microarray preprint

	Bibliography on Microarray Data Analysis	front\| books \| preprints \| 2009 \| 2008 \| 2007 \| 2006 \| 2005 \| 2004 \| 2003 \| 2002 \| 2001 \| 2000 \| 1999 \| 1998 \| 1997 \| 1996 \| 1995 \| 1994 \| 1993 \| core facilities\| data\| mailing \| programs(free) \| analysis groups \| labs \| companies \| short-courses\| lists \| mirror © Copyright, 1999-2009 Wentian Li of North Shore LIJ Research Institute
http://www.nslij-genetics.org/microarray/

preprints, unpublished documents, thesis

see also, Nature precedings: http://precedings.nature.com/
Collection of Biostatistics Research Archive (COBRA): http://www.biostatsresearch.com/repository/
and arXiv.org "quantitative biology" section: http://www.arxiv.org/archive/q-bio

Joke Allemeersch (2006), Statistical Analysis of Microarray Data: Applications in Platform Comparison, Compendium Data, and Array CGH Ph.D Thesis, Department Elektrotechniek, Katholieke Universiteit Leuven
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KV Ballman, Grill DE, Oberg AL, Therneau TM (2003), "Faster cyclic loess: normalizing DNA arrays via linear models", Mayo Foundation Technical Report #68.
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Dieter Beule, Johannes Schuchhardt, Hanspeter Herzel, "Clustering gene expression time series", preprint.
Therese Biedl, Brona Brejova, Erik D. Demaine, Angele M. Hamel, Tomas Vinar "Optimal arrangement of leaves in the tree representing hierarchical clustering of gene expression data", preprint #14 (Computer Science Dept, Univ Waterloo, April 2001)
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David R Bickel , "Robust cluster analysis of DNA microarray data: An application of nonparametric correlation dissimilarity", 2001 Proceedings of the Joint Statistical Meetings of the American Statistical Association (Biometrics Section).
Sven Bilke (2000), "Shuffling yeast gene expression data", arXiv e-print, physics/0006050
[abstract]
Sven Bilke, T. Breslin, M. Sigvardsson (2003), "Probabilistic estimation of microarray data reliability and underlying gene expression", arXiv e-print, q-bio.QM/0309006.
[abstract]
BM Bolstad, RA Irizarry, M Astrand, TP Speed, "A comparison of normalization methods for high density oligonucleotide array data based on bias and variance", submitted.
LD Burgoon, DR Boverhof, JE Eckel, C Gennings, TM Therneau, TR Zacharewski (2004), "Normalization of Two-Channel Microarray Experiments: A Semiparametric Approach", Mayo Foundation Technical Report #69.
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S Busygin, G Jacobsen, E Krämer "Double conjugated clustering applied to Leukemia microarray data", Contentsoft preprint. see also: "Double conjugated clustering and its applicability to node-driven algorithms", Contentsoft preprint.
Viann Chan, Nick Hontzeas, Vincent Park, "Gene expression", preprint (Univ Warterloo).
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Vera Cherepinsky, Jiawu Feng, Marc Rejali, Bud Mishra (2003), "Shrinkage-based similarity metric for cluster analysis of microarray data", NYU Courant Institute technical report (TR2003-845).
JA Correa, S Dudoit, DR Goldstein, "Multiple testing in the survival analysis of microarray data", preprint.
X Cui, GA Churchill (2003), "How many mice and how many arrays? Replication in mouse cDNA microarray experiments", submitted to CAMDA '02 proceedings
X Cui, MK Kerr, GA Churchill, "Data transformation for cDNA microarray data", preprint.
Somnath Datta (2004), "An empirical Bayes adjustment to multiple p-values for the detection of differentially expressed genes in microarray experiments", Proceedings of the Second Asia-Pacific bioinformatics conference on Bioinformatics 2004, to appear.
Marcel Dettling, Peter Buhlmann "How to use boosting for tumor classification with gene expression data", preprint (ETH Zurich, 2002).
Marcel Dettling, Peter Buhlmann "Supervised clustering of genes", preprint (ETH Zurich, 2001).
JM Deutsch (2001), "Algorithm for finding optimal gene sets in microarray prediction", arXiv preprint, physics/0108011
[ abstract]
KA Do, GJ McLachlan, RW Bean, S Wen (2002), "A comparison of two methods of clustering gene microarray data", Technical Report, Centre for Statistics, University of Queensland.
Adrian Dobra, Chris Hans, Beatrix Jones, Joseph R Nevins, Mike West (2003), "Sparse graphical models for exploring gene expression data", Working Paper 03-11 (Institute of Statistics and Decision Science, Duke Univ).
Eytan Domany (2002) "Cluster analysis of gene expression data", arXiv preprint, physics/0206056. [abstract]
RO Dror, "Noise models in gene array analysis", Area exam report, MIT Department of Electrical Engineering and Computer Science (2001).
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Sandrine Dudoit, J Fridlyand, "Bagging to improve the accuracy of a clustering procedure", preprint #600 (Statistics Dept, UC Berkeley).
B Durbin, J Hardin, D Hawkins, DM Rocke, "A variance-stabilizing transformation for gene expression microarray data", preprint.
Bradley Efron, Robert Tibshirani (2006), "On testing the significance of sets of genes", arXiv e-print, math.ST/0610667.
[abstract]
Bradley Efron, Robert Tibshirani, Virginia Goss, Gilbert Chu, "Microarrays and their use in a comparative experiment", preprint #37B/213 (Dept Statistics, Stanford Univ, Nov 2000).
S Draghici, O Kulaeva, A Petrov, B Hoff, A Kuklin, S Shams, M Tainsky , "Computational methods for the selection of differentially regulated genes in cell immortalization", submitted.
Yevgeniya Jane M Fridlyand, Resampling Methods for Variable Selection and Classification: Applications to Genomics Ph.D Thesis (2001), Department of Statistics, UC Berkeley.
Shmuel Friedland, Mostafa Kaveh, Amir Niknejad, Hossein Zare (2005), "An Algorithm for Missing Value Estimation for DNA Microarray Data", arXiv e-print, q-bio.GN/0510047.
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Wen Fury, Franak Batliwalla, Peter K. Gregersen, Wentian Li (2006), "Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion", arXiv e-print, q-bio.QM/0606017.
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Sue C Geller, Jeff P Gregg, Paul Hagerman, David M Rocke, "Transformation and normalization of oligonucleotide microarray data", preprint.
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Robert Gentleman, Markus Ruschhaupt, and Wolfgang Huber (2005), "On the synthesis of microarray experiments", Bioconductor Project Working Papers.
D Ghosh, "Penalized regression models for the classification of tumors from gene expression data", submitted.
D Ghosh, "Finding cancer subtypes in microarray data using random projections", submitted.
D Ghosh, TR Barrette, D Rhodes, AM Chinnaiyan, "Statistical issues and methods for high-throughput cross-validation of microarray data, with applications to prostate cancer", preprint.
Liang Goh, Qun Song, Nikola Kasabo (2004), "A novel feature selection method to improve classification of gene expression data", Proceedings of the Second Asia-Pacific bioinformatics conference on Bioinformatics 2004, to appear.
Mika Gustafsson, Michael Hornquist, Anna Lombardi (2004), "Large-scale reverse engineering by the Lasso", arXiv e-print, q-bio.MN/0403012.
[abstract]
AJ Hartemink, DK Gifford, TS Jaakkola, RA Young, "Maximum likelihood estimation of optimal scaling factors for expression array normalization", MIT preprint.
Y He, W Pan, J Lin (2005), "Cluster Analysis Using Multivariate Normal Mixture Models to Detect Differential Gene Expression With Microarray Data", Research Report 2005-010, Division of Biostatistics, University of Minnesota.
http://www.biostat.umn.edu./rrs.php
T. Heim, L.-C. Tranchevent, E. Carlon, G. T. Barkema (2006), "Physics-based analysis of Affymetrix microarray data", arXiv e-print, q-bio.BM/0605008.
[abstract]
WH Hsu, Deng, R Joehanes (2003), "Score-based methods for learning structure of graphical models of gene expression from microarray data", submitted to Journal of Artificial Intelligence in Medicine.
Inako Inza, Pedro Larranaga, Rosa 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).
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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.
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L Lazzeroni, Art Owen, "Plaid models for gene expression data", preprint #211 (Dept Statistics, Stanford Univ, June 2000).
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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
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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.
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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 A. Lim, Nila Patil, Marcelo O. Magnasco (2001), "From features to expression: High-density oligonucleotide array analysis revisited", arXiv e-print, physics/0102010
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Radhakrishnan Nagarajan, Meenakshi Upreti (2005), "Correlation statistics for cDNA microarray image analysis", arXiv e-print, q-bio.GN/0511030.
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Radhakrishnan Nagarajan, Meenakshi Upreti (2006), "Qualitative assessment of gene expression in Affymetrix genechip arrays", arXiv e-print, q-bio.GN/0604015.
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MA Newton, A Noueiry, D Sarkar, P Ahlquist "Detecting differential gene expression with a semiparametric hierarchical mixture method", Technical Report 1074 (Dept Statistics, Univ Wisconsin), 2003.
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W Pan, J Lin, C Le (2001), "A Mixture model approach to detecting differentially expressed genes with microarray data", preprint (Biostat, U Minnesota, #2001-011)
P Pavlidis, J Weston, J Cai, WS Nobel, "Learning gene functional classifications from multiple data types." preprint.
P Pavlidis, WN Grundy "Classification of genes using probabilistic models of microarray expression profiles", preprint.
P Pavlidis, WN Grundy "Statistical analysis of strain and regional variation in gene expression in mouse brain", preprint.
Leif E Peterson, Kwong Lau "Observation of intermittency in gene expression on cDNA microarrays", Genome Biology, deposited research article 0005 (2002).
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Jennifer Pittman, Erich Huang, Holly Dressman, Cheng-Fang Horng, Skye H Cheng, Mei-Hua Tsou, Chii-Ming Chen, Andrea Bild, Edwin S Iversen, Ming Liao, Andrew T Huang, Joseph R Nevins Mike West (2003), "Integrated modelling of clinical and gene expression information for personalized prediction of disease outcomes", Working Paper 03-07 (Institute of Statistics and Decision Science, Duke Univ).
Jennifer Pittman, Erich Huang, Joseph Nevins, Mike West (2003), "Bayesian analysis of binary prediction tree models for retrospectively sampled outcomes", Working Paper 03-10 (Institute of Statistics and Decision Science, Duke Univ).
Jennifer Pittman, Erich Huang, Joseph Nevins, Mike West (2003), "Prediction tree models in clinico-genomics", Working Paper 03-13 (Institute of Statistics and Decision Science, Duke Univ).
Katherine S. Pollard and Mark J. van der Laan (2005), "Cluster analysis of genomic data with applications in R", U.C. Berkeley Division of Biostatistics Working Paper Series
P Provero (2002), "Gene networks from DNA microarray data: centrality and lethality", arXiv e-print, cond-mat/0207345.
[abstract]
Li-Xuan Qin and Steven G. Self (2005), "The clustering of regression models method with applications in gene expression data", UW Biostatistics Working Paper Series
J Sunil Rao, Jingjin Li , "Parametric and nonparametric analysis of gene expression curves", preprint.
Robert B. Scharpf, Christine A. Iacobuzio-Donahue, Julie B. Sneddon, and Giovanni Parmigiani (2005), "When should one substract background fluorescence in two color microarrays?", Johns Hopkins University, Dept. of Biostatistics Working Papers
Mark R. Segal (2005), "Microarray gene expression data with linked survival phenotypes: diffuse large-B-cell lymphoma revisited", Center for Bioinformatics & Molecular Biostatistics, UCSF
SK Shevade and SS Keerthi (2002), "A simple and efficient algorithm for gene selection using sparse logistic regression", Technical Report No. CD-02-22, Control Division, Department of Mechanical Engineering, National University of Singapore.
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M Smolkin, D Ghosh, "Cluster stability scores for microarray data in cancer studies", submitted.
JD Storey (2005), "The optimal discovery procedure I: a new approach to simultaneous significance testing", UW Biostatistics Working Paper Series
JD Storey, James Y. Dai, and Jeffrey T. Leek (2005), "The optimal discovery procedure II: applications to comparative microarray experiments", UW Biostatistics Working Paper Series
JD Storey, R Tibshirani (2001), "Estimating false discovery rates under dependence, with applications to DNA microarrays", Technical Report 2001-28 (Dept Stat, Stanford Univ).
M Rattray, N Morrison, D Hoyle, A Brass, "DNA microarray normalisation, PCA and a related latent variable model", preprint.
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K Rho, H Jeong, B Kahng (2003), "Identification of essential and functionally moduled genes through the microarray assay", arXiv e-print, cond-mat/0301110
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Rainer Spang, Harry Zuzan, Mike West, Joseph Nevins, Carrie Blanchette, Jeffrey R Marks (2000), "Prediction and uncertainty in the analysis of gene expression profiles", Working Paper 00-31 (Institute of Statistics and Decision Science, Duke Univ).
JE Steinbachs, "Microarray analysis: statistical perils and data-mining conundrums", preprint.
[ webpage from the authors]
Robert Tibshirani, Eric Bair (2003), "Improved detection of differential gene expression through the singular value decomposition", preprint.
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Willy Valdivia-Granda, Christopher Dwan (2006), "Microarray data management. an enterprise information approach: implementations and challenges", arXiv e-print, q-bio.GN/0605005.
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Willy Valdivia-Granda, William Perrizo, Edward Deckard, Francis Larson (2006), "Peano count trees (P-trees) and rule association mining for gene expression profiling of microarray data", arXiv e-print, cs.DS/0610076.
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Jean-Philippe Vert, Minoru Kanehisa (2002), "Graph-driven features extraction from microarray data", arXiv e-print, physics/0206055
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Mike West (2000), "Bayesian regression analysis in the large p, small n paradigm", Working Paper 00-22 (Institute of Statistics and Decision Science, Duke Univ).
Mike West (2002), "Bayesian factor regression models in the large p, small n paradigm", Working Paper 02-12 (Institute of Statistics and Decision Science, Duke Univ).
Mike West, Joseph R Nevins, Jeffrey R Marks, Rainer Spang, Carrie Blanchette, Harry Zuzan (2000), "DNA microarray data analysis and regression modeling for genetic expression profiling", Working Paper 00-15 (Institute of Statistics and Decision Science, Duke Univ).
EC Wit, A Nobile, R Khanin (2004), "Simulated annealing for near-optimal dual-channel microarray designs", Technical Report 04-7, Department of Statistics, Univ of Glasgow, UK.
B Wu (2004), "A unified statistical framework for differential gene expression detection and sample classification using penalized linear regression models" Research Report 2004-030, Division of Biostatistics, University of Minnesota.
http://www.biostat.umn.edu./rrs.php?mode=view&year=2004
Lei Xu (2007), A Novel Statistical Method for Microarray Data Integration: Applications to Cancer Research , Ph.D Thesis, Johns Hopkins University.
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Ka Yee Yeung, David R Haynor, Walter L Ruzzo, "Validating clustering for gene expression data", preprint.
Larry TH Yu, Fu-lai Chung, Stephen CF Chan (2004), "Using emerging pattern based projected clustering and gene expression data for cancer detection", Proceedings of the Second Asia-Pacific bioinformatics conference on Bioinformatics 2004, to appear.
Harry Zuzan, Carrie Blanchette, Holly Dressman, Erich Huang, Seiichi Ishida, Jeffrey R Marks, Joseph R Nevins, Rainer Spang, Mike West, Valen E Johnson (2002), "Estimation of probe cell locations in high-density synthetic-oligonucleotide DNA microarrays", Working Paper 02-05 (Institute of Statistics and Decision Science, Duke Univ).
Shu-Dong Zhang, Timothy W. Gant (2005), "Effect of pooling samples on the efficiency of comparative studies using microarrays", arXiv e-print, q-bio.QM/0510024.
[abstract]

preprints, unpublished documents, thesis