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DNA Microarray: Publications Revealing Problems with the Technology
Sydney Brenner, Peng Liang, Stephen Cooper, Nat Goodman and others weigh in

This is a list of publications that GenHunter has compiled from well-known scientists including recent Nobel Prize winner Sydner Brenner, Richard Klausner, Thomas Cebula, Arthur Pardee, Peng Liang, Stephen Cooper, Nat Goodman and many others. These publications reveal some of the problems and common pitfalls of Microarray technology.

  • 1) Brenner, S.: Sillycon valley fever. Current Biology. 1999, 9:R671.

  • 2) Richmond, C.S. et al: Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 1999, 27:3821-3835.

  • 3) Wooster, R.: Cancer classification with DNA microarrays: is less more? Trends in Genetics. 2000, 16:327-329.

  • 4) Liang, P.: Gene discovery using differential display. Genetic Engineering News. 2000, 20:37.

  • 5) Mir, K. U.: The hypothesis is there is no hypothesis. Trends in Genetics. 2000, 16:63-64.

  • 6) Gibbs, W. W.: Shrinking to enormity: DNA microarrays are reshaping basic biology – but scientists fear they may soon drown in the data. Scientific American. 2001, 284:33-34.

  • 7) Marshall, E.: Affymetrix settles suit, fixes mouse chips. Science. 2001, 291:2535.

  • 8) Mills, J.C, Roth, K.A, Cagan, R.L, Gordon, J.I.: DNA microarrays and beyond: completing the journey from tissue to cell. Nature Cell Biology. 2001, 8:E175-178.

  • 9) Goryachev, A.B, Macgregor, P.F, Edwards, A.M.: Unfolding of microarray data. J Comput. Biol. 2001, 8:443-461.

  • 10) King, H.C. and A. A. Sinha.: Gene expression profile analysis by DNA microarrays: promise and pitfalls. JAMA. 2001, 14:286(18):2280-2288.

  • 11) Knight, J.: When the chips are down. Nature. 2001, 410:860-861.

  • 12) Knight, J.: Geneticists’ work in disarray as DNA-chip producer pulls the plug. Nature. 2001, 414:135-136.

  • 13) Ramdas, L. et al: Sources of nonlinearity in cDNAmicroarray expression measurements. Genome Biology. 2001, 2:Research0047.

  • 14) Shedden, K. and Cooper, S.: Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization. Proc. Natl Acad. Sci. U S A. 2002, 99:4379-4384.

  • 15) Liang P.: A decade of differential display. Biotechniques. 2002, 33:338-346.

  • 16) Cooper, S.: Cell cycle analysis and microarrays. Trends in Genetics. 2002, 18:289-290.

  • 17) Liang P.: SAGE Genie: A suite with panoramic view of gene expression. Proc. Natl Acad. Sci. U S A. 2002, 99:11547-11548.

  • 18) Jenssen T.-K.; Langaas M.; Kuo W.P.; Smith-Sorensen B.; Myklebost O.; and Hovig E.: Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res. 2002, 30:3235-3244.

  • 19) Kuo, W.P.; Jenssen, T.-K.; Butte, A.J.; Ohno-Machado, L; and Kohane, I.S.: Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 2002, 18: 405-412.

  • 20) Kothapalli, R.; Yoder, S.J.; Mane, S.; and Loughran, T.P.: Microarray results: how accurate are they? BMC Bioinformatics. 2002, 3:22.

  • 21) Petricoin, E.F. III; Hackett, J.L.; Lesko, L.J.; Puri, R.K.; Gutman, S.I.; Chumakov, K.; Woodcock, J.; Feigal, D.W., Jr.; Zoon, K.C.; and Sistare, F.D.: Medical applications of microarray technologies: a regulatory science perspective.Nature Genetics (supplement). 2002, 32:474-479.

  • 22) McGowan, K.: The need to make microarrays mainstream. Genome Technology. 2002, 22:77-81.

  • 23) Goodman, N.: Microarrays: Hazardous to your science. Genome Technology. 2003, 32:42-45.

  • 24) Worms and science: An interview with Sydney Brenner, Distinguished Research Professor at The Salk Institute, La Jolla, USA, and one of the winners of the 2002 Nobel Prize for Physiology and Medicine. EMBO reports. 2003, 4: 224-226.

  • 25) Brenner, S.: The worm’s turn. Current Biology. 2003, 12: R713.

  • 26) Tilstone, C.: Vital statistics. Nature. 2003, 424:610-612.

  • 27) Krochmal, M.: Cross platform, should researchers vanquish Venn diagrams? Genome Technology. 2003, 36:46.

  • 28) Liang, P. and Pardee, A.B.: Analysing differential gene expression in cancer. Nature Reviews Cancer. 2003. 3:869-876.

  • 29) Ransohoff, D.F.: Developing molecular markers for cancer. Science. 2003, 299:1679-1680.

  • 30) Ransohoff, D.F.: Discovery-based research and fishing. Gastroenterology. 2003, 125:290.

  • 31) Tan, P.K. et al: Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res.. 2003, 31:5676-5684.

  • 32) Marshall, E.: Getting the noise out of gene arrays. Science. 2004, 306:630-631.

  • 33) Sherlock, G.: Of fish and chips. Nature Methods. 2005, 2:329-330.

  • 34) Larkin, J.E. et al.: Independence and reproducibility across microarray platforms. Nature Methods. 2005, 2:337-343.

  • 35) Irizarry, R.A. et al: Multiple-laboratory comparison of microarray platforms. Nature Methods. 2005, 2:345-349.

  • 36) Weis, B.K. et al: Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods. 2005, 2:351-356.

  • 37) Liang, P: MAQC papers over the cracks. Nature Biotechnology. 2006, 25:27-28.

Because of several major advantages, Differential Display (DD) continues to lead other competing technologies including Microarray, Oligo Array, and SAGE in total publication numbers. To see the latest comparison of publications numbers as well as a list of advantages of DD technology, please click here.

For more information about our DD Kits and FDD Services, please click here. Our FDD Service has been utilized by both academic and industry customers including 52 different institutions from 8 different countries. For a list of our FDD Service clients, click here. In addition, a list of more than 500 selected DD publications, organized chronologically and by fields of application, shows the wide range of organisms and experiements that can be performed.

Please feel free to contact us with any technical questions or comments.

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