. 531-540.
    by Jens Stougaard
    posted to nodulin by talponer on 2008-03-28 11:00:51 as **
  • Nod factor structures, responses, and perception during initiation of nodule development
    Glycobiology, Vol. 12, No. 6. (1 June 2002), pp. 79R-105.
    by Wim D'Haeze, Marcelle Holsters
    posted to nodulin by talponer on 2008-03-28 11:00:08 as **
  • Quantile smoothing of array CGH data
    Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 1146-1153.
    by HC Eilers, X de Menezes
    posted to microarray tiling by talponer on 2008-03-25 09:50:03 as **
  • Summaries of Affymetrix GeneChip probe level data.
    Nucleic Acids Res, Vol. 31, No. 4. (15 February 2003)
    by RA Irizarry, BM Bolstad, F Collin, LM Cope, B Hobbs, TP Speed
    posted to microarray by talponer on 2008-03-11 12:07:36 as ** along with 11 people pcahan1 RMGraze aviad_work vplagnol ghattem heliopais wirawan waszak rschulz bertelsen srp33
  • A physical model for tiling array analysis.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by HR Chung, D Kostka, M Vingron
    posted to microarray by talponer on 2008-03-06 12:35:48 as ** along with 3 people GeeSharpMinor sebastien_vigneau jyuh
  • Model-based analysis of tiling-arrays for ChIP-chip.
    Proc Natl Acad Sci U S A, Vol. 103, No. 33. (15 August 2006), pp. 12457-12462.
    by WE Johnson, W Li, CA Meyer, R Gottardo, JS Carroll, M Brown, XS Liu
    posted to microarray by talponer on 2008-03-06 12:35:03 as ** along with 6 people and 1 group GeeSharpMinor kengg nicholso caseybrown bertelsen bozdagd Plantandetc
  • Virus-Induced Host Gene Shutoff in Animals and Plants
    Virology, Vol. 243, No. 2. (10 April 1998), pp. 261-267.
    by Miguel Aranda, Andrew Maule
    posted to tesi by talponer on 2008-03-05 11:51:23 as **
  • Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
    Neuroscience Letters, Vol. 339, No. 1. (13 March 2003), pp. 62-66.
    by Christian Ramakers, Jan M Ruijter, Ronald H Deprez, Antoon F Moorman
    posted to no-tag by talponer on 2008-03-05 10:50:29 as **
  • Genevestigator. Facilitating Web-Based Gene-Expression Analysis
    Plant Physiol., Vol. 141, No. 4. (1 August 2006), pp. 1164-1166.
    by Aleel K Grennan
    posted to tesi by talponer on 2008-03-04 17:24:11 as **
  • The Gene Ontology (GO) database and informatics resource.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by MA Harris, J Clark, A Ireland, J Lomax, M Ashburner, R Foulger, K Eilbeck, S Lewis, B Marshall, C Mungall, J Richter, GM Rubin, JA Blake, C Bult, M Dolan, H Drabkin, JT Eppig, DP Hill, L Ni, M Ringwald, R Balakrishnan, JM Cherry, KR Christie, MC Costanzo, SS Dwight, S Engel, DG Fisk, JE Hirschman, EL Hong, RS Nash, A Sethuraman, CL Theesfeld, D Botstein, K Dolinski, B Feierbach, T Berardini, S Mundodi, SY Rhee, R Apweiler, D Barrell, E Camon, E Dimmer, V Lee, R Chisholm, P Gaudet, W Kibbe, R Kishore, EM Schwarz, P Sternberg, M Gwinn, L Hannick, J Wortman, M Berriman, V Wood, N de la Cruz, P Tonellato, P Jaiswal, T Seigfried, R White,
    posted to tesi by talponer on 2008-03-04 17:21:30 as ** along with 9 people and 2 groups katerinakal setar balajis nuke2005 benny dullhunk bundschu sgoetz waghsk mlkd generif_paper
  • Expression of stress-response proteins upon whitefly-mediated inoculation of Tomato yellow leaf curl virus in susceptible and resistant tomato plants
    Molecular Plant-Microbe Interactions, Vol. 20, No. 11. (November 2007), pp. 1376-1383.
    by R Gorovits, F Akad, H Beery, F Vidavsky, A Mahadav, H Czosnek
    posted to no-tag by talponer on 2008-03-03 16:03:34 as **
  • A heat shock transcription factor in pea is differentially controlled by heat and virus replication
    The Plant Journal, Vol. 20, No. 2. (1999), pp. 153-161.
    by Miguel A Aranda, Margarita Escaler, Carole L Thomas, Andrew J Maule
    posted to tesi by talponer on 2008-03-03 15:55:02 as **
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