My microarray journal watch - year 1999  [ this week | 2004 Oct-Dec | 2004 Jul-Sep | 2004 Apr-Jun | 2004 Jan-Mar | 2003 Oct-Dec | 2003 Jul-Sep | 2003 Apr-Jun | 2003 Jan-Mar | 2002 Jul-Dec |  2002 Jan-Jun | 2001 Jul-Dec | 2001 Jan-Jun | 2000 | 1999 | 1998 | 1997 | 1996 & before ]

General
Nature Genetics volume 21, Supplement (1999) The chipping forecast
Monitoring cell response, gene expression, clustering and profiling
Genetic analysis
Disease screening and clinical practice
Pharmacogenomics and pharmacogenetics
Technical development
Other related technical issue; microdissection; linear amplification of RNA (aRNA)
Data analysis
Tissue microarray
Protein array
Biochip/ lab-on-a-chip/ micro-Total Analysis System (uTAS)
Alternative array		 Can't find the microarray article published in 1999 in my site? 
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General

  1. Niehrs C, Pollet N. Synexpression groups in eukaryotes. Nature. 1999 Dec 2;402(6761):483-7. Review [PubMed]
  2. Ekins R, Chu FW. Microarrays: their origins and applications. Trends Biotechnol. 1999 Jun;17(6):217-8. [PubMed]
  3. Khan J, Bittner ML, Chen Y, Meltzer PS, Trent JM. DNA microarray technology: the anticipated impact on the study of human disease. Biochim Biophys Acta. 1999 Mar 25;1423(2):M17-28. Review. [PubMed]
  4. Gerhold D, Rushmore T, Caskey CT. DNA chips: promising toys have become powerful tools.Trends Biochem Sci. 1999 May;24(5):168-73. Review. [PubMed]
  5. Graves DJ. Powerful tools for genetic analysis come of age. Trends Biotechnol. 1999 Mar;17(3):127-134 [link to article]
  6. Phimister B. Going global. Nat Genet. 1999 Jan;21(1 Suppl):1. [pdf]
  7. Collins FS. Microarrays and macroconsequences Nat Genet. 1999 Jan;21(1 Suppl):2. [pdf]
  8. Lander ES. Array of hope. Nat Genet. 1999 Jan;21(1 Suppl):3-4. [pdf]
  9. Bowtell DD. Options available--from start to finish--for obtaining expression data by microarray. Nat Genet. 1999 Jan;21(1 Suppl):25-32. Review. [PubMed][pdf]
  10. Brown PO, Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 1999 Jan;21(1 Suppl):33-7. Review. [PubMed][pdf]
  11. Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods Enzymol. 1999;303:179-205. [PubMed][pdf]

Nature Genetics volume 21, Supplement (1999) The chipping forecast

  1. Phimister B. Going global. Nat Genet. 1999 Jan;21(1 Suppl):1. [pdf]
  2. Collins FS. Microarrays and macroconsequences Nat Genet. 1999 Jan;21(1 Suppl):2. [pdf]
  3. Lander ES. Array of hope. Nat Genet. 1999 Jan;21(1 Suppl):3-4. [pdf]
  4. Southern E, Mir K, Shchepinov M. Molecular interactions on microarrays. Nat Genet. 1999 Jan;21(1 Suppl):5-9. Review. [PubMed][pdf]
  5. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Expression profiling using cDNA microarrays. Nat Genet. 1999 Jan;21(1 Suppl):10-4. Review. [PubMed][pdf]
  6. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G. Making and reading microarrays. Nat Genet. 1999 Jan;21(1 Suppl):15-9. Review. [PubMed][pdf]
  7. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays. Nat Genet. 1999 Jan;21(1 Suppl):20-4. Review. [PubMed][pdf]
  8. Bowtell DD. Options available--from start to finish--for obtaining expression data by microarray. Nat Genet. 1999 Jan;21(1 Suppl):25-32. Review. [PubMed][pdf]
  9. Brown PO, Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 1999 Jan;21(1 Suppl):33-7. Review. [PubMed][pdf]
  10. Cole KA, Krizman DB, Emmert-Buck MR. The genetics of cancer--a 3D model. Nat Genet. 1999 Jan;21(1 Suppl):38-41. Review. [PubMed][pdf]
  11. Hacia JG. Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet. 1999 Jan;21(1 Suppl):42-7. Review. [PubMed][pdf]
  12. Debouck C, Goodfellow PN. DNA microarrays in drug discovery and development. Nat Genet. 1999 Jan;21(1 Suppl):48-50. Review. [PubMed][pdf]
  13. Bassett DE Jr, Eisen MB, Boguski MS. Gene expression informatics--it's all in your mine. Nat Genet. 1999 Jan;21(1 Suppl):51-5. Review. [PubMed][pdf]
  14. Chakravarti A. Population genetics--making sense out of sequence. Nat Genet. 1999 Jan;21(1 Suppl):56-60. Review. [PubMed][pdf]

Monitoring cell response, gene expression, clustering and profiling

  1. White KP, Rifkin SA, Hurban P, Hogness DS. Microarray analysis of Drosophila development during metamorphosis.Science. 1999 Dec 10;286(5447):2179-84. [PubMed]
  2. Niehrs C, Pollet N. Synexpression groups in eukaryotes. Nature. 1999 Dec 2;402(6761):483-7. Review [PubMed]
  3. Ferea TL, Brown PO.  Observing the living genome.  Curr Opin Genet Dev. 1999 Dec; 9(6): 715-22. Review. [PubMed]
  4. Johannes G, Carter MS, Eisen MB, Brown PO, Sarnow P. Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray.  Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13118-23. [PubMed][pdf]
  5. Khan J, Bittner ML, Saal LH, Teichmann U, Azorsa DO, Gooden GC, Pavan WJ, Trent JM,Meltzer PS. cDNA microarrays detect activation of a myogenic transcription program by the PAX3-FKHR fusion oncogene. Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13264-9. [PubMed][pdf]
  6. Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc Natl Acad Sci U S A. 1999 Oct 26; 96(22): 12833-8. [PubMed][pdf]
  7. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 1999 Sep;23(1):41-6. [PubMed][pdf][web supplement]
  8. Ferea TL, Botstein D, Brown PO, Rosenzweig RF.  Systematic changes in gene expression patterns following adaptive evolution in yeast.  Proc Natl Acad Sci U S A. 1999 Aug 17; 96(17): 9721-6. [PubMed][pdf][web supplement]
  9. Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT, Pergamenschikov A, Williams  CF, Zhu SX, Lee JC, Lashkari D, Shalon D, Brown PO, Botstein D. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9212-7. [PubMed][pdf][web supplement]
  10. Wolfsberg TG, Gabrielian AE, Campbell MJ, Cho RJ, Spouge JL, Landsman D. Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomycescerevisiae. Genome Res. 1999 Aug;9(8):775-92. [PubMed]
  11. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet. 1999 Jul;22(3):281-5. [PubMed]
  12. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6745-50. [PubMed][pdf][web_supplement]
  13. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2907-12. [PubMed][pdf]
  14. Yang GP, Ross DT, Kuang WW, Brown PO, Weigel RJ.  Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes.  Nucleic Acids Res. 1999 Mar 15; 27(6): 1517-23. [PubMed]
  15. Hilsenbeck SG, Friedrichs WE, Schiff R, O'Connell P, Hansen RK, Osborne CK, Fuqua SA. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J Natl Cancer Inst. 1999 Mar 3;91(5):453-9. [PubMed]
  16. Khan J, Saal LH, Bittner ML, Chen Y, Trent JM, Meltzer PS. Expression profiling in cancer using cDNA microarrays. Electrophoresis. 1999 Feb;20(2):223-9. Review. [PubMed]
  17. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Expression profiling using cDNA microarrays. Nat Genet. 1999 Jan;21(1 Suppl):10-4. Review. [PubMed][pdf]
  18. Myers LC, Gustafsson CM, Hayashibara KC, Brown PO, Kornberg RD.  Mediator protein mutations that selectively abolish activated transcription.  Proc Natl Acad Sci U S A. 1999 Jan 5; 96(1): 67-72. [PubMed][pdf]
  19. Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson J Jr, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO. The transcriptional program in the response of human fibroblasts to serum. Science. 1999 Jan 1;283(5398):83-7. [PubMed][pdf][web supplement]

    20.  

Genetic analysis

  1. Syvanen AC. From gels to chips: "minisequencing" primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat. 1999;13(1):1-10. Review. [PubMed]
  2. Hacia JG. Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet. 1999 Jan;21(1 Suppl):42-7. Review. [PubMed][pdf]
  3. Chakravarti A. Population genetics--making sense out of sequence. Nat Genet. 1999 Jan;21(1 Suppl):56-60. Review. [PubMed][pdf]

Disease screening and clinical practice

     
  1. Stephenson J. Lab-on-a-chip shows promise in defining and diagnosing cancers. JAMA. 1999 Nov 17;282(19):1801-2. [PubMed]
  2. Friend SH. How DNA microarrays and expression profiling will affect clinical practice. BMJ. 1999 Nov 13;319(7220):1306-7. [PubMed]
  3. Bubendorf L, Kolmer M, Kononen J, Koivisto P, Mousses S, Chen Y, Mahlamaki E, Schraml P, Moch H, Willi N, Elkahloun AG, Pretlow TG, Gasser TC, Mihatsch MJ, Sauter G, Kallioniemi OP. Hormone therapy failure in human prostate cancer: analysis by complementary DNA and tissue microarrays. J Natl Cancer Inst. 1999 Oct 20;91(20):1758-64. [PubMed]
  4. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999 Oct 15;286(5439):531-7. [PubMed]
  5. Khan J, Saal LH, Bittner ML, Chen Y, Trent JM, Meltzer PS. Expression profiling in cancer using cDNA microarrays. Electrophoresis. 1999 Feb;20(2):223-9. Review. [PubMed]
  6. Cole KA, Krizman DB, Emmert-Buck MR. The genetics of cancer--a 3D model. Nat Genet. 1999 Jan;21(1 Suppl):38-41. Review. [PubMed][pdf]
  7. Alizadeh A, Eisen M, Davis RE, Ma C, Sabet H, Tran T, Powell JI, Yang L, Marti GE, Moore DT, Hudson JR, Chan WC, Greiner T, Weisenburger D, Armitage JO,  Lossos I, Levy R, Botstein D, Brown PO, Staudt LM.  The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes.  Cold Spring Harb Symp Quant Biol. 1999;64:71-8. [PubMed]

Pharmacogenomics and pharmacogenetics

  1. Hilsenbeck SG, Friedrichs WE, Schiff R, O'Connell P, Hansen RK, Osborne CK, Fuqua SA. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J Natl Cancer Inst. 1999 Mar 3;91(5):453-9. [PubMed]
  2. Debouck C, Goodfellow PN. DNA microarrays in drug discovery and development. Nat Genet. 1999 Jan;21(1 Suppl):48-50. Review. [PubMed][pdf]
  3. Chakravarti A. Population genetics--making sense out of sequence. Nat Genet. 1999 Jan;21(1 Suppl):56-60. Review. [PubMed][pdf]

Technical development

  1. Kwiatkowski M, Fredriksson S, Isaksson A, Nilsson M, Landegren U. Inversion of in situ synthesized oligonucleotides: improved reagents for hybridization and primer extension in DNA microarrays. Nucleic Acids Res. 1999 Dec 15;27(24):4710-4. [PubMed]
  2. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. [PubMed]
  3. Loftus SK, Chen Y, Gooden G, Ryan JF, Birznieks G, Hilliard M, Baxevanis AD, Bittner M, Meltzer P, Trent J, Pavan W. Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis. Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9277-80. [PubMed][pdf]
  4. Regnier FE, He B, Lin S, Busse J. Chromatography and electrophoresis on chips: critical elements of future integrated, microfluidic analytical systems for life science. Trends Biotechnol. 1999 Mar;17(3):101-106
  5. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays. Nat Genet. 1999 Jan;21(1 Suppl):20-4. Review. [PubMed][pdf]
  6. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G. Making and reading microarrays. Nat Genet. 1999 Jan;21(1 Suppl):15-9. Review. [PubMed][pdf]
  7. Southern E, Mir K, Shchepinov M. Molecular interactions on microarrays. Nat Genet. 1999 Jan;21(1 Suppl):5-9. Review. [PubMed][pdf]

Other related technical issue; microdissection; linear amplification of RNA (aRNA)

  1. Mahadevappa M, Warrington JA. A high-density probe array sample preparation method using 10- to 100-fold fewer cells. Nat Biotechnol. 1999 Nov;17(11):1134-6. [PubMed]
  2. Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999 Mar;19(3):1720-30. [PubMed]
  3. Suarez-Quian CA, Goldstein SR, Pohida T, Smith PD, Peterson JI, Wellner E, Ghany M, Bonner RF.  Laser capture microdissection of single cells from complex tissues.  Biotechniques. 1999 Feb;26(2):328-35. [PubMed]
  4. Luo L, Salunga RC, Guo H, Bittner A, Joy KC, Galindo JE, Xiao H, Rogers KE, Wan JS, Jackson MR, Erlander MG. Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med. 1999 Jan;5(1):117-22. [PubMed]
  5. Kacharmina JE, Crino PB, Eberwine J. Preparation of cDNA from single cells and subcellular regions. Methods Enzymol. 1999;303:3-18. [PubMed]

Data analysis

  1. Ben-Dor A, Shamir R, Yakhini Z. Clustering gene expression patterns. J Comput Biol. 1999 Fall-Winter;6(3-4):281-97. [PubMed][ps][pdf]
  2. Wolfsberg TG, Gabrielian AE, Campbell MJ, Cho RJ, Spouge JL, Landsman D. Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomycescerevisiae. Genome Res. 1999 Aug;9(8):775-92. [PubMed]
  3. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet. 1999 Jul;22(3):281-5. [PubMed]
  4. Bittner M, Meltzer P, Trent J. Data analysis and integration: of steps and arrows.Nat Genet. 1999 Jul;22(3):213-5 [PubMed]
  5. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2907-12. [PubMed][pdf]
  6. Hilsenbeck SG, Friedrichs WE, Schiff R, O'Connell P, Hansen RK, Osborne CK, Fuqua SA. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J Natl Cancer Inst. 1999 Mar 3;91(5):453-9. [PubMed]]
  7. Wittes J, Friedman HP.  Searching for evidence of altered gene expression: a comment on statistical analysis of microarray data.  J Natl Cancer Inst. 1999 Mar 3;91(5):400-1. [PubMed]
  8. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Expression profiling using cDNA microarrays.Nat Genet. 1999 Jan;21(1 Suppl):10-4. Review. [PubMed][pdf]
  9. Bassett DE Jr, Eisen MB, Boguski MS. Gene expression informatics--it's all in your mine. Nat Genet. 1999 Jan;21(1 Suppl):51-5. Review. [PubMed][pdf]
  10. Mjolsness, E., Castano, R., Mann, T., Roden, J., Gray, A., and Wold, B. (1999) Clustering methods for the analysis of C. elegans gene expression array data. Technical report JPL-ICTR-99-1. [you can find the full text pdf from their web]
  11. E. Mjolsness, R. Castaño, A. Gray. Multi-Parent Clustering Algorithms for Large-Scale Gene Expression Analysis. Technical Report JPL-ICTR-99-5. [you can find the full text pdf from their web]
  12. E. Mjolsness, T. Mann, R. Castaño, B. Wold. From Coexpression to Coregulation: An Approach to Inferring Transcriptional Regulation among Gene Classes from Large-Scale Expression Data. In: Neural Information Processing Systems (NIPS) 1999. Also avail. as Technical Report JPL-ICTR-99-4. [you can find full text pdf from their web]
  13. Claverie JM. Computational methods for the identification of differential and coordinated gene expression.Hum Mol Genet. 1999;8(10):1821-32. [PubMed]
  14. Hartuv E,  Schmitt E, Lange J, Meier-Ewert S, Lehrach H, and Shamir R. An algorithm for clustering cDNAs for gene expression analysis. Third annual international conference on Computational molecular biology (RECOMB '99) [abstract][ps][pdf][pdf(2nd location)]
  15. Chen T, Filkov V, Skiena SS. Identifying gene regulatory networks from experimental data. Third annual international conference on Computational molecular biology (RECOMB '99) [abstract][ps][pdf][pdf(2nd location)]
  16. Karp RM, Stoughton R, Yeung KY. Algorithms for choosing differential gene expression experiments. Third annual international conference on Computational molecular biology (RECOMB '99) [pdf]
  17. Szallasi Z. Genetic network analysis in light of massively parallel biological data acquisition. Pac Symp Biocomput. 1999;:5-16. [PubMed][pdf]
  18. Akutsu T, Miyano S, Kuhara S. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac Symp Biocomput. 1999;:17-28. [PubMed][pdf]

Tissue microarray

  1. Bubendorf L, Kolmer M, Kononen J, Koivisto P, Mousses S, Chen Y, Mahlamaki E, Schraml P, Moch H, Willi N, Elkahloun AG, Pretlow TG, Gasser TC, Mihatsch MJ, Sauter G, Kallioniemi OP. Hormone therapy failure in human prostate cancer: analysis by complementary DNA and tissue microarrays. J Natl Cancer Inst. 1999 Oct 20;91(20):1758-64. [PubMed]
  2. Schraml P, Kononen J, Bubendorf L, Moch H, Bissig H, Nocito A, Mihatsch MJ, Kallioniemi OP, Sauter G. Tissue microarrays for gene amplification surveys in many different tumor types. Clin Cancer Res. 1999 Aug;5(8):1966-75. [PubMed]

Protein array

  1. Bieri C, Ernst OP, Heyse S, Hofmann KP, Vogel H.  Micropatterned immobilization of a G protein-coupled receptor and direct detection of G protein activation.  Nat Biotechnol. 1999 Nov;17(11):1105-8. [PubMed]
  2. Lueking A, Horn M, Eickhoff H, Bussow K, Lehrach H, Walter G.  Protein microarrays for gene expression and antibody screening. Anal Biochem. 1999 May 15;270(1):103-11. [PubMed]

Biochip/ lab-on-a-chip/ micro-Total Analysis System (uTAS)

  1. Wilding P, Kricka LJ. Micro-microchips: just how small can we go? Trends Biotechnol. 1999 Dec;17(12):465-8. Review. [PubMed]
  2. Gilles PN, Wu DJ, Foster CB, Dillon PJ, Chanock SJ.  Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips.  Nat Biotechnol. 1999 Apr;17(4):365-70. [PubMed]
  3. Regnier FE, He B, Lin S, Busse J.  Chromatography and electrophoresis on chips: critical elements of future integrated, microfluidic analytical systems for life science. Trends Biotechnol. 1999 Mar;17(3):101-6. Review. [PubMed]

Alternative array


last updated: 4 Nov 2001
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