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shigepong's library [306 articles]

Recent papers added to shigepong's library.
  • Apparently low reproducibility of true differential expression discoveries in microarray studies.
    Bioinformatics (Oxford, England) (16 July 2008)
    by Min Zhang, Chen Yao, Zheng Guo, Jinfeng Zou, Lin Zhang, Hui Xiao, Dong Wang, Da Yang, Xue Gong, Jing Zhu, Yanhui Li, Xia Li
    posted to fdr by shigepong on 2008-07-23 07:13:55 as *****
  • A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?
    Bioinformatics (Oxford, England) (17 July 2008)
    by B Haibe-Kains, C Desmedt, C Sotiriou, G Bontempi
    posted to microarray classifier by shigepong on 2008-07-23 07:13:38 as ****
  • PathCluster: a framework for gene set-based hierarchical clustering.
    Bioinformatics (Oxford, England) (15 July 2008)
    by Tae-Min M Kim, Seon-Hee H Yim, Yong-Bok B Jeong, Yu-Chae C Jung, Yeun-Jun J Chung
    posted to clustering by shigepong on 2008-07-19 01:29:15 as ** along with 1 person maralena
  • A unified approach to false discovery rate estimation
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Korbinian Strimmer
    posted to fdr by shigepong on 2008-07-12 07:44:21 as ** along with 4 people joaocarrico nuin barriot chad_davis
  • On correcting the overestimation of the permutation based false discovery rate estimator.
    Bioinformatics (Oxford, England) (23 June 2008)
    by Shuo Jiao, Shunpu Zhang
    posted to fdr by shigepong on 2008-06-27 17:05:52 as ***** along with 1 person djkt
  • Multiple tests of association with biological annotation metadata
    (20 May 2008)
    by Sandrine Dudoit, Sündüz Keleş, Mark J van der Laan
    posted to networkestimation fdr by shigepong on 2008-05-22 02:06:23 as ****
  • GraphWeb: mining heterogeneous biological networks for gene modules with functional significance.
    Nucleic acids research (6 May 2008)
    by Jüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler, Jaak Vilo
    posted to networkestimation by shigepong on 2008-05-09 09:52:23 as **** along with 4 people ptrobajo jyuh maralena pinney
  • A correction for estimating error when using the Local Pooled Error Statistical Test.
    Bioinformatics (Oxford, England) (1 May 2008)
    by Carl Murie, Robert Nadon
    posted to msht fdr by shigepong on 2008-05-07 10:02:57 as *****
  • The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks
    BMC Bioinformatics, Vol. 9 (02 May 2008), 227.
    by Anatolij P Potapov, Bjorn Goemann, Edgar Wingender
    posted to networkestimation by shigepong on 2008-05-07 09:59:54 as **** along with 2 people joaocarrico bootsy
  • An efficient method to identify differentially expressed genes in microarray experiments.
    Bioinformatics (Oxford, England) (3 May 2008)
    by Huaizhen Qin, Tao Feng, Scott A A Harding, Chung-Jui J Tsai, Shuanglin Zhang
    posted to microarray differential by shigepong on 2008-05-07 09:57:47 as ***** along with 2 people Stew natstreet
  • A Note on the False Discovery Rate and Inconsistent Comparisons between Experiments.
    Bioinformatics (Oxford, England) (19 April 2008)
    by Roger Higdon, Gerald van V Belle, Eugene Kolker
    posted to microarray fdr by shigepong on 2008-04-23 08:23:39 as ** along with 6 people braynor renatomilani giovenko wisdom_love girschick jyuh
  • Missing value imputation improves clustering and interpretation of gene expression microarray data
    BMC Bioinformatics, Vol. 9 (18 April 2008), 202.
    by Johannes Tuikkala, Laura L Elo, Olli S Nevalainen, Tero Aittokallio
    posted to missing microarray by shigepong on 2008-04-23 08:16:00 as ** along with 2 people jyuh bertelsen
  • A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Harri Kiiveri
    posted to microarray by shigepong on 2008-04-17 11:00:57 as **** along with 5 people akastrin jyuh joaocarrico osilander iceman2995
  • Predicting cancer involvement of genes from heterogeneous data
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Ramon Aragues, Chris Sander, Baldo Oliva
    posted to cancer differential by shigepong on 2008-04-03 04:28:11 as *** along with 7 people and 1 group reyez aheilbut cerami barriot renatomilani smgomez henryk69 GomezLab
  • Neurobiological models of two-choice decision making can be reduced to a one-dimensional nonlinear diffusion equation.
    PLoS Comput Biol, Vol. 4, No. 3. (March 2008)
    by A Roxin, A Ledberg
    posted to mind by shigepong on 2008-03-31 00:49:38 as ****
  • PCCA: a program for phylogenetic canonical correlation analysis
    Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 1018-1020.
    by Liam J Revell, Alexis S Harrison
    posted to furuya matrixdecomposition by shigepong on 2008-03-26 23:57:59 as **** along with 1 person vrich
  • Unequal group variances in microarray data analyses.
    Bioinformatics (14 March 2008)
    by Meaza Demissie, Barbara Mascialino, Stefano Calza, Yudi Pawitan
    posted to differential by shigepong on 2008-03-21 05:03:23 as ***** along with 3 people jfr aviad_work jyuh
  • ChIPCodis: Mining complex regulatory systems in yeast by concurrent enrichment analysis of Chip-on-chip data.
    Bioinformatics (12 March 2008)
    by Federico Abascal, Pedro Carmona-Saez, Jose-Maria M Carazo, Alberto Pascual-Montano
    posted to causality networkestimation by shigepong on 2008-03-16 09:12:30 as ****
  • Merging Two Gene Expression Studies via Cross Platform Normalization.
    Bioinformatics (5 March 2008)
    by Andrey A A Shabalin, Håkon Tjelmeland, Cheng Fan, Charles M M Perou, Andrew B B Nobel
    posted to microarray microarrayimage by shigepong on 2008-03-09 07:46:51 as ****
  • Language affects patterns of brain activation associated with perceptual decision.
    Proc Natl Acad Sci U S A (3 March 2008)
    by Li Hai H Tan, Alice H D H Chan, Paul Kay, Pek-Lan L Khong, Lawrance K C K Yip, Kang-Kwong K Luke
    posted to misc by shigepong on 2008-03-06 13:16:56 as **** along with 1 person briordan
  • How reliably can we predict the reliability of protein structure predictions?
    BMC Bioinformatics, Vol. 9 (03 March 2008), 137.
    by Istvan Miklos, Adam Novak, Balazs Dombai, Jotun Hein
    posted to bayesian by shigepong on 2008-03-06 09:09:28 as **
  • Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays.
    Bioinformatics (3 March 2008)
    by Jin Xu, Xinping Cui
    posted to differential microarray by shigepong on 2008-03-06 09:05:03 as ***** along with 5 people bertelsen GeeSharpMinor kengg jyuh chrys
  • Causality and Pathway Search in Microarray Time Series Experiment.
    Bioinformatics (26 February 2008)
    by Radhakrishnan Nagarajan, Meenakshi Upreti
    posted to causality microarray timeseries by shigepong on 2008-03-01 17:03:56 as **** along with 1 person jyuh
  • Merging microarray data from separate breast cancer studies provides a robust prognostic test
    BMC Bioinformatics, Vol. 9 (27 February 2008), 125.
    by Lei Xu, Aik C Tan, Raimond L Winslow, Donald Geman
    posted to cancer microarray prognosis by shigepong on 2008-03-01 08:10:23 as ** along with 1 person chrisamiller
  • Effects of dependence in high-dimensional multiple testing problems
    BMC Bioinformatics, Vol. 9 (25 February 2008), 114.
    by Kyung I Kim, Mark A van de Wiel
    posted to fdr by shigepong on 2008-02-28 14:34:46 as ***** along with 3 people jfr jyuh barriot
  • Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
    Bioinformatics (21 February 2008)
    by Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, D Stephen S Charnock-Jones, Cristin Print, Satoru Miyano
    posted to networkestimation by shigepong on 2008-02-24 08:42:51 as ** along with 2 people jyuh bertelsen
  • Predicting Human Interactive Learning by Regret-Driven Neural Networks
    Science, Vol. 319, No. 5866. (22 February 2008), pp. 1111-1113.
    by Davide Marchiori, Massimo Warglien
    posted to science by shigepong on 2008-02-24 08:40:49 as ** along with 5 people and 1 group mdimmic brian Koh zwang shivakmr VisionLab
  • Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics.
    Bioinformatics (19 February 2008)
    by Yung-Keun K Kwon, Kwang-Hyun H Cho
    posted to networkestimation networkphysics by shigepong on 2008-02-23 01:52:15 as ** along with 3 people jyuh grahamc bootsy
  • Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs.
    Bioinformatics (19 February 2008)
    by Juby Jacob, Marcel Jentsch, Dennis Kostka, Stefan Bentink, Rainer Spang
    posted to networkestimation by shigepong on 2008-02-23 01:52:06 as ** along with 1 person ptrobajo
  • Statistical methodology for the analysis of dye-switch microarray experiments
    BMC Bioinformatics, Vol. 9 (13 February 2008), 98.
    by Tristan Mary-Huard, Julie Aubert, Nadera Mansouri-Attia, Olivier Sandra, Jean-Jacques Daudin
    posted to microarray microarrayimage by shigepong on 2008-02-16 07:01:05 as ** along with 3 people jfr jyuh GeeSharpMinor
  • Manifold parametrizations by eigenfunctions of the Laplacian and heat kernels.
    Proc Natl Acad Sci U S A (7 February 2008)
    by Peter W W Jones, Mauro Maggioni, Raanan Schul
    posted to kernel misc by shigepong on 2008-02-10 23:53:39 as ****
  • The kernel energy method of quantum mechanical approximation carried to fourth-order terms.
    Proc Natl Acad Sci U S A (4 February 2008)
    by Lulu Huang, Lou Massa, Jerome Karle
    posted to interesting by shigepong on 2008-02-07 07:51:05 as **
  • Bayesian models based on test statistics for multiple hypothesis testing problems.
    Bioinformatics (1 February 2008)
    by Yuan Ji, Yiling Lu, Gordon B B Mills
    posted to bayesian fdr multipletesting by shigepong on 2008-02-07 02:04:10 as ***** along with 8 people craigwilson06 jyuh jfr djkt GeeSharpMinor bertelsen mailund maralena
  • Computation of significance scores of unweighted Gene Set Enrichment Analyses
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Andreas Keller, Christina Backes, Hans P Lenhof
    posted to enrichment-analyses by shigepong on 2008-02-05 08:52:54 as ** along with 4 people and 1 group heliopais jfr ealloza GeeSharpMinor BioinfoCIPF
  • Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction.
    Proc Natl Acad Sci U S A (31 January 2008)
    by Xing Zhang, Ethan Settembre, Chen Xu, Philip R R Dormitzer, Richard Bellamy, Stephen C C Harrison, Nikolaus Grigorieff
    posted to superresolution by shigepong on 2008-02-04 12:44:09 as ** along with 1 person TOchi
  • A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes.
    Bioinformatics, Vol. 17, No. 6. (June 2001), pp. 509-519.
    by P Baldi, AD Long
    posted to differential by shigepong on 2008-02-03 05:23:46 as ** along with 7 people and 1 group textoris lyongu dquest daniel_quest jeremymiller jo_davies baldigroup GeschwindLab
  • Estimating Large Scale Signaling Networks through Nested Effect Models with Intervention Effects from Microarray Data.
    Bioinformatics (28 January 2008)
    by Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beissbarth
    posted to networkestimation by shigepong on 2008-02-03 02:35:10 as ** along with 2 people czeller jyuh
  • Why is Real-World Visual Object Recognition Hard?
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e27.
    by Nicolas Pinto, David D Cox, James J Dicarlo
    posted to visualobjectrecognition by shigepong on 2008-02-03 02:34:56 as ** along with 5 people napvasconcelos edgarbc alterego alexstorer cwr
  • Getting Started in Text Mining
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e20.
    by Bretonnel K Cohen, Lawrence Hunter
    posted to textmining by shigepong on 2008-02-03 02:34:39 as ** along with 13 people and 1 group jfr quianominorleo TheresaNiederberger ulmer jyuh y4su0 yas dullhunk hpiwowar sebastien_vigneau cjeans wchapman sci91078 dbmi-nlp
  • Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Cornelia Froemke, Ludwig Hothorn, Siegfried Kropf
    posted to differential fdr by shigepong on 2008-02-03 02:30:46 as ***** along with 2 people jyuh mijam
  • Inferring gene expression dynamics via functional regression analysis.
    BMC Bioinformatics, Vol. 9, No. 1. (28 January 2008)
    by Hans-Georg G Muller, Jeng-Min M Chiou, Xiaoyan Leng
    posted to networkestimation by shigepong on 2008-02-03 02:25:04 as **
  • Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by David Smith, Pal Saetrom, Ola Snove, Cathryn Lundberg, Guillermo Rivas, Carlotta Glackin, Garrett Larson
    posted to metaanalysismicroarray by shigepong on 2008-02-03 02:24:48 as ** along with 3 people and 1 group jfr heliopais xili03 microRNA
  • Using repeated measurements to validate hierarchical gene clusters.
    Bioinformatics (19 January 2008)
    by Laurent Bréhélin, Olivier Gascuel, Olivier Martin
    posted to clustering by shigepong on 2008-01-23 07:26:31 as ** along with 3 people jyuh jfr dfournier
  • Sparse representation and Bayesian detection of genome copy number alterations from microarray data.
    Bioinformatics (18 January 2008)
    by Roger Pique-Regi, Jordi Monso-Varona, Antonio Ortega, Robert Seeger, Timothy Triche, Shahab Asgharzadeh
    posted to cgh by shigepong on 2008-01-23 07:26:18 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 differential microarray by shigepong on 2008-01-23 07:22:12 as *** along with 4 people jyuh cannin jfr jdiezperezj
  • Reconstruction of genetic association networks from microarray data: A partial least squares approach.
    Bioinformatics (18 January 2008)
    by Vasyl Pihur, Somnath Datta, Susmita Datta
    posted to furuya networkestimation by shigepong on 2008-01-23 07:21:40 as ** along with 6 people winterschlaefer jyuh cannin jfr aconesa sotacam
  • Function approximation approach to the inference of reduced NGnet models of genetic networks
    BMC Bioinformatics, Vol. 9 (14 January 2008), 23.
    by Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura, Mariko Hatakeyama
    posted to networkestimation by shigepong on 2008-01-21 13:45:44 as **
  • Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models
    BMC Bioinformatics, Vol. 9 (10 January 2008), 14.
    by Harald Binder, Martin Schumacher
    posted to cancer microarray survival by shigepong on 2008-01-13 11:50:13 as ***** along with 3 people jyuh jfr msierk
  • Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
    by Yoav Benjamini, Yosef Hochberg
    posted to fdr by shigepong on 2008-01-11 14:39:52 as ** along with 13 people and 2 groups isimpson dragonrez jyuh RMGraze oannes vplagnol frohike grahamc ccr axelon ugengma amsantos rschulz Bioinformatics Regulomics_UCHSC
  • Supervised inference of gene-regulatory networks
    BMC Bioinformatics, Vol. 9 (04 January 2008), 2.
    by Cuong C To, Jiri Vohradsky
    posted to furuya networkestimation by shigepong on 2008-01-09 08:56:02 as ** along with 1 person gracio
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