Reading List by Topic

Text: Microarray Gene Expression Data Analysis: A Beginner's Guide [ILLUSTRATED] (Paperback)
by Helen Causton, John Quackenbush, Alvis Brazma

Introduction & Basic Array Design - April 9

• Text: Chapter 1, 2.4
• Review: [On-line] "Genomics, gene expression and DNA arrays", Lockhart DJ, Winzeler EA, Nature 2000 Jun 15; 405:827-36.

Experimental Design - April 11

Text: Rest of Chapter 2

• Review: ** "DNA arrays for analysis of gene expression", Eisen MB, Brown PO, Methods Enzymol 1999; 303:179-205. [Pickup from class papers location given in class]

Journal Club - April 13

• 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.

• 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.

Spotted Array Design - April 16

• Text: Chapter 3

Types of Experiments / Array Databases - April 18

• Text: Chapter 4

Journal Club - April 20

• 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.

Additional Data Acquisition & Basic Analysis Papers

• 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.

• 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.

GenePix 6.0 - Introduction Lab - April 23

•    GenePix 6.0 Manual -- please read chapters 1-3, then look over the tutorial (Chapter 4) in preparation for the first lab

Introduction to R & Bioconductor - April 25

• Intro to Bioconductor workshop slides from 2003 Tutorial (Katie Pollard)  -- reviewed in class
• Intro to R tutorial slides
  

Journal Club - April 27

• Research paper: [On-line] "Ammonium toxicity and potassium limitation in yeast",Hess DC, Lu W, Rabinowitz JD, Botstein D.,  PLoS Biol. 2006 Oct;4(11):e351
  

Bioconductor Lab / Normalization Issues - April 30

• Research paper: [On-line] "Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes",
  Alicia Oshlack , Dianne Emslie , Lynn M Corcoran  and Gordon K Smyth,  Genome Biology 2007, 8:R2
• Research paper: [On-line] "Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.", Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Nucleic Acids Res. 2002 Feb 15;30(4):e15.
• Research paper: [On-line] "Monitoring global messenger RNA changes in externally controlled microarray experiments", Jeroen van de Peppel, Patrick Kemmeren1, Harm van Bakel, Marijana Radonjic, Dik van Leenen, Frank C.P. Holstege,  EMBO Rep. 2003 Apr;4(4):387-93.

Reproducibility of Arrays / Microarray Quality Control Project (MAQC) - May 2

• Research paper [On-line] "A study of inter-lab and inter-platform agreement of DNA microarray data." Wang H, He X, Band M, Wilson C, Liu L., BMC Genomics. 2005 May 11;6(1):71
  
  
• News & Views: [On-line] "Of fish and chips", Nature Methods 2005; 2, 329-330.
• Research paper: [On-line] "Independence and reproducibility across microarray platforms", Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J., Nat Methods. 2005 May;2(5):337-44.
• Research paper: [On-line] "Multiple-laboratory comparison of microarray platforms", Irizarry RA, Warren D, et al.,  Nat Methods. 2005 May;2(5):345-50.
  
• Research paper: [On-line] "Standardizing global gene expression analysis between laboratories and across platforms." Bammler T, Beyer RP, et al., Nat Methods. 2005 May;2(5):351-6.
  

• Review: [On-line] "Arrays of hope" Strauss E., Cell. 2006 Nov 17;127(4):657-9.
• Research paper: [On-line] "Evaluation of DNA microarray results with quantitative gene expression platforms." Canales RD, Luo Y, et al., Nat Biotechnol. 2006 Sep;24(9):1115-22.
• Research paper [On-line] "The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.", MAQC Consortium, Nat Biotechnol. 2006 Sep;24(9):1151-61.
• Critical Comment on MAQC studies: [On-line] "Statistical methods and microarray data.", Klebanov L, Qiu X, Welle S, Yakovlev A., Nat Biotechnol. 2007 Jan;25(1):25-6.
• Critical Comment on MAQC studies: [On-line] "MAQC papers over the cracks", Liang P. Nat Biotechnol. 2007 Jan;25(1):27-8.
  

Gene Expression Clustering - May 10 & 11

• Review Paper: [On-line] - "Clustering Microarray Data", Golub J, Sherlock G, Methods in Enzymology 2006 411:194-213.
  
• 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.
• Application Note: [On-line] "Genesis: cluster analysis of microarray data", Alexander Sturn, John Quackenbush, Zlatko Trajanoski , Bioinformatics 2002 18:207-208.
  

Advanced Analysis - Integrating Microarray Data with Genomics - May 16

• 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.
  
• Methods Paper: [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
• Research Paper:  [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.

Web Resources for Microarray Analysis and Databases - May 17

• Application Note: [On-line] "CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis",
  Johannes Rainer, Fatima Sanchez-Cabo, Gernot Stocker, Alexander Sturn, and Zlatko Trajanoski, Nucleic Acids Res. 2006, v34(Web Server issue): W498–W503.
• [Extensive Web Software & Database Links page]: Nice listing of links and summary of features for many free and commercial microarray resources
   compiled by Y.F. Leung (current through ~mid 2004)
  

Evolution of Gene Expression - May 18

• Review Paper: [On-line] - "Evolution of primate gene expression" Khaitovich P, Enard W, Lachmann M, Paabo S.
  Nat Rev Genet. 2006 Sep;7(9):693-702.
• Research Paper: [On-line] - "Expression profiling in primates reveals a rapid evolution of human transcription factors.", Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP. Nature. 2006 Mar 9;440(7081):242-5.
  
• Research Paper: [On-line] - "Comparison of protein and mRNA expression evolution in humans and chimpanzees" Fu N, Drinnenberg I, Kelso J, Wu JR, Paabo S, Zeng R, Khaitovich P.  PLoS ONE. 2007 Feb 14;2:e216.
  

Additional Applications of DNA Array Technology

• 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
• Research Paper: [On-line] "Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans", Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, Kim SK, Proc Natl Acad Sci U S A 2001 Jan 2; 98:218-23.
• 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.

Addtional Advanced Analysis Methods

• Review: [On-line] "Analysis of large-scale gene expression data", Sherlock G, Curr Opin Immunol 2000 Apr; 12:201-5.
• 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] "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.
• Research Paper:  [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.

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.