Microarray bibliography and links (no date) [incomplete]

Here are some resources if you (as I) are just starting to learn about microarray data analysis.

Bioconductor and related links

BioConductor: open source software for bioinformatics. Bates D, Carey V, Dettling M, Dudoit S, Ellis B, Gautier L, Gentleman R, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Maechler M, Rossini A, Sawitzki G, Tierney L, Yang JYH, Zhang JJ. Accessed on 2003-04-10. www.bioconductor.org/

The Comprehensive R Archive Network. Leisch F. Accessed on 2003-04-10. cran.r-project.org/

The R Project for Statistical Computing. Leisch F, Gentleman R, Ihaka R. Accessed on 2003-04-10. www.r-project.org/

The Spot Users Guide. Yang J. Accessed on 2004-05-22. www.cmis.csiro.au/IAP/Spot/spotmanual.htm

Other software links

Here are some other lists of microarray software:

Web links

http://www.statsci.org/micrarra/annotate.html

http://www.cato.com/biotech/bio-software.html#Informatics

http://www.msri.org/publications/ln/hosted/nas/2001/speed/1/index.html

Bagging survival trees. Berthold L, Hothorn T, Lausen B, Benner A, Troeger MR. Accessed on 2003-01-02. www.mathpreprints.com/math/Preprint/blausen/20020518/2/

Home Page of Andreas Buja. Buja A. Accessed on 2003-01-02. This page has some good papers on multivariate approaches, especially "bagging." www.research.att.com/~andreas/

Perl Documentation. Ramirez C. Accessed on 2003-01-17. Perl is a popular language in Bioinformatics. One of it's greatest strengths is the ability to sort and filter large amounts of text information. www.perldoc.com/

PIDEX: a Statistical Approach for Screening Differentially Expressed Genes Using Microarrays Analysis. Ge N, Huang F, Shaw P, Wu CFJ. Accessed on 2003-04-08. www.stat.lsa.umich.edu/~jeffwu/publication/pidex.pdf

Supervised Learning from Micro-Array Data. Hastie T. Accessed on 2003-04-08. www.insightful.com/events/2001uc/hastie.pdf

References

Rosenthal NEJM 338, 122 (1998) "In Search of Perverse Polymorphisms"

DNA microarrays in medical practice. Aitman TJ. British Medical Journal 2001: 323(7313); 611-5. [Full text] [PDF]

A systematic statistical linear modeling approach to oligonucleotide array experiments. Chu TM, Weir B, Wolfinger R. Math Bioscience 2002: 176(1); 35-51. [PDF]

Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays. Chudin E, Walker R, Kosaka A, Wu SX, Rabert D, Chang TK, Kreder DE. Genome Biol 2002: 3(1); RESEARCH0005. [Abstract] [Full text] [PDF]

Computational methods for the identification of differential and coordinated gene expression. Claverie JM. Hum Mol Genet 1999: 8(10); 1821-32. [PDF]

Bayesian Models for Gene Expression With DNA Microarray. Ibrahim JG, Chen M-H, Gray RJ. J American Statistical Association 2002 March: 97(457); 88-99. [PDF]

Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P. J Biol Chem 2001: 276(23); 19937-44. [Abstract] [Full text] [PDF]

Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Naef F, Hacker CR, Patil N, Magnasco M. Genome Biol 2002: 3(4); RESEARCH0018. [Abstract] [Full text] [PDF]

Prediction of central nervous system embryonal tumour outcome based on gene expression. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JYE, Goumnerova LC, Black PM. Nature 2002: 415436-442. [Abstract]

Analyzing high-density oligonucleotide gene expression array data. Schadt EE, Li C, Su C, Wong WH. Journal of Cellular Biochemistry 2000: 80(2); 192-202. [PDF]

Significance analysis of microarrays applied to the ionizing radiation response. Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci U S A 2001: 98(9); 5116-21. [Abstract] [Full text] [PDF]

A gene-expression signature as a predictor of survival in breast cancer. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R. N Engl J Med 2002: 347(25); 1999-2009.  [Abstract]

Computational method for reducing variance with Affymetrix microarrays. Welle S, Brooks AI, Thornton CA. BMC Bioinformatics 2002: 3(1); 23. [Abstract] [Full text] [PDF]

Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis. Zhou Y, Abagyan R. BMC Bioinformatics 2002: 3(1); 3. [Abstract] [Full text]

Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Jr., Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Nature 2000: 403(6769); 503-11. [Medline] [Abstract] [Full text] [PDF]

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