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  • xslink
    read the discussion below about constant definitions before trying to compile The Makefile we are distributing uses the gcc compiler distributed by the Free Software Foundation If gcc is not available to you or you would like to use the cc compiler instead you can change this by When you issue the make command add the tag CC cc this will override the setting in Makefile e g make xslink CC cc In general we recommend using gcc instead of cc because gcc produces faster machine code If you are unfamiliar with these concepts and want help see your system administrator for information about how your particular system is organized Constant definitions VERY IMPORTANT There are 4 constants that are defined in commondefs h and 2 constants that are defined in moddefs h that you will want to set before compiling This means that you will edit the files to put in the appropriate numbers and then compile The constants in commondefs h are maxhap maxclasssize maxneed maxprobclass maxhap and maxneed have been in the programs all along the other two are new The constants in moddefs h are AUTOSOMAL RUN The reasons to set the constants correctly are If the constants are too low you may get the wrong answer If the constants are too high you may run out of space unnecessarily If the constants are too high it slows down the program unnecessarily So set the constants MAXHAP is the maximum number of possible joint haplotypes It is the product of the number of alleles at each locus in the analysis For example if you want to do a 3 locus SLINK run in which the 3 loci have 2 3 and 5 alleles respectively set maxhap to 30 which is 2x3x5 MAXCLASSSIZE is the maximum size of an isozygote class for one individual It should be set to 2 k 1 where k is the number of loci In numbers Use 2 for 2 loci Use 4 for 3 loci Use 8 for 4 loci Use 16 for 5 loci and so on MAXNEED is the number of different recombination probabilities needed Let k 3 be the number of loci The formula to compute maxneed is maxneed C k 0 1 2 C k 1 1 2 C k 2 2 2 C k 3 4 2 C k 4 8 2 C k 5 16 2 C k k maxclassize maxclasssize The notation C k i stands for the binomial coefficient k choose i That is the number of ways of choosing i objects out of k when order doesn t matter and repetition is not allowed Three important values for maxneed are maxneed 7 for 2 loci use this value for LODSCORE maxneed 32 for 3 loci maxneed 157 for 4 loci maxneed 782 for 5 loci MAXPROBCLASS The formula for maxprobclass is similar to maxneed It is maxprobclass C k 0 1 C k 1 1 C k 2 2 C k 3

    Original URL path: http://linkage.rockefeller.edu/soft/xslink.html (2012-11-26)
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  • micrarray books
    Advanced Analysis of Gene Expression Microarray Data World Scientific List price 87 edited by Wei Zhang Ilya Shmulevich 2006 Computational and Statistical Approaches to Genomics second edition Springer 2005 David B Allison 2005 DNA Microarrays and Related Genomic Techniques Design Analysis and Interpretation of Experiments Chapman Hall CRC List price 89 95 Jode Edwards David Allison Grier Page T Mark Beasley 2005 DNA Microarrays and Related Genomics Techniques Design Analysis and Interpretation of Experiments CRC Press List price 93 95 edited by Robert Gentleman Wolfgang Huber Vincent J Carey Rafael A Irizarry and Sandrine Dudoit 2005 Bioinformatics and Computational Biology Solutions Using R and Bioconductor Springer List price 89 95 Hans Joachim Müller Thomas Roeder 2005 Microarrays Academic Press List price 54 95 Jennifer S Shoemaker Simon M Lin 2005 Methods Of Microarray Data Analysis IV Springer Verlag List price 109 Nature Genetics vol 37 Supplement 6s Chipping Forecast III June 2005 http www nature com ng journal v37 n6s index html 2004 ed Dev Kambhampati 2004 Protein Microarray Technology John Wiley Sons List price 135 00 Steen Knudsen 2004 Guide to Analysis of DNA Microarray Data John Wiley Sons 2nd edition List price 31 79 Robert Matson 2004 Applying Genomic and Proteomic Microarray Technology in Drug Discovery CRC Press List price 185 95 Mei Ling Ting Lee 2004 Analysis of Microarray Gene Expression Data Springer List price 69 95 Geoffrey J McLachlan Kim Anh Do 2004 Analyzing Microarray Gene Expression Data John Wiley Sons List price 94 95 Mark Schena 2004 Protein Microarrays Jones Bartless List price 124 95 Richard M Simon Edward L Korn Lisa M McShane Michael D Radmacher George W Wright Yingdong Zhao 2004 Design and Analysis of DNA Microarray Investigations Springer Verlag List price 59 95 Ernst Wit John McClure 2004 Statistics for Microarrays Design Analysis and Inference John Wiley Sons List price 90 Wei Zhang Ilya Shmulevich Jaakko Astola 2004 Microarray Quality Control Wiley Liss List price 69 95 2003 Dhammika Amaratunga Javier Cabrera 2003 Exploration and Analysis of DNA Microarray and Protein Array Data John Wiley Sons List price 89 95 edited by Daniel P Berrar Werner Dubitzky Martin Granzow 2003 A Practical Approach to Microarray Data Analysis Kluwer Academic List price 99 50 ed EM Blalock 2003 A Beginner s Guide to Microarray Kluwer Academic List price 85 00 Helen C Causton John Quackenbush Alvis Brazma 2003 Microarray Gene Expression Data Analysis A Beginner s Guide Blackwell List price 54 95 Sorin Draghici 2003 Data Analysis Tools for DNA Microarrays Chapman Hall List price 79 95 Gary Hardimann 2003 Microarrays Methods and Applications Nuts Bolts DNA Press List price 42 50 Ian Humphery Smith Joanna Albala 2003 Protein Arrays Biochips and Proteomics The Next Phase of Genomic Discovery CRC Press List price 195 95 edited by Kimberly F Johnson and Simon M Lin 2003 Methods of Microarray Data Analysis III Papers from CAMDA 02 Kluwer Academic List price 99 50 edited by G Parmigiani ES Garrett RA Irizarry SL Zeger 2003 The

    Original URL path: http://linkage.rockefeller.edu/microarray/book.html (2012-11-26)
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  • microarray preprint
    Blanco Antonio J Cerrolaza 2003 Filter versus wrapper gene selection approaches in DNA microarray domains submitted to Journal of Artificial Intelligence in Medicine Rafael A Irizarry Zhijin Wu and Harris A Jaffee 2005 Comparison of Affymetrix geneChip expression measures Johns Hopkins University Dept of Biostatistics Working Papers S Keles MJ van der Laan S Dudoit SE Cawley 2004 Multiple testing methods for ChIP Chip high density oligonucleotide array data working paper 147 Biostatistics UC Berkeley Andrew D Keller Michel Schummer Walter L Ruzzo Lee Hood Bayesian classification of DNA array expression data preprint 08 01 Computer Science and Engineering Univ Washington Aug 2000 PDF CM Kendziorski H Lan AD Attie The efficiency of mRNA pooling in microarray experiments preprint Technical Report 168 Department of Biostatistics and Medical Informatics University of Wisconsin Madison Nicola Lama Patrizia Boracchi Elia Mario Biganzoli 2006 Exploration of distributional models for a novel intensity dependent normalization COBRA preptint Paper 14 Istituto di Statistica Medica e Biometria Universita di Milano Jobst Landgrebe Frank Bretz Edgar Brunner 2004 Efficient design and analysis of two colour factorial microarray experiments Universitat Gottingen preprint PDF L Lazzeroni Art Owen Plaid models for gene expression data preprint 211 Dept Statistics Stanford Univ June 2000 PDF or Postscript Michael LeBlanc Charles Kooperberg Tom Grogan Tom Miller Directed indices for exploring gene expression data preprint Fred Hutchinson Cancer Research Center William J Lemon Jeffrey JT Palatini Ralf Krahe Fred A Wright Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays submitted Robert J Lesurf 2006 An overview of the integration of gene expression datasets paper 109 School of COMputing Queen s Uninv Canada PDF H Li C Zhang A mixture Rasch model for microarray gene expression data submitted Jinyan Li Huiqing Liu Limsoon Wong 2004 Use of built in features in the interpretation of high dimensional cancer diagnosis data Proceedings of the Second Asia Pacific bioinformatics conference on Bioinformatics 2004 to appear Wentian Li Young Ju Suh Jingshan Zhang 2006 Does logarithm transformation of microarray data affect ranking order of differentially expressed genes arXiv e print q bio QM 0606018 abstract Yi Lin Samuel T Nadler Alan D Attie Brian S Yandell Mining for low abundance transcripts in microarray data preprint Technical Report 1031 Univ Wisconsin Department of Statistics protein Mwanatumu Mbwana Daniel Panagoulis Joshua D Levin Detection of proteins in micrarray format using protein detector microarray dot blot kits tech report KPL Inc PDF GJ McLachlan 2003 On a resampling approach for tests on the number of clusters with mixture model based clustering of tissue samples Technical Report Centre for Statistics University of Queensland GJ McLachlan SU Chang C Ambroise 2003 On the simultaneous use of clinical and microarray expression data in the cluster analysis of tissue samples Proceedings of the Second Asia Pacific bioinformatics conference on Bioinformatics 2004 to appear S Mukherjee P Tamayo JP Mesirov D Slonim A Verri T Poggio 1999 Support vector machine classification of microarray Data MIT CBCL Paper 182 AI Memo 1677 Felix Naef Daniel

    Original URL path: http://linkage.rockefeller.edu/microarray/preprint.html (2012-11-26)
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  • microarray 2012
    Reinhard Schneider 2012 PathVar analysis of gene and protein expression variance in cellular pathways using microarray data Bioinformatics 28 3 446 447 abstract Bettina Grun Theresa Scharl Friedrich Leisch 2012 Modelling time course gene expression data with finite mixtures of linear additive models Bioinformatics 28 2 222 228 abstract Ming Hu Yu Zhu Jeremy M G Taylor Jun S Liu Zhaohui S Qin 2012 Using Poisson mixed effects model to quantify transcript level gene expression in RNA Seq Bioinformatics 28 1 63 68 abstract Natalia Jimenez Lozano Joan Segura José Ramón Macías Juanjo Vega José María Carazo 2012 Integrating human and murine anatomical gene expression data for improved comparisons Bioinformatics 28 3 397 402 abstract Alla Karnovsky Terry Weymouth Tim Hull V Glenn Tarcea Giovanni Scardoni Carlo Laudanna Maureen A Sartor Kathleen A Stringer H V Jagadish Charles Burant Brian Athey Gilbert S Omenn 2012 Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data Bioinformatics 28 3 373 380 abstract Raivo Kolde Sven Laur Priit Adler Jaak Vilo 2012 Robust rank aggregation for gene list integration and meta analysis Bioinformatics 28 4 573 580 abstract VM Kvam P Liu Y Si 2012 A comparison

    Original URL path: http://linkage.rockefeller.edu/microarray/2012.html (2012-11-26)
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  • microarray 2011
    Varodom Charoensawan Alexander van Oudenaarden Sarah A Teichmann 2011 RNA sequencing reveals two major classes of gene expression levels in metazoan cells Molecular Systems Biology 7 497 abstract Lars Juhl Jensen1 Alex Bateman 2011 The rise and fall of supervised machine learning techniques editorial Bioinformatics 27 24 3331 3332 abstract Andre Koschmieder Karin Zimmermann Silke Trià l Thomas Stoltmann Ulf Leser 2011 Tools for managing and analyzing microarray data Briefings in Bioinformatics to appear abstract Radha Krishna Murthy Karuturi 2011 Heterogeneity of differential expression in cancer studies algorithms and methods in Algorithms in Computational Molecular Biology Techniques Approaches and Applications eds M Mlloumi AY Zomaya pp 691 722 Wiley Leo Lahti Laura L Elo Tero Aittokallio Samuel Kaski 2011 Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays IEEE ACM Transactions on Computational Biology and Bioinformatics 8 1 217 225 J Lee Y Ji S Liang G Cai P Muller 2011 On differential gene expression using RNA Seq data Cancer Informatics 10 205 215 Ker Chau Li 2011 Liquid association and related ideas in quantifying changes in correlation in Handbook of Statistical Bioinformatics part 3 pp 389 404 Springer abstract Alan Wee Chung Liew Xiangchao Gan 2011 Microarray gene expression data analysis in Algorithms in Computational Molecular Biology Techniques Approaches and Applications eds M Mlloumi AY Zomaya pp 625 650 Wiley A W C Liew N F Law H Yan 2011 Missing value imputation for gene expression data computational techniques to recovermissing data from available information Briefings in Bioinformatics to appear Jun Lu Robnet T Kerns Shyamal Peddada Pierre R Bushel 2011 Principal component analysis based filtering improves detection for Affymetrix gene expression arrays Nucleic Acids Research 39 13 e86 Shuangge Ma Xiao Song 2011 Ranking prognosis markers in cancer genomic studies Briefings in Bioinformatics

    Original URL path: http://linkage.rockefeller.edu/microarray/2011.html (2012-11-26)
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  • microarray 2010
    abstract Dexiang Gao Jihye Kim Hyunmin Kim Tzu L Phang Heather Selby Aik Choon Tan Tiejun Tong 2010 A survey of statistical software for analysing RNA seq data Human Genomics 5 1 56 60 Jian Guo 2010 Simultaneous variable selection and class fusion for high dimensional linear discriminant analysis Biostatistics 11 4 599 608 abstract Thomas J Hardcastle Krystyna A Kelly 2010 baySeq Empirical Bayesian methods for identifying differential expression in sequence count data BMC Bioinformatics 11 422 abstract Sepp Hochreiter Ulrich Bodenhofer Martin Heusel Andreas Mayr Andreas Mitterecker Adetayo Kasim Tatsiana Khamiakova Suzy Van Sanden Dan Lin 0 Willem Talloen Luc Bijnens Hinrich W H Göhlmann Ziv Shkedy Djork Arné Clevert 2010 FABIA factor analysis for bicluster acquisition Bioinformatics 26 12 1520 1527 abstract Xu Hui Linchao Pu Fu lai Chung Shitong Wang 2010 Analyzing noisy gene experimental data using uncertainty support vector domain description Biostatistics Bioinformatics and Biomathematics 1 2 3 Robert R Kitchen Vicky S Sabine Andrew H Sims E Jane Macaskill Lorna Renshaw Jeremy S Thomas Jano I van Hemert J Michael Dixon John MS Bartlett 2010 Correcting for intra experiment variation in Illumina BeadChip data is necessary to generate robust gene expression profiles BMC Genomics 11 134 abstract Shuo Jiao Shunpu Zhang 2010 Estimating the proportion of equivalently expressed genes in microarray data based on transformed test statistics Journal of Computational Biology 17 2 177 187 abstract Chungyeul Kim Soonmyung Paik 2010 Gene expression based prognostic assays for breast cancer Nature Reviews Clinical Oncology 7 340 347 abstract E Laing CP Smith 2010 RankProdIt a web interactive rank products analysis tool BMC Research Notes 3 1 221 abstract Shili Lin 2010 Space oriented rank based data integration Statistical Applications in Genetics and Molecular Biology 9 1 20 abstract Sara López Pintado Juan Romo Aurora Torrente 2010 Robust depth based tools for the analysis of gene expression data Biostatistics 11 2 254 264 abstract Yong Lu Roni Rosenfeld Gerard J Nau Ziv Bar Joseph 2010 Cross species expression analysis of innate immune response Journal of Computational Biology 17 3 253 268 abstract S Ma M Shi Y Li D Yi BC Shia 2010 Incorporating gene co expression network in identification of cancer prognosis markers BMC Bioinformatics 11 271 abstract P Mahata 2010 Exploratory consensus of hierarchical clusterings for melanoma and breast cancer IEEE ACM Transactions on Computational Biology and Bioinformatics 7 1 138 152 abstract Matthew N McCall Benjamin M Bolstad Rafael A Irizarry 2010 Frozen robust multiarray analysis fRMA Biostatistics 11 2 242 253 abstract Hisashi Noma Shigeyuki Matsui Takashi Omori Tosiya Sato 2010 Bayesian ranking and selection methods using hierarchical mixture models in microarray studies Biostatistics 11 2 281 289 abstract Massimiliano Orsini Enrico Capobianco 2010 Coupling genomic expression with copy number variation in brain cancer regulation studies Biostatistics Bioinformatics and Biomathematics 1 1 5 Alicia Oshlack Mark D Robinson Matthew D Young 2010 From RNA seq reads to differential expression results Genome Biology 11 220 abstract Mark D Robinson Davis J McCarthy Gordon

    Original URL path: http://linkage.rockefeller.edu/microarray/2010.html (2012-11-26)
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  • microarray 2009
    Flight and Peter D Wentzell 2009 Potential Bias in GO TermFinder Briefings in Bioinformatics 10 289 294 abstract Johannes M Freudenberg Vineet K Joshi Zhen Hu Mario Medvedovic 2009 CLEAN CLustering Enrichment ANalysis BMC Bioinformatics 10 234 abstract Andre Fujita Joao Ricardo Sato Marcos Angelo Almeida Demasi Mari Cleide Sogayar Carlos Eduardo Ferreira Satoru Miyano 2009 Comparing Pearon Spearman and Hoeffding s D measure for gene expression association Analysis Journal of Bioinformatics and Computational Biology 7 4 663 684 abstract D Ghosh AM Chinnaiyan 2009 Genomic outlier profile analysis mixture models null hypotheses and nonparametric estimation Biostatistics 10 1 60 69 abstract Jesse Gillis Paul Pavlidis 2009 A methodology for the analysis of differential coexpression across the human lifespan BMC Bioinformatics 10 306 abstract Enrico Glaab Jonathan M Garibaldi Natalio Krasnogor 2009 ArrayMining a modular web application for microarray analysis combining ensemble and consensus methods with cross study normalization BMC Bioinformatics 10 358 abstract Galina V Glazko and Frank Emmert Streib 2009 Unite and conquer univariate and multivariate approaches for finding differentially expressed gene sets Bioinformatics 25 18 2348 2354 abstract Daniel Glez Peña Fernando Díaz Jesús M Hernández Juan M Corchado Florentino Fdez Riverola 2009 geneCBR a translational tool for multiple microarray analysis and integrative information retrieval for aiding diagnosis in cancer research BMC Bioinformatics 10 187 abstract MR Guarracino S Cuciniello PM Pardalos 2009 Classification and characterization of gene expression data with generalized eigenvalues Journal of Optimization Theory and Applications 141 3 533 545 abstract B Han X Chen X Wang M Michaelis 2009 Integrating multiple microarray data for cancer pathway analysis using bootstrapping K S test Journal of Biomedicine and Biotechnology 2009 article707580 abstract Xiyi Hang Fang Xiang Wu 2009 Sparse representation for classification of tumors using gene expression data Journal of Biomedicine and Biotechnology 2009 article403689 abstract Ruth Heller Elisabetta Manduchi Gregory R Grant Warren J Ewens 2009 A flexible two stage procedure for identifying gene sets that are differentially expressed Bioinformatics 25 8 1019 1025 abstract Ruth Heller Elisabetta Manduchi Dylan S Small 2009 Matching methods for observational microarray studies Bioinformatics 25 7 904 909 abstract Jérôme Hennetin Petri Pehkonen Michel Bellis 2009 Construction and use of gene expression covariation matrix BMC Bioinformatics 10 214 abstract Yvonne Hey and Stuart D Pepper 2009 Interesting times for microarray expression profiling Briefings in Functional Genomics and Proteomics 8 3 170 173 abstract Brian E Howard Beate Sick Steffen Heber 2009 Unsupervised assessment of microarray data quality using a Gaussian mixture model BMC Bioinformatics 10 191 abstract Da Wei Huang Brad T Sherman Richard A Lempicki 2009 Bioinformatics enrichment tools paths toward the comprehensive functional analysis of large gene lists Nucleic Acids Research 37 1 1 13 abstract Paul J Hurd and Christopher J Nelson 2009 Advantages of next generation sequencing versus the microarray in epigenetic research Briefings in Functional Genomics and Proteomics 8 3 174 183 abstract JP Ioannidis Allison DB Ball CA Coulibaly I Cui X Culhane AC Falchi M Furlanello C Game L Jurman G Mangion J Mehta T Nitzberg M Page GP Petretto E van Noort V 2009 Repeatability of published microarray gene expression analyses Nature Genetics 41 2 149 155 Rafael A Irizarry Chi Wang Yun Zhou Terence P Speed 2009 Gene set enrichment analysis made simple Statistical Methods in Medical Research 18 565 575 abstract Natalia Jiménez Lozano Joan Segura José Ramón Macías Juanjo Vega and José María Carazo 2009 aGEM an integrative system for analyzing spatial temporal gene expression information Bioinformatics 25 19 2566 2572 abstract Eun Youn Kim Seon Young Kim Daniel Ashlock Dougu Nam 2009 MULTI K accurate classification of microarray subtypes using ensemble k means clustering BMC Bioinformatics 10 260 abstract Lee J Lancashire Christophe Lemetre and Graham R Ball 2009 An introduction to artificial neural networks in bioinformatics application to complex microarray and mass spectrometry datasets in cancer studies Briefings in Bioinformatics 10 3 315 329 abstract William B Langdon Graham J G Upton and Andrew P Harrison 2009 Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips Briefings in Bioinformatics 10 259 277 abstract Z Liu RB Gartenhaus XW Chen CD Howell M Tan 2009 Survival prediction and gene identification with penalized global AUC maximization Journal of Computational Biology 16 12 1661 1670 abstract A H M Mahbub Latif Frank Bretz and Edgar Brunner 2009 Robustness considerations in selecting efficient two color microarray designs Bioinformatics 25 18 2355 2361 abstract Shili Lin Jie Ding 2009 Integration of ranked lists vcia cross entropy Monte Carlo with applications to mRNA and microRNA studies Biometrics 65 9 18 abstract Xue Lin Bahman Afsari Luigi Marchionni Leslie Cope Giovanni Parmigiani Daniel Naiman Donald Geman 2009 The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations BMC Bioinformatics 10 256 abstract Yong Lu Peter Huggins Ziv Bar Joseph 2009 Cross species analysis of microarray expression data Bioinformatics 25 12 1476 1483 abstract Ke Shiuan Lynn Li Lan Li Yen Ju Lin Chiuen Huei Wang Shu Hui Sheng Ju Hwa Lin Wayne Liao Wen Lian Hsu Wen Harn Pan 2009 A neural network model for constructing endophenotypes of common complex diseases an application to male young onset hypertension microarray data Bioinformatics 25 8 981 988 abstract Shuangge Ma Michael R Kosorok 2009 Identification of differential gene pathways with principal component analysis Bioinformatics 25 7 882 889 abstract Davis J McCarthy Gordon K Smyth 2009 Testing significance relative to a fold change threshold is a TREAT Bioinformatics 25 6 765 771 abstract Anirban Mukhopadhyay Ujjwal Maulik Sanghamitra Bandyopadhyay 2009 A novel coherence measure for discovering scaling biclusters from gene expression data Journal of Bioinformatics and Computational Biology 7 5 853 868 abstract protein E Shannon Neeley Steven M Kornblau Kevin R Coombes Keith A Baggerly 2009 Variable slope normalization of reverse phase protein arrays Bioinformatics 25 11 1384 1389 abstract L Omberg J R Meyerson K Kobayashi L S Drury J F X Diffley O Alter 2009 Global effects of

    Original URL path: http://linkage.rockefeller.edu/microarray/2009.html (2012-11-26)
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  • microarray 2008
    2008 Optimization of minuscule samples for use with cDNA microarrays Journal of Biochemical and Biophysical Methods to appear abstract BH Hwang HJ Cha 2008 Quantitative oligonucleotide microarray data analysis with an artificial standard probe strategy Biosensors Bioelectronics to appear W Jiang S Varma R Simon 2008 Calculating confidence intervals for prediction error in microarray classification using resampling Statistical Applications in Genetics and Molecular Biology 7 8 A Joshi Y Van de Peer T Michoel 2008 Analysis of a Gibbs sampler method for model based clustering of gene expression data Bioinformatics 24 176 183 abstract Tommy S Jørstad Herman Midelfart Atle M Bones 2008 A mixture model approach to sample size estimation in two sample comparative microarray experiments BMC Bioinformatics 9 117 abstract Giuseppe Jurman Stefano Merler Annalisa Barla Silvano Paoli Antonio Galea Cesare Furlanello 2008 Algebraic stability indicators for ranked lists in molecular profiling Bioinformatics 24 258 264 abstract Koji Kadota Yuji Nakai Kentaro Shimizu 2008 A weighted average difference method for detecting differentially expressed genes from microarray data Algorithms for Molecular Biology 3 8 abstract Rei Kakuhata Masahiro Watanabe Takenori Yamamoto Eriko Obana Naoshi Yamazaki Masatoshi Kataoka Toshihiko Ooie Yoshinobu Baba Tomoshige Hori Yasuo Shinohara 2008 Importance of probe location for quantitative comparison of signal intensities among genes in microarray analysis Journal of Biochemical and Biophysical Methods to appear abstract Andreas Keller Christina Backes Maher Al Awadhi Andreas Gerasch Jan Küntzer Oliver Kohlbacher Michael Kaufmann Hans Peter Lenhof 2008 GeneTrailExpress a web based pipeline for the statistical evaluation of microarray experiments BMC Bioinformatics 9 552 abstract Ryan Kelley Hoda Feizi Trey Ideker 2008 Correcting for gene specific dye bias in DNA microarrays using the method of maximum likelihood Bioinformatics 24 71 77 abstract G Kerr HJ Ruskin M Crane P Doolan 2008 Techniques for clustering gene expression data Computers in Biology and Medicine 38 3 283 293 abstract Chang Sik Kim 2008 Self organizing maps with statistical phase synchronization SOMPS for analyzing cell cycle specific gene expression data Statistical Applications in Genetics and Molecular Biology 7 1 abstract Jaehee Kim Haseong Kim 2008 Clustering of change patterns using Fourier coefficients Bioinformatics 24 184 191 abstract Tae Min Kim Seon Hee Yim Yong Bok Jeong Yu Chae Jung Yeun Jun Chung 2008 PathCluster a framework for gene set based hierarchical clustering Bioinformatics 24 17 1957 1958 abstract TA Knijnenburg LFA Wessels MJT Reinders 2008 Creating gene set activity profiles with time series expression data International Journal of Bioinformatics Research and Applications 4 3 306 323 abstract H Koltai C Weingarten Baror 2008 Specificity of DNA microarray hybridization characterization effectors and approaches for data correction Nucleic Acids Research to appear X Kong V Mas KJ Archer 2008 A non parametric meta analysis approach for combining independent microarray datasets application using two microarray datasets pertaining to chronic allograft nephropathy BMC Genomics 9 98 abstract Tomokazu Konishi 2008 Data distribution of short oligonucleotide expression arrays and its application to the construction of a generalized intellectual framework Statistical Applications in Genetics and Molecular Biology 7 25 abstract Tomokazu Konishi Fumikazu Konishi Shigeru Takasaki Kohei Inoue Koji Nakayama Akihiko Konagaya 2008 Coincidence between transcriptome analyses on different microarray platforms using a parametric framework PLoS ONE 3 10 e3555 abstract Sun Yuan Kung Man Wai Mak 2008 Feature selection for self supervised classification with applications to microarray and sequence data IEEE Journal of Selected Topics in Signal Processing 2 3 297 309 abstract Yinglei Lai 2008 Genome wide co expression based prediction of differential expressions Bioinformatics 24 5 666 673 abstract Chang Tsun Li Yinyin Yuan Roland Wilson 2008 An unsupervised conditional random fields approach for clustering gene expression time series Bioinformatics 24 2467 2473 abstract Guo Zheng Li Hua Long Bu Mary Qu Yang Xue Qiang Zeng Jack Y Yang 2008 Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis BMC Genomics 9 suppl 2 S24 abstract J Li JP Fine 2008 ROC analysis with multiple classes and multiple tests methodology and its application in microarray studies Biostatistics to appear Heng Lian 2008 MOST detecting cancer differential gene expression Biostatistics 9 411 418 abstract Illumina SM Lin P Du W Huber WA Kibbe 2008 Model based variance stabilizing transformation for Illumina microarray data Nucleic Acids Research 36 2 e11 Rongheng Lin Shuangshuang Dai Richard D Irwin Alexandra N Heinloth Gary A Boorman Leping Li 2008 Gene set enrichment analysis for non monotone association and multiple experimental categories BMC Bioinformatics 9 481 abstract BH Liu CH Goh LL Ooi KM Hui 2008 Identification of unique and common low abundance tumour specific transcripts by suppression subtractive hybridization and oligonucleotide probe array analysis Oncogene to appear affymetrix Hsi Che Liu Chien Yu Chen Yu Ting Liu Cheng Bang Chu Der Cherng Liang Lee Yung Shih Chih Jen Lin 2008 Cross generation and cross laboratory predictions of Affymetrix microarrays by rank based methods Journal of Biomedical Informatics to appear abstract James Long Mitchell Roth 2008 Synthetic microarray data generation with RANGE and NEMO Bioinformatics 24 132 134 abstract Fabrício Martins Lopes David Corrêa Martins Jr Roberto M Cesar Jr 2008 Feature selection environment for genomic applications BMC Bioinformatics 9 451 abstract Correction 10 285 2009 abstract Shuangge Ma and Jian Huang 2009 Penalized feature selection and classification in bioinformatics Briefings in Bioinformatics 9 392 403 abstract Paolo Magni Fulvia Ferrazzi Lucia Sacchi Riccardo Bellazzi 2008 TimeClust a clustering tool for gene expression time series Bioinformatics 24 3 430 432 abstract protein N Marthandan S Klyza S Li YU Kwon T Kodadek HR Garner 2008 Construction and evaluation of an automated light directed protein detecting microarray synthesizer IEEE Transactions on Nanobioscience 7 1 20 27 Daniele Masotti Christine Nardini Simona Rossi Elena Bonora Giovanni Romeo Stefano Volinia Luca Benini 2008 TOM enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders Bioinformatics 24 3 428 429 abstract PE Meyer C Schretter G Bontempi 2008 Information iheoretic feature selection in microarray data using variable complementarity IEEE Journal of Selected Topics in

    Original URL path: http://linkage.rockefeller.edu/microarray/2008.html (2012-11-26)
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