Application and Analysis of Microarrays
BME 210
, Winter 2004

Reading List



Reading Assignments


Note: All the articles with [On-line] links should be accessible from with the "" campus domain, or off campus using the SlugLink proxy-server. For instructions on setting up the proxy server, go here.

Overview of Course


  • Causton: Chapter 1
  • Review: [On-line] "Genomics, gene expression and DNA arrays", Lockhart DJ, Winzeler EA, Nature 2000 Jun 15; 405:827-36.
    Additional Reviews
  • Review: [On-line] "Exploring the new world of the genome with DNA microarrays", Brown PO, Botstein D, Nat Genet 1999 Jan; 21(Suppl):33-7.
  • Review: [On-line] "DNA microarrays for expression profiling", Hughes TR, Shoemaker DD, Curr Opin Chem Biol 2001 Feb; 5:21-5.

Introduction & Basic Array Design


  • Causton: Chapter 2.4
  • Research Paper: [On-line] "Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization", Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B, Mol Biol Cell 1998 Dec; 9:3273-97. Referenced in class]
  • Review: [On-line] "Computational analysis of microarray data", Quackenbush J., Nat Rev Genet 2001 Jun; 2:418-27.

Spotted DNA Array Construction


  • Handout: Foreword by Ed Southern

Crossing the Digital Divide


  • Causton: Rest of Chapter 2

Experimental Design

Assigned (please read by next Tuesday)

  • Review: ** "DNA arrays for analysis of gene expression", Eisen MB, Brown PO, Methods Enzymol 1999; 303:179-205. [Pickup from location given in class]
  • Research Paper: [On-line] "The transcriptional program of sporulation in budding yeast", Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I, Science 1998 Oct 23; 282:699-705.
  • Research Paper: [On-line]"Genomic expression programs in the response of yeast cells to environmental changes", Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO, Mol Biol Cell 2000 Dec; 11:4241-57.
  • Research Paper: [On-line]"Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications", Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lonning P, Borresen-Dale AL, Proc Natl Acad Sci U S A 2001 Sep 11; 98:10869-74.

GenePix Lab

(Please look over for lab on thursday 1/22)

Data Acquisition


  • Review Paper: [On-line] "Gene expression informatics--it's all in your mine", Bassett DE Jr, Eisen MB, Boguski MS, Nat Genet 1999 Jan; 21 (Suppl 1):51-5.
  • Method Paper: [On-line] "Cluster analysis and display of genome-wide expression patterns", Eisen MB, Spellman PT, Brown PO, Botstein D, Proc Natl Acad Sci U S A 1998 Dec 8; 95:14863-8.
  • Research Paper: [On-line] "Functional discovery via a compendium of expression profiles", Hughes TR, et al., Cell 2000 Jul 7; 102:109-26.
  • Research Paper: [On-line] "A gene expression database for the molecular pharmacology of cancer", Scherf U, et al., Nat Genet 2000 Mar; 24:236-44.
  • Research Paper: [On-line] "Replication dynamics of the yeast genome", Raghuraman MK, et al., Science 2001 Oct 5; 294:115-21
  • Research Paper: [On-line] "Transcriptional regulation and function during the human cell cycle", Cho RJ, et al., Nat Genet 2001 Jan; 27:48-54.
  • Supplemental Reading: Re-Analysis of Cho Human Cell Cycle Paper (mentioned in class): [On-line] "Analysis of Cell-Cycle-Specific Gene Expression in Human Cells as Determined by Microarrays and Double-Thymidine Block Synchronization", Shedden K, Cooper S, PNAS preprint, 2001.

Normalization and Assessment of Data Analysis Results

  • Research Paper: [On-line] ""Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments", Kerr MK, Churchill GA, Proc Natl Acad Sci U S A 2001 Jul 31; 98:8961-5
  • Research Paper: [On-line] "Normalization strategies for cDNA microarrays", Schuchhardt J, Beule D, Malik A, Wolski E, Eickhoff H, Lehrach H, Herzel H., Nucleic Acids Res 2000 May 15; 28:E47
  • Research Paper: [On-line] "Molecular classification of cancer: class discovery and class prediction by gene expression monitoring", Golub TR, et al., Science 1999 Oct 15; 286:531-7

Advanced Analysis I

  • Review: [On-line] "Analysis of large-scale gene expression data", Sherlock G, Curr Opin Immunol 2000 Apr; 12:201-5.
  • Research Paper: [On-line] "Knowledge-based analysis of microarray gene expression data by using support vector machines", Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D, Proc Natl Acad Sci U S A 2000 Jan 4; 97:262-7
  • Research Paper: [On-line] "Singular value decomposition for genome-wide expression data processing and modeling", Alter O, Brown PO, Botstein D, Proc Natl Acad Sci U S A 2000 Aug 29; 97:10101-6.
  • Supplemental Reading - (material presented by guest speaker) [On-line] "Missing value estimation methods for DNA microarray", Olga Troyanskaya, Michael Cantor, Gavin Sherlock, Pat Brown, Trevor Hastie, Robert Tibshirani, David Botstein, and Russ B. Altman, Bioinformatics 2001 17: 520-525.

Advanced Analysis II

  • Research Paper: [On-line ]"Bioprospector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-expressed genes", Liu X, Brutlag DL, Liu JS, Pac Symp Biocomput 2001; 127-38.
  • Research Paper: [On-line] "Identifying regulatory networks by combinatorial analysis of promoter elements", Pilpel Y, Sudarsanam P, Church GM, Nat Genet 2001 Oct; 29:153-9.
  • Research Paper: [On-line] "Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles", Chiang DY, Brown PO, Eisen MB, Bioinformatics 2001; 17 Suppl 1:S49-55. [On-line] "'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns", Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P, Genome Biol 2000;1(2):Research0003.1-00003.21
  • Supplemental Reading - (material presented by guest speaker) [On-line] "Evolutionarily conserved sequences on human chromosome 21", Frazer KA, Sheehan JB, Stokowski RP, Chen X, Hosseini R, Cheng JF, Fodor SP, Cox DR, Patil N, Genome Res 2001 Oct; 11:1651-9.
  • Supplemental Reading - (material presented by guest speaker) [On-line] "Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association", Lieb JD, Liu X, Botstein D, Brown PO, Nat Genet 2001 Aug; 28:327-34.

Other Kinds of Arrays

  • Review Paper: [On-line] "Tissue microarray (TMA) technology: miniaturized pathology archives for high-throughput in situ studies.", Bubendorf L, Nocito A, Moch H, Sauter G., J Pathol 2001 Sep;195(1):72-9.
  • Research Paper: [On-line] "Scanometric DNA array detection with nanoparticle probes", Taton TA, Mirkin CA, Letsinger RL, Science 2000 Sep 8; 289:1757-60.
  • Research Paper: [On-line] "Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays", Brenner S, et al., Nat Biotechnol 2000 Jun; 18:630-4.
  • Supplemental Review Paper: [On-line] "Large-scale functional analysis using peptide or protein arrays", Emili AQ, Cagney G., Nat Biotechnol 2000 Apr; 18:393-7.
  • Supplemental Reading: [On-line] "Printing proteins as microarrays for high-throughput function determination", MacBeath G, Schreiber SL., Science 2000 Sep 8; 289:1760-3.

** Access information provided in class.





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