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References & Papers

  1. G. McGall, J. Labadie, P. Brock, G. Wallraff, T. Nguyen, W. Hinsberg, Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists, PNAS, Vol. 93, Nov. 1996, 13555-13560
  2. http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494
  3. Eric S. Lander, et. al. (~3,000 authors), Initial sequencing and analysis of the human genome, Nature, Vol. 409, Feb, 15, 2001.
  4. J. Craig Venter, The Sequence of the Human Genome, Science 2001 February 16; 291: 1304-1351.
  5. K. J. Luebke, R. P. Balog, D. Mittelman and H.R. Garner, Digital Optical Chemistry: A Novel System for the Rapid Fabrication of Custom Oligonucleotide Arrays, a chapter in Microfabricated Sensors, Application of Optical Technology for DNA Analysis, Richard Kordal, Author Usmani and Wai Tak Law, editors, American Chemical Society Publications, 2002.  (the book cover featured one of our arrays)
  6. G. Miller J. Jacklevic, and H.R. Garner, chapter in  Instrumentation for the Genome Project, Annual Reviews of Biomedical Engineering, Joe Jacklevic, editor, 1999.
  7. H.R. Garner, “Custom Hardware and Software for Genome Center Operations:  From Robotic Control to Databases,” included in  Automated Technologies for Genome Characterization, edited by Dr. Tony J. Beugelsdijk, 1997.
  8. H. R. Garner, R. P. Balog and K. J. Luebke, The Evolution of Custom Microarray Manufacture,  IEEE Engineering in Biology and Medicine, in print
  9. Robert P. Balog, Y. Emi Ponce de Souza, Hue M. Tang, Gina M. DeMasellis, Boning Gao, Adrian Avila, Desmond J. Gaban, David Mittelman, John D. Minna, Kevin J. Luebke, and Harold R. Garner, Parallel Assessment of CpG Methylation by Two-Color Hybridization with Oligonucleotide Arrays, submitted, Analytical Biochemistry.
  10. Kevin J. Luebke, Robert P. Balog, and Harold R. Garner, Prioritized Selection of Oligonucleotide Probes for Efficient Hybridization to RNA Transcripts, submitted, Nucleic Acids Research
  11. L.J. Hornbeck, Digital Light Processing for high-brightness, high-resolution applications, Texas Instruments White paper, http://www.ti.com/dlp/docs/business/resources/white/index.html, and many other articles on DLP.
  12. S. Rayner, S. Brignac, R. Bumeister, Y. Belodludtsev, T. Ward, O. Grant, K. O’Brien, G.A. Evans and H.R. Garner, “MerMade:  A 2 x 96-Well Plate Oligo Synthesizer For High Throughput Production”, Genome Research, Vol. 8, 741-747, 1998.
  13. Rudert, F. Genomics and proteomics tools for the clinic. [Review] [59 refs]. Current Opinion in Molecular Therapeutics, 2: 633-642, 2000.
  14. Hughes, T. R. and Shoemaker, D. D. DNA microarrays for expression profiling. [Review] [50 refs]. Current Opinion in Chemical Biology, 5: 21-25, 2001.
  15. Young, R. A. Biomedical discovery with DNA arrays. [Review] [36 refs]. Cell, 102: 9-15, 2000.
  16. Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., Kidd, M. J., King, A. M., Meyer, M. R., Slade, D., Lum, P. Y., Stepaniants, S. B., Shoemaker, D. D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., and Friend, S. H. Functional discovery via a compendium of expression profiles. Cell, 102: 109-126, 2000.
  17. Cole, K. A., Krizman, D. B., and Emmert-Buck, M. R. The genetics of cancer--a 3D model. [Review] [47 refs]. Nature Genetics, 21: 38-41, 1999.
  18. Brown, P. O. and Botstein, D. Exploring the new world of the genome with DNA microarrays. [Review] [27 refs]. Nature Genetics, 21: 33-37, 1999.
  19. Duggan, D. J., Bittner, M., Chen, Y., Meltzer, P., and Trent, J. M. Expression profiling using cDNA microarrays. [Review] [33 refs]. Nature Genetics, 21: 10-14, 1999.
  20. Pandey, A. and Mann, M. Proteomics to study genes and genomes. [Review] [88 refs]. Nature, 405: 837-846, 2000.
  21. Keiser, N., Venkataraman, G., Shriver, Z., and Sasisekharan, R. Direct isolation and sequencing of specific protein-binding glycosaminoglycans. Nature Medicine, 7: 123-128, 2001.
  22. Gerhold, D., Rushmore, T., and Caskey, C. T. DNA chips: promising toys have become powerful tools. [Review] [28 refs]. Trends in Biochemical Sciences, 24: 168-173, 1999.
  23. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. [see comments]. Science, 270: 467-470, 1995.
  24. Shena, M., Heller, R. A., Theriault, T. P., Konrad, K., Lachenmeier, E., and Davis, R. W. Microarrays: biotechnology's discovery platform for functional genomics. [see comments]. [Review] [33 refs]. Trends in Biotechnology, 16: 301-306, 1998.
  25. http://www.nimblegen.com/NimbleGen.html
  26. http://www.febit.com/
  27. http://www.xeotron.com/
  28. http://spores.nci.nih.gov/
  29. R. A. Schultz, T. Nielsen, J.R. Zavaleta, R. Ruch, R. Wyatt and H.R. Garner, “Hyperspectral Imaging: A Novel Approach For Microscopic Analysis,” Vol. 43, pgs. 239-247, Cytometry, 2001.
  30. Michael L. Huebschman, Roger A. Schultz, and Harold R. Garner, Hyperspectral Imaging, Review article, Encyclopedia of Modern Optics, Academic Press, 2002
  31. M.R. Weil, T. Macatee, and H. R. Garner, Towards a universal standard: Comparing two methods for standardizing spotted microarray data, in press, Biotechniques, 32(6), June 2002.
  32. Adel M. Talaat, Susan T. Howard, Walker Hale IV, Rick Lyons, Harold R. Garner  and Stephen Albert Johnston, Genomic DNA Standards For Gene Expression Profiling of Mycobacterium tuberculosis, accepted, Nucleic Acids Research.
  33. Jonathan D Wren, T. Macatee, Amit Kulkarni, Charles Epstein, Ron Butow, Harold R Garner, Microarray Cross-Hybridization,  IEEE Engineering in Biology and Medicine, pgs. 71-75, March, 2002.
  34. J. Schageman, M. Basit, T. Gallardo, and H.R. Garner  R.V. Shohet, MarC-V:  A Spreadsheet-Based Tool for Analysis, Normalization, and Visualization of Single cDNA Microarray Experiments, Biotechniques 32:338-344, Feb. 2002.
  35. A. Kulkarni, D. Mittelman, N. Williams, A. Pertsemlidis, Y. Lian, H. R. Garner, ARROGANT- Array Organizing Tool, A software tool to compile, analyze and merge large gene collections, in print, BioInformatics.
  36. B. Liao, C. Epstein, W. Hale, R. Butow, H.R. Garner, “MAD ­ A microarray database”, Bioinformatics, 2000.
  37. A. Pertsemlidis, B. Miller, A. Pande, P. Schilling, M. H. Wei, M. I. Lerman, J. D. Minna and H. R. Garner, "PANORAMA - An integrated web based sequence analysis tool and its role in gene discovery," Genomics 70, ppg 300-306, 2000.
  38. Wren JD, Mittleman D, Garner HR "SIGNAL ­ Sequence Iterative GeNomic AnaLysis" Computer Methods and Programs in Biomedicine 2002 May; 68(2): 177-181
  39. Wren, JD and Garner, HR, Heuristics for Identification of Acronym-Definition Patterns within Text: Towards an Automated Construction, Methods of Information in Medicine, in press.
  40. Wren JD and Garner HR, "Knowledge Discovery by Implicit and Shared Relationship Analysis", submitted, Science
  41. A.Pertsemlidis and H.R. Garner, eTBLAST: text comparison for mining the biomedical literature, submitted, PNAS
  42. M. Horvath, J. Fondon and H.R. Garner, SNP database analyis: Synonymous and nonsynonymous point mutations are non-randomly distributed across codons, submitted, Genome Research.
  43. Riggs, A. & Pfeifer, G. X-chromosome inactivation and cell memory. Trends in Genetics 8, 169-174 (1992).
  44. Sekido, Y., Fong, K.M. & Minna, J.D. Progress in understanding the molecular pathogenesis of human lung cancer. Biochimica et Biophysica Acta 1378, F21-59 (1998).
  45. Zochbauer-Muller, S. et al. Aberrant promoter methylation of multiple genes in non-small cell lung cancers. Cancer Research 61, 249-255 (2001).
  46. Burbee, D.G. et al. Epigenetic inactivation of RASSF1A in lung and breast cancers and malignant phenotype suppression. Journal of the National Cancer Institute 93, 691-699 (2001).
  47. Pinkel et al. (1998) Nat. Genet. 20, 207-211.
  48. Kallioniemi et al. (1992) Science 258, 818-821
  49. Pollack et al. (1999) Nat. Genet. 23, 41-46
  50. http://www.operon.com/
  51. Lin, C.H., et al., Genome-wide hypomethylation in hepatocellular carcinogenesis. Cancer Res, 2001. 61(10): p. 4238-43.
  52. Baylin, S.B., et al., Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet, 2001. 10(7): p. 687-92.
  53. Leonhardt, H. and M.C. Cardoso, DNA methylation, nuclear structure, gene expression and cancer. J Cell Biochem, 2000. Suppl(35): p. 78-83.
  54. Bulyk, Gentalen, Lockhart, and Church (1999) Nature Biotech. 17(6) 573-577
  55. Bulyk, Huang, Cho, and Church (2001) PNAS 98(13) 7158-7163
  56. SantaLucia, Allawi, and Seneviratne (1996) Biochemistry 35, 3555-3562
  57. Borer, Dengler, Tinoco, and Uhlenbeck (1974) J. Mol. Biol. 86, 843-853
  58. Strobl, L.J., Zimber-Strobl, Y. Magnetic DNA Affinity Purification of a Cellular Transcription Factor, Methods in Mol. Biol. 2001, 174, 271-277.