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Tag r [323 articles]

Recent papers classified by the tag r.
  • notes MedlineR: an open source library in R for Medline literature data mining.
    Bioinformatics, Vol. 20, No. 18. (12 December 2004), pp. 3659-3661.
    by SM Lin, P McConnell, KF Johnson, J Shoemaker
    posted to r by za on 2007-02-14 12:58:10 as ** along with 5 people and 2 groups cisevol druvus irenas Enro BioGeek BergmanLab dbk-lab
  • notes ROCR: visualizing classifier performance in R.
    Bioinformatics (11 August 2005)
    by Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
    posted to r roc stat by za on 2007-02-14 12:53:34 as *** along with 11 people and 4 groups natstreet druvus BragilMassoud ana barry Ayest lyongu marcius schlauchi gokhan bertelsen structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • The SNPMaP package for R: A framework for genome-wide association using DNA pooling on microarrays.
    Bioinformatics (Oxford, England) (12 November 2008)
    by Oliver S P S Davis, Robert Plomin, Leonard C C Schalkwyk
    posted to snp r by ykadi on 2008-12-04 14:20:19 as **
  • Pvclust: an R package for assessing the uncertainty in hierarchical clustering.
    Bioinformatics, Vol. 22, No. 12. (15 June 2006), pp. 1540-1542.
    by R Suzuki, H Shimodaira
    posted to clustering hierarchical r software by wnpx on 2006-09-02 11:32:40 as ** along with 8 people druvus jfr maryee josepe ghattem elfar quianominorleo briordan
  • Proposed design for gR, a graphical models toolkit for R
    by Kevin P Murphy
    posted to bayesian bayesnet design r software by wnpx on 2006-07-13 17:55:43 as ** along with 2 people markusd CarlosSantos
  • Fast manipulation of multi-dimensional arrays in Matlab
    (2002)
    by K Murphy
    posted to implementation matlab programming r by wnpx on 2006-07-13 18:00:49 as **
  • BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network.
    Bioinformatics (27 September 2006)
    by Xiaohui Chen, Ming Chen, Kaida Ning
    posted to bayesian bayesnet gene network r regulation by wnpx on 2006-11-18 18:09:29 as ** along with 6 people guhjy frohike jhatrimatri shigepong ramakris waszak
  • From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Rainer O Rhein, Korbinian Strimmer
    posted to inference r by wnpx on 2007-08-06 16:19:58 as ** along with 5 people nolodie druvus GeeSharpMinor jo_davies heliopais
  • MDQC: a new quality assessment method for microarrays based on quality control reports
    Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3162-3169.
    by Cohen, Zsuzsanna Hollander, Enqing Shen, Ruben H Zamar, Robert Balshaw, Andreas Scherer, Bruce Mcmanus, Paul Keown, Robert W Mcmaster, Raymond T Ng
    posted to microarray quality r software by waszak on 2007-12-10 14:29:13 as ** along with 2 people guhjy aviad_work
  • An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays
    Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1278-1285.
    by Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Tomoharu Agata, Akiko Kashiwagi, Hiroshi Shimizu, Tetsuya Yomo
    posted to algorithm microarray normalization r by waszak on 2008-05-17 18:08:10 as ** along with 2 people heliopais giovenko
  • A comparison study: applying segmentation to array CGH data for downstream analyses
    Bioinformatics, Vol. 21, No. 22. (15 November 2005), pp. 4084-4091.
    by Hanni Willenbrock, Jane Fridlyand
    posted to software r cnp cgh algorithm acgh by waszak on 2008-10-08 15:15:21 as ** along with 2 people shigepong ellakat
  • RReportGenerator : Automatic reports from routine statistical analysis using R
    Bioinformatics (24 November 2007), btm556.
    by Wolfgang Raffelsberger, Yannick Krause, Luc Moulinier, David Kieffer, Anne-Laure Morand, Laurent Brino, Olivier Poch
    posted to affymetrix r by waszak on 2007-12-03 20:39:09 as ** along with 7 people natstreet druvus guhjy jfr mailund maralena GeeSharpMinor
  • A robust statistical method for case-control association testing with copy number variation.
    Nature genetics (7 September 2008)
    by Chris Barnes, Vincent Plagnol, Tomas Fitzgerald, Richard Redon, Jonathan Marchini, David Clayton, Matthew E E Hurles
    posted to software snp r ld gmm em cnv associationstudy algorithm affymetrix by waszak on 2008-10-08 15:01:08 as ** along with 12 people and 1 group pengchy ptrobajo vplagnol caseybrown Zephyrus dakelley buyske misonneh djkt rdiaz Stew guhjy Roswell Cancer Crosstalk
  • Transcript mapping with high-density oligonucleotide tiling arrays
    Bioinformatics, Vol. 22, No. 16. (15 August 2006), pp. 1963-1970.
    by Wolfgang Huber, Joern Toedling, Lars M Steinmetz
    posted to tiling software r normalization microarray algorithm by waszak on 2008-10-08 15:07:35 as ** along with 6 people raiyar johncumbers jtaylor ptrobajo tresch GeeSharpMinor
  • oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language
    Bioinformatics (17 September 2007), btm469.
    by Remo Sanges, Francesca Cordero, Raffaele A Calogero
    posted to affymetrix bioconductor r software by waszak on 2007-12-10 14:27:34 as ** along with 2 people guhjy rdiaz
  • Applied Statistics Using SPSS, STATISTICA, MATLAB and R
    (20 July 2007)
    by Joaquim
    posted to statistics r matbal book by treangen on 2008-11-20 13:57:44 as ** along with 2 people natstreet druvus
  • R/parallel - speeding up bioinformatics analysis with R
    BMC Bioinformatics, Vol. 9 (22 September 2008), 390.
    by Gonzalo Vera, Ritsert C Jansen, Remo L Suppi
    posted to r parallel by talponer on 2008-10-28 11:57:57 as ** along with 19 people and 1 group siebert operon dipenps guhjy dakelley chad_davis ptrobajo pengchy shikin robertlischke chrisamiller cisevol druvus renatomilani rdiaz nuin GeeSharpMinor neils jandot BergmanLab
  • beadarray: R classes and methods for Illumina bead-based data
    Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2183-2184.
    by Mark J Dunning, Mike L Smith, Matthew E Ritchie, Simon Tavare
    posted to beadarray illumina r by Stew on 2008-08-04 17:27:25 as ** along with 4 people heliopais raylim srp33 guhjy
  • GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.
    Bioinformatics (12 May 2007)
    by Sean Davis, Paul S S Meltzer
    posted to r database by shikin on 2008-12-02 16:16:43 as **** along with 7 people guhjy jfr ugengma giovenko ablejec zhouyu bertelsen
  • Identifying differentially-expressed subnetworks with MMG
    Bioinformatics (25 September 2008), btn499.
    by Josselin Noirel, Guido Sanguinetti, Phillip C Wright
    posted to subnetwork r model mixture implementation graphs expressed differentially by sg45653 on 2008-12-02 15:22:44 as ** along with 8 people pengchy behindtherabbit roys jiayi369 tmmurali bertelsen guhjy rdiaz
  • Data Analysis and Graphics Using R: An Example-based Approach (Cambridge Series in Statistical and Probabilistic Mathematics)
    (26 December 2006)
    by John Maindonald, John Braun
    posted to r software-guide by sfcheung on 2008-08-15 14:31:43 as ** along with 4 people jfelipe fheintz bigbossman quianominorleo
  • Fractals and Statistics: an R package called ifs
    by Stefano M Iacus, Davide La Torre
    posted to fractal ifs r statistics by scis0000001 on 2006-09-07 15:01:54 as **
  • A Conserved Carboxylesterase Is a SUPPRESSOR OF AVRBST-ELICITED RESISTANCE in Arabidopsis
    Plant Cell, Vol. 19, No. 2. (1 February 2007), pp. 688-705.
    by Sebastien Cunnac, Ariane Wilson, Jamie Nuwer, Angela Kirik, Gayathri Baranage, Mary B Mudgett
    posted to r ttss by saru on 2007-04-21 05:20:29 as **
  • Tobacco mosaic virus regulates the expression of its own resistance gene N.
    Plant Physiol, Vol. 135, No. 4. (August 2004), pp. 2392-2397.
    by M Levy, O Edelbaum, I Sela
    posted to n r by saru on 2007-07-07 08:49:47 as **
  • Gene expression signatures from three genetically separable resistance gene signaling pathways for downy mildew resistance.
    Plant Physiol, Vol. 135, No. 2. (June 2004), pp. 1129-1144.
    by T Eulgem, VJ Weigman, HS Chang, JM McDowell, EB Holub, J Glazebrook, T Zhu, JL Dangl
    posted to r rpp4 rpp7 rpp8 by saru on 2007-02-27 01:46:15 as ** along with 1 person and 1 group wrowell Cline_lab
  • From the Cover: Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes
    PNAS, Vol. 103, No. 23. (6 June 2006), pp. 8888-8893.
    by Peter N Dodds, Gregory J Lawrence, Ann-Maree Catanzariti, Trazel Teh, Ching-I Wang, Michael A Ayliffe, Bostjan Kobe, Jeffrey G Ellis
    posted to l r by saru on 2007-02-17 05:52:05 as read along with 2 people and 1 group cmm tale FAB-lab
  • Downy mildew (Peronospora parasitica) resistance genes in Arabidopsis vary in functional requirements for NDR1, EDS1, NPR1 and salicylic acid accumulation.
    Plant J, Vol. 22, No. 6. (June 2000), pp. 523-529.
    by JM McDowell, A Cuzick, C Can, J Beynon, JL Dangl, EB Holub
    posted to r rpp8 rps7 by saru on 2007-02-27 01:36:59 as **
  • Members of the Arabidopsis HRT/RPP8 family of resistance genes confer resistance to both viral and oomycete pathogens.
    Plant Cell, Vol. 12, No. 5. (May 2000), pp. 663-676.
    by MB Cooley, S Pathirana, HJ Wu, P Kachroo, DF Klessig
    posted to hrt r by saru on 2006-10-06 08:43:34 as read
  • Type III Effector Activation via Nucleotide Binding, Phosphorylation, and Host Target Interaction
    PLoS Pathogens, Vol. 3, No. 3. (1 March 2007), e48.
    by Darrell Desveaux, Alex U Singer, Ai-Jiuan Wu, Brian C Mcnulty, Laura Musselwhite, Zachary Nimchuk, John Sondek, Jeffery L Dangl
    posted to avr r structure by saru on 2007-05-01 06:41:10 as **
  • Plant–fungal associations Cue for the branching connection
    Nature, Vol. 435, No. 7043. (08 June 2005), pp. 750-751.
    by Martin Parniske
    posted to r review by saru on 2007-05-28 03:21:09 as **
  • Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae.
    Plant Cell, Vol. 15, No. 2. (February 2003), pp. 317-330.
    by Y Tao, Z Xie, W Chen, J Glazebrook, HS Chang, B Han, T Zhu, G Zou, F Katagiri
    posted to basal r transcript by saru on 2007-06-18 02:24:43 as **
  • The Mi-1-Mediated Pest Resistance Requires Hsp90 and Sgt1.
    Plant Physiol (9 March 2007)
    by Kishor K K Bhattarai, Qi Li, Yule Liu, Savithramma P P Dinesh-Kumar, Isgouhi Kaloshian
    posted to hsp90 mi-1 r sgt1 by saru on 2007-03-15 03:21:10 as ** along with 1 person kikubh
  • Genome-Wide Analysis of NBS-LRR-Encoding Genes in Arabidopsis
    Plant Cell, Vol. 15, No. 4. (1 April 2003), pp. 809-834.
    by Blake C Meyers, Alexander Kozik, Alyssa Griego, Hanhui Kuang, Richard W Michelmore
    posted to r by saru on 2006-08-08 10:31:25 as read along with 2 people and 2 groups bsmagic talponer Bioinformatics bioinplant
  • EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels.
    Plant J (23 January 2007)
    by Thomas Eulgem, Tokuji Tsuchiya, Xiao-Jun J Wang, Britt Beasley, Alayne Cuzick, Mahmut Tör, Tong Zhu, John M M McDowell, Eric Holub, Jeffery L L Dangl
    posted to edm2 r rpp7 by saru on 2007-02-16 01:18:02 as read
  • The Pto kinase of tomato, which regulates plant immunity, is repressed by its myristoylated N terminus.
    J Biol Chem, Vol. 281, No. 36. (8 September 2006), pp. 26578-26586.
    by VM Andriotis, JP Rathjen
    posted to pto r by saru on 2007-02-27 02:02:00 as **
  • Interaction between domains of a plant NBS-LRR protein in disease resistance-related cell death.
    EMBO J, Vol. 21, No. 17. (2 September 2002), pp. 4511-4519.
    by P Moffett, G Farnham, J Peart, DC Baulcombe
    posted to r rx by saru on 2007-02-26 03:24:10 as **
  • A viral resistance gene from common bean functions across plant families and is up-regulated in a non-virus-specific manner
    PNAS (31 July 2006), 0604815103.
    by Young-Su Seo, Maria R Rojas, Jung-Youn Lee, Sang-Won Lee, Jong-Seong Jeon, Pamela Ronald, William J Lucas, Robert L Gilbertson
    posted to r by saru on 2006-08-08 10:45:57 as read
  • Plant disease resistance protein signaling: NBS-LRR proteins and their partners.
    Curr Opin Plant Biol, Vol. 7, No. 4. (August 2004), pp. 391-399.
    by Y Belkhadir, R Subramaniam, JL Dangl
    posted to r review by saru on 2007-03-05 10:32:55 as ** along with 1 person kikubh
  • Single amino acid alterations in Arabidopsis thaliana RCY1 compromise resistance to Cucumber mosaic virus, but differentially suppress hypersensitive response-like cell death.
    Plant Mol Biol (29 August 2006)
    by Ken-Taro T Sekine, Takeaki Ishihara, Shu Hase, Tomonobu Kusano, Jyoti Shah, Hideki Takahashi
    posted to r by saru on 2006-09-06 09:49:00 as read
  • The transcriptome of Arabidopsis thaliana during systemic acquired resistance.
    Nat Genet, Vol. 26, No. 4. (December 2000), pp. 403-410.
    by K Maleck, A Levine, T Eulgem, A Morgan, J Schmid, KA Lawton, JL Dangl, RA Dietrich
    posted to r review sar transcriptome by saru on 2008-01-28 10:56:37 as **
  • Plant disease susceptibility conferred by a "resistance" gene
    Proceedings of the National Academy of Sciences (5 September 2007), 0702572104.
    by Jennifer M Lorang, Teresa A Sweat, Thomas J Wolpert
    posted to lov1 r by saru on 2007-09-07 03:22:42 as **
  • Expression of RPS4 in tobacco induces an AvrRps4-independent HR that requires EDS1, SGT1 and HSP90.
    Plant J, Vol. 40, No. 2. (October 2004), pp. 213-224.
    by Y Zhang, S Dorey, M Swiderski, JD Jones
    posted to r rps4 by saru on 2007-02-26 03:53:58 as **
  • The genomic dynamics and evolutionary mechanism of the Pi2/9 locus in rice.
    Mol Plant Microbe Interact, Vol. 20, No. 1. (January 2007), pp. 63-71.
    by B Zhou, M Dolan, H Sakai, GL Wang
    posted to pi29 r by saru on 2007-01-28 01:09:13 as **
  • Resistance proteins: molecular switches of plant defence
    Current Opinion in Plant Biology, Vol. 9, No. 4. (August 2006), pp. 383-390.
    by Frank LW Takken, Mario Albrecht, Wladimir IL Tameling
    posted to r review by saru on 2007-05-29 10:37:06 as **
  • Indirect activation of a plant nucleotide binding site-leucine-rich repeat protein by a bacterial protease.
    Proc Natl Acad Sci U S A (2 February 2007)
    by Jules Ade, Brody J J Deyoung, Catherine Golstein, Roger W W Innes
    posted to rps5 r by saru on 2007-02-07 07:13:12 as read
  • Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice.
    J Genet Genomics, Vol. 34, No. 3. (March 2007), pp. 247-257.
    by L Gu, R Guo
    posted to alternative r by saru on 2007-05-17 01:17:34 as **
  • MAP kinases function at the downstream of HSP90 and upstream of mitochondria in TMV-resistance gene N-mediated hypersensitive cell death.
    Plant Cell Physiol (8 February 2007)
    by Reona Takabatake, Yuko Ando, Shigemi Seo, Shinpei Katou, Shinya Tsuda, Yuko Ohashi, Ichiro Mitsuhara
    posted to mapk n r by saru on 2007-03-05 10:43:39 as **
  • RPP13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica.
    Plant J, Vol. 21, No. 2. (January 2000), pp. 177-188.
    by PD Bittner-Eddy, IR Crute, EB Holub, JL Beynon
    posted to r rpp13 by saru on 2007-03-05 10:37:58 as **
  • Overexpression of CRK13, an Arabidopsis cysteine-rich receptor-like kinase, results in enhanced resistance to Pseudomonas syringae.
    Plant J (5 April 2007)
    by Biswa R R Acharya, Surabhi Raina, Shahina B B Maqbool, Guru Jagadeeswaran, Stephen L L Mosher, Heidi M M Appel, Jack C C Schultz, Daniel F F Klessig, Ramesh Raina
    posted to crk kinase r by saru on 2007-04-24 07:35:01 as **
  • Arabidopsis RPP4 is a member of the RPP5 multigene family of TIR-NB-LRR genes and confers downy mildew resistance through multiple signalling components.
    Plant J, Vol. 29, No. 4. (February 2002), pp. 439-451.
    by EA van der Biezen, CT Freddie, K Kahn, JE Parker, JD Jones
    posted to r by saru on 2006-09-07 04:40:36 as **
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