My microarray journal watch - year 2000  [ 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
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
Database
Tissue microarray
Protein array
Biochip/ lab-on-a-chip/ micro-Total Analysis System (uTAS)
Alternative array		 Can't find the microarray article published in 2000 in my site? 
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General

  1. Watson SJ, Meng F, Thompson RC, Akil H. The "chip" as a specific genetic tool.  Biol Psychiatry. 2000 Dec 15;48(12):1147-56. [PubMed]
  2. Harkin DP. Uncovering functionally relevant signaling pathways using microarray-based expression profiling. Oncologist. 2000;5(6):501-7. [PubMed]
  3. Rudd KE. New tools for an old workhorse. Nat Biotechnol. 2000 Dec;18(12):1241-1242. [PubMed]
  4. Wisman E, Ohlrogge J. Arabidopsis Microarray Service Facilities. Plant Physiol. 2000 Dec;124(4):1468-1471. [PubMed]
  5. Zubritsky E.  Spotting a microarray system.  Anal Chem. 2000 Dec 1;72(23):761A-767A. [PubMed]
  6. Snijders AM, Meijer GA, Brakenhoff RH, van den Brule AJ, van Diest PJ. Microarray techniques in pathology: tool or toy?  Mol Pathol. 2000 Dec;53(6):289-94. [PubMed]
  7. Rudert F. Genomics and proteomics tools for the clinic.  Curr Opin Mol Ther. 2000 Dec;2(6):633-42. [PubMed]
  8. Schulze A, Downward J. Analysis of gene expression by microarrays: cell biologist's gold mine or minefield? J Cell Sci. 2000;113(Pt 23):4151-4156. [PubMed]
  9. Nadis S. Whitehead enters into array deal. Nature 2000. Nov 2; 6-7 [PubMed]
  10. When is a chip not a chip? Trends Biotechnol. 2000. Nov; 18: 439-440
  11. Schwarz DG.  DNA chips and development: prospects and problems Genesis. 2000 Nov;28(3-4):134 [PubMed]
  12. Zanders ED.  Gene expression analysis as an aid to the identification of drug targets. Pharmacogenomics. 2000 Nov;1(4):375-84. [PubMed]
  13. Hayes A. Meeting Review: the Second International Meeting on Microarray Data Standards, Annotations,Ontologies and Databases. Yeast. 2000 Sep 30;17(3):238-240. [PubMed]
  14. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques. 2000 Sep;29(3):548-54, 556, 558-60 passim. [PubMed][pdf]
  15. Corning chips in. Nat Biotechnol. 2000 Oct;18(10):1023. [PubMed]
  16. Meldrum D. Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends. Genome Res. 2000 Sep;10(9):1288-1303. [PubMed]
  17. Jorge D. Cortese. The array of today: biomolecule arrays become the 21st century's test tube. The Scientist 2000 Sep 4;14(17):25 [Web link][Supplementary info: A,B]
  18. Ishii M, Hashimoto Si, Tsutsumi S, Wada Y, Matsushima K, Kodama T, Aburatani H. Direct Comparison of GeneChip and SAGE on the Quantitative Accuracy in Transcript Profiling Analysis. Genomics. 2000 Sep 1;68(2):136-143. [PubMed]
  19. Wang J. SURVEY AND SUMMARY: From DNA biosensors to gene chips. Nucleic Acids Res. 2000 Aug 15;28(16):3011-3016.[PubMed]
  20. Jain KK.  Applications of biochip and microarray systems in pharmacogenomics.  Pharmacogenomics. 2000 Aug;1(3):289-307. [PubMed]
  21. Jain KK. Biotechnological applications of lab-chips and microarrays. Trends Biotechnol. 2000 Jul;18(7):278-80.[PubMed]
  22. Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays.  Nature. 2000 Jun 15;405(6788):827-36. Review. [PubMed]
  23. Ivanov I, Schaab C, Planitzer S, Teichmann U, Machl A, Theml S, Meier-Ewert S, Seizinger B, Loferer H. DNA microarray technology and antimicrobial drug discovery. Pharmacogenomics. 2000 May;1(2):169-78. [PubMed]
  24. Jurecic R, Belmont JW. Long-distance DD-PCR and cDNA microarrays.  Curr Opin Microbiol. 2000 Jun;3(3):316-21. Review. [PubMed]
  25. Dangond F. Chips around the world: proeedings from the Nature Genetics Microarray Meeting. Physiol Genomics. 2000 Mar; 2: 53-58 [PubMed]
  26. Brazma A, Robinson A, Cameron G, Ashburner M. One-stop shop for microarray data. Nature. 2000 Feb 17;403(6771):699-700. [PubMed]
  27. Mir KU. The hypothesis is there is no hypothesis.The Microarray Meeting, Scottsdale, Arizona, USA, 22-5 September 1999 [Meeting Report]. Trends Genet. 2000 Feb;16(2):63-64 [link to article]
  28. Dalton R. DIY microarrayers promise DNA chips with everything. Nature. 2000 Jan 20;403(6767):234. [PubMed]
  29. Stewart DJ. Making and using DNA microarrays: a short course at Cold Spring Harbor Laboratory. Genome Res. 2000 Jan;10(1):1-3. [PubMed]
  30. Staudt LM, Brown PO.  Genomic views of the immune system.  Annu Rev Immunol. 2000; 18: 829-59. Review. [PubMed]
  31. Coffey RJ, Threadgill D.  Microarray foray. Breast Cancer Res. 2000;2(1):8-9 [PubMed]

Monitoring cell response, gene expression, clustering and profiling

  1. Yazaki J, Kishimoto N, Nakamura K, Fujii F, Shimbo K, Otsuka Y, Wu J, Yamamoto K, Sakata K, Sasaki T, Kikuchi S. Embarking on rice functional genomics via cDNA microarray: use of 3' UTR probes for specific gene expression analysis. DNA Res. 2000 Dec 31;7(6):367-70. [PubMed]
  2. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA.  Genome-wide location and function of DNA binding proteins. Science. 2000 Dec 22;290(5500):2306-9. [PubMed]
  3. Petersen M, Brodersen P, Naested H, Andreasson E, Lindhart U, Johansen B, Nielsen HB, Lacy M, Austin MJ, Parker JE, Sharma SB, Klessig DF, Martienssen R, Mattsson  O, Jensen AB, Mundy J. Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance.  Cell. 2000 Dec 22;103(7):1111-1120. [PubMed]
  4. Evans JD, Wheeler DE. Expression profiles during honeybee caste determination. Genome Biology 2000 Dec 20;2(1): research0001.1-0001.6 [link to article][pdf]
  5. Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14668-14673. [PubMed][pdf]
  6. Tenenbaum SA, Carson CC, Lager PJ, Keene JD. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14085-14090. [PubMed][pdf]
  7. Yang J, Moravec CS, Sussman MA, DiPaola NR, Fu D, Hawthorn L, Mitchell CA, Young JB, Francis GS, McCarthy PM, Bond M. Decreased SLIM1 expression and increased gelsolin expression in failing human hearts measured by high-density oligonucleotide arrays.  Circulation. 2000 Dec 19;102(25):3046-52. [PubMed]
  8. Bertucci F, Houlgatte R, Benziane A, Granjeaud S, Adelaide J, Tagett R, Loriod B, Jacquemier J, Viens P, Jordan B, Birnbaum D, Nguyen C. Gene expression profiling of primary breast carcinomas using arrays of candidate genes. Hum Mol Genet. 2000 Dec 12;9(20):2981-2991.[PubMed]
  9. Callow MJ, Dudoit S, Gong EL, Speed TP, Rubin EM. Microarray expression profiling identifies genes with altered expression oin HDL-Deficient Mice. Genome Res. 2000 Dec; 10(12): 2022-2029 [PubMed]
  10. Andrews J, Bouffard GG, Cheadle C, Lü J, Becker KG, Oliver B. Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis. Genome Res. 2000 Dec; 10(12): 2030-2043 [PubMed]
  11. Ogawa N, DeRisi J, Brown PO. New Components of a System for Phosphate Accumulation and Polyphosphate Metabolism in  Saccharomyces cerevisiae Revealed by Genomic Expression Analysis. Mol Biol Cell. 2000 Dec;11(12):4309-4321. [PubMed][web supplement]
  12. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO.   Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes.  Mol Biol Cell. 2000 Dec.; 11(12): 4241-4257. [PubMed][web supplement]
  13. Shiffman D, Mikita T, Tai JT, Wade DP, Porter JG, Seilhamer JJ, Somogyi R, Liang S, Lawn RM. Large scale gene expression analysis of cholesterol loaded macrophages. J Biol Chem. 2000 Dec 1;275(48):37324-32 [PubMed]
  14. Vertegaal ACO, Kuiperij B, van Laar T, Scharnhorst V, van der Eb AH, Zantema A. cDNA micro array identification of a gene differentially expressed in adenovirus type 5- versus type 12-transformed cells. FEBS Lett. 2000 Dec; 487: 151-155
  15. Klevecz RR. Dynamic architecture of the yeast cell cycle uncovered by wavelet decomposition of expression microarray data. Funct Integr Genomics 2000. 1:186-192 [PubMed]
  16. Svaren J, Ehrig T, Abdulkadir SA, Ehrengruber MU, Watson MA, Milbrandt J. EGR1 Target Genes in Prostate Carcinoma Cells Identified by Microarray Analysis. J Biol Chem. 2000 Dec 8;275(49):38524-38531. [PubMed]
  17. Zou S, Meadows S, Sharp L, Jan LY, Jan YN. Genome-wide study of aging and oxidative stress response in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13726-13731. [PubMed][pdf]
  18. Futcher B. Microarrays and cell cycle transcription in yeast. Curr Opin Cell Biol. 2000 Dec;12(6):710-5. [PubMed]
  19. Primig M, Williams RM, Winzeler EA, Tevzadze GG, Conway AR, Hwang SY, Davis RW, Esposito RE. The core meiotic transcriptome in budding yeasts. Nat Genet. 2000 Dec;26(4):415-423. [PubMed]
  20. Maleck K, Levine A, Eulgem T, Morgan A, Schmid J, Lawton KA, Dangl JL, Dietrich RA. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet. 2000 Dec;26(4):403-410. [PubMed]
  21. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol. 2000 Dec;18(12):1262-1268. [PubMed]
  22. Aguan K, Carvajal JA, Thompson LP, Weiner CP. Application of a functional genomics approach to identify differentially expressed genes in human myometrium during pregnancy and labour. Mol Hum Reprod. 2000 Dec;6(12):1141-1145. [PubMed]
  23. Girke T, Todd J, Ruuska S, White J, Benning C, Ohlrogge J. Microarray Analysis of Developing Arabidopsis Seeds. Plant Physiol. 2000 Dec;124(4):1570-1581. [PubMed]
  24. Wolf M, El-Rifai W, Tarkkanen M, Kononen J, Serra M, Eriksen EF, Elomaa I, Kallioniemi A, Kallioniemi O, Knuutila S. Novel findings in gene expression detected in human osteosarcoma by cDNA microarray. Cancer Genetics and Cytogenetics 2000. Dec; 123:128-132 [PubMed]
  25. Futcher B. Microarrays and cell cycle transcription in yeast. Curr Opin Cell Biol. 2000 Dec 1;12(6):710-715. [PubMed]
  26. Bouton CM, Pevsner J.  Effects of lead on gene expression.  Neurotoxicology. 2000 Dec;21(6):1045-55. [PubMed]
  27. Reid JL, Iyer VR, Brown PO, Struhl K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase.  Mol Cell. 2000 Dec.; 6(6): 1297-1307. [PubMed]
  28. Yamada M, Yamada M, Yamazaki S, Takahashi K, Nishioka G, Kudo K, Ozawa H, Yamada S, Kiuchi Y, Kamijima K, Higuchi T, Momose K. Identification of a Novel Gene with RING-H2 Finger Motif Induced after Chronic Antidepressant Treatment in Rat Brain. Biochem Biophys Res Commun. 2000 Nov 11;278(1):150-157. [PubMed]
  29. Lucito R, West J, Reiner A, Alexander J, Esposito D, Mishra B, Powers S, Norton L, Wigler M. Detecting Gene Copy Number Fluctuations in Tumor Cells by Microarray Analysis of Genomic Representations. Genome Res. 2000 Nov;10(11):1726-1736. [PubMed]
  30. Aschheim K. Gene detection by array. Nat Biotechnol. 2000 Nov;18(11):1129. [PubMed]
  31. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M. Analysis of yeast protein kinases using protein chips. Nat Genet. 2000 Nov;26(3):283-289. [PubMed]
  32. Penn SG, Rank DR, Hanzel DK, Barker DL. Mining the human genome using microarrays of open reading frames. Nat Genet. 2000 Nov;26(3):315-318. [PubMed]
  33. Dieckgraefe BK, Stenson WF, Korzenik JR, Swanson PE, Harrington CA. Analysis of mucosal gene expression in inflammatory bowel disease by parallel oligonucleotide arrays. Physiol Genomics. 2000 Nov; 4:1-11 [PubMed]
  34. Ben-Dor A, Bruhn L, Friedman N, Nachman I, Schummer M, Yakhini Z. Tissue Classification with Gene Expression Profiles.  J Comput Biol. 2000 Nov;7(3):559-583. [PubMed]
  35. Gore MA, Morshedi MM, Reidhaar-Olson JF. Gene expression changes associated with cytotoxicity identified using cDNA arrays. Funct Integr Genomics. 2000 1:114-126
  36. Hill AA, Hunter CP, Tsung BT, Tucker-Kellogg G, Brown EL. Genomic analysis of gene expression in C. elegans. Science 2000. Oct 27; 290:809-812
  37. Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, Yanofsky C. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12170-12175. [PubMed][pdf]
  38. Brachat A, Pierrat B, Brungger A, Heim J. Comparative microarray analysis of gene expression during apoptosis-induction by growth factor deprivation or protein kinase C inhibition. Oncogene. 2000 Oct 19;19(44):5073-82. [PubMed]
  39. Puga A, Maier A, Medvedovic M. The transcriptional signature of dioxin in human hepatoma HepG2 cells.  Biochem Pharmacol. 2000 Oct 15;60(8):1129-1142. [PubMed]
  40. Takizawa PA, DeRisi JL, Wilhelm JE, Vale RD. Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. Science. 2000 Oct 13;290(5490):341-4. [PubMed]
  41. Gross C, Kelleher M, Iyer VR, Brown PO, Winge DR.  Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays.  J Biol Chem. 2000 Oct 13; 275(41): 32310-6. [PubMed]
  42. Schenk PM, Kazan K, Wilson I, Anderson JP, Richmond T, Somerville SC, Manners JM. Coordinated plant defense responses in arabidopsis revealed by microarray analysis. Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11655-60. [PubMed][pdf]
  43. Drawid A, Jansen R, Gerstein M. Genome-wide analysis relating expression level with protein subcellular localization.Trends Genet. 2000 Oct;16(10):426-430. [PubMed]
  44. Mirnics K, Middleton FA, Marquez A, Lewis DA, Levitt P. Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex. Neuron. 2000. Oct; 28:53-67
  45. Liotta L, Petricoin E. Molecular profiling of human cancer. Nature reviews genetics. 2000 Oct; 1:48-56.
  46. Qi L, Sit KH.  Suicidal differential housekeeping gene activity in apoptosis induced by DCNP.  Apoptosis. 2000 Oct;5(4):379-88. [PubMed]
  47. Brady G. Expression profiling of single mammalian cells - small is beautiful. Yeast. 2000 Sep 30;17(3):211-217. [PubMed]
  48. Wada R, Tifft CJ, Proia RL. Microglial activation precedes acute neurodegeneration in Sandhoff disease and is suppressed by bone marrow transplantation. Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):10954-10959. [PubMed][pdf]
  49. Geschwind DH. Mice, microarrays, and the genetic diversity of the brain. Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):10676-10678. [PubMed]
  50. Arfin SM, Long AD, Ito ET, Tolleri L, Riehle MM, Paegle ES, Hatfield GW. Global Gene Expression Profiling in Escherichia coli K12. THE EFFECTS OF INTEGRATION HOST FACTOR.J Biol Chem. 2000 Sep 15;275(38):29672-29684. [PubMed]
  51. Nadimpalli R, Yalpani N, Johal GS, Simmons CR. Prohibitins, Stomatins, and Plant Disease Response Genes Compose a Protein Superfamily That Controls Cell Proliferation, Ion Channel Regulation, and Death. J Biol Chem. 2000 Sep 15;275(38):29579-29586. [PubMed]
  52. Samir AA, Ropolo A, Grasso D, Tomasini R, Dagorn JC, Dusetti N, Iovanna JL, Vaccaro MI.  Cloning and Expression of the Mouse PIP49 (Pancreatitis Induced Protein 49) mRNA Which Encodes a New Putative Transmembrane Protein  Activated in the Pancreas with Acute Pancreatitis.   Mol Cell Biol Res Commun. 2000 Sep;4(3):188-193. [PubMed]
  53. Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10209-13. [PubMed][pdf]
  54. Eickhoff H, Schuchhardt J, Ivanov I, Meier-Ewert S, O'Brien J, Malik A, Tandon N, Wolski EW, Rohlfs E, Nyarsik L, Reinhardt R, Nietfeld W, Lehrach H. Tissue Gene Expression Analysis Using Arrayed Normalized cDNA Libraries. Genome Res. 2000 Aug;10(8):1230-1240. [PubMed]
  55. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D.  Molecular portraits of human breast tumours. Nature. 2000 Aug 17;406(6797):747-52. [PubMed][pdf][web supplement]
  56. Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9419-24. [PubMed][pdf]
  57. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A, Sampas N, Dougherty E, Wang E, Marincola F, Gooden C, Lueders J, Glatfelter A, Pollock P, Carpten J,Gillanders E, Leja D, Dietrich K, Beaudry C, Berens M, Alberts D, Sondak V. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000 Aug 3;406(6795):536-40. [PubMed][pdf]
  58. Clark EA, Golub TR, Lander ES, Hynes RO.  Genomic analysis of metastasis reveals an essential role for RhoC.  Nature. 2000 Aug 3;406(6795):532-5. [PubMed][pdf]
  59. Ridley A. Molecular switches in metastasis. Nature. 2000 Aug 3;406(6795):466-7. [PubMed][pdf]
  60. Tanaka TS, Jaradat SA, Lim MK, Kargul GJ, Wang X, Grahovac MJ, Pantano S, Sano Y, Piao Y, Nagaraja R, Doi H, Wood WH 3rd, Becker KG, Ko MS. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9127-32. [PubMed][pdf]
  61. Shaffer AL, Yu X, He Y, Boldrick J, Chan EP, Staudt LM. BCL-6 represses genes that function in lymphocyte differentiation, inflammation, and cell cycle control. Immunity. 2000 Aug;13(2):199-212 [PubMed]
  62. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD,Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH. Functional discovery via a compendium of expression profiles. Cell. 2000 Jul 7;102(1):109-26. [PubMed]
  63. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature. 2000 Jul 6;406(6791):90-4. [PubMed]
  64. Lyons TJ, Gasch AP, Gaither LA, Botstein D, Brown PO, Eide DJ. Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc Natl Acad Sci U S A. 2000 Jul 5;97(14):7957-62. [PubMed][pdf]
  65. Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D, Burchard J, Dow S, Ward TR, Kidd MJ, Friend SH, Marton MJ. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet. 2000 Jul;25(3):333-7. [PubMed]
  66. Lee CK, Weindruch R, Prolla TA. Gene-expression profile of the ageing brain in mice. Nat Genet. 2000 Jul;25(3):294-7. [PubMed]
  67. Posas F, Chambers JR, Heyman JA, Hoeffler JP, de Nadal E, Arino J. The transcriptional response of yeast to saline stress. J Biol Chem. 2000 Jun 9;275(23):17249-55. [PubMed]
  68. Friddle CJ, Koga T, Rubin EM, Bristow J. Expression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6745-50. [PubMed][pdf]
  69. Kelly DL, Rizzino A. DNA microarray analyses of genes regulated during the differentiation of embryonic stem cells. Mol Reprod Dev. 2000 Jun;56(2):113-23. [PubMed]
  70. Cristofalo VJ. A DNA chip off the aging block. Nat Med. 2000 May;6(5):507. [PubMed]
  71. Harrington CA, Rosenow C, Retief J. Monitoring gene expression using DNA microarrays. Curr Opin Microbiol. 2000 Jun;3(3):285-91. Review. [PubMed]
  72. Derocq JM, Jbilo O, Bouaboula M, Segui M, Clere C, Casellas P. Genomic and functional changes induced by the activation of the peripheral cannabinoid receptor CB2 in the promyelocytic cells HL-60. Possible involvement of the CB2 receptor in cell differentiation. J Biol Chem. 2000 May 26;275(21):15621-8. [PubMed]
  73. Luthi-Carter R, Strand A, Peters NL, Solano SM, Hollingsworth ZR, Menon AS, Frey AS, Spektor BS, Penney EB, Schilling G, Ross CA, Borchelt DR, Tapscott SJ, Young AB, Cha JH, Olson JM. Decreased expression of striatal signaling genes in a mouse model of Huntington's disease. Hum Mol Genet. 2000 May 22;9(9):1259-71. [PubMed]
  74. Stanton LW, Garrard LJ, Damm D, Garrick BL, Lam A, Kapoun AM, Zheng Q, Protter AA, Schreiner GF, White RT. Altered patterns of gene expression in response to myocardial infarction. Circ Res. 2000 May 12;86(9):939-45. [PubMed]
  75. Rogge L, Bianchi E, Biffi M, Bono E, Chang SY, Alexander H, Santini C, Ferrari G, Sinigaglia L, Seiler M, Neeb M,Mous J, Sinigaglia F, Certa U. Transcript imaging of the development of human T helper cells using oligonucleotide arrays. Nat Genet. 2000 May;25(1):96-101. [PubMed]
  76. Diehn M, Eisen MB, Botstein D, Brown PO. Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat Genet. 2000 May;25(1):58-62. [PubMed][pdf][web supplement]
  77. Lyn D, Liu XW, Bennett NA, Emmett NL. Gene expression profile in mouse myocardium after ischemia. Physiol Genomics 2000 May 2:93-100.[PubMed]
  78. Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M. Comparison of human adult and fetal expression and identification of 535 housekeeping/ maintenance genes. Physiol Genomics 2000 May 2:143-147. [PubMed]
  79. Zhao R, Gish K, Murphy M, Yin Y, Notterman D, Hoffman WH, Tom E, Mack DH, Levine AJ. Analysis of p53-regulated gene expression patterns using oligonucleotide arrays. Genes Dev. 2000 Apr 15;14(8):981-93. [PubMed]
  80. Cohen P, Bouaboula M, Bellis M, Baron V, Jbilo O, Poinot-Chazel C, Galiegue S, Hadibi EH, Casellas P. Monitoring cellular responses to Listeria monocytogenes with oligonucleotide arrays. J Biol Chem. 2000 Apr 14;275(15):11181-90. [PubMed]
  81. Yun CW, Ferea T, Rashford J, Ardon O, Brown PO, Botstein D, Kaplan J, Philpott CC. Desferrioxamine-mediated iron uptake in Saccharomyces cerevisiae. Evidence for two  pathways of iron uptake.  J Biol Chem. 2000 Apr 7; 275(14): 10709-15. [PubMed]
  82. Casagrande R, Stern P, Diehn M, Shamu C, Osario M, Zuniga M, Brown PO, Ploegh H. Degradation of proteins from the ER of S. cerevisiae requires an intact unfolded protein response pathway.  Mol Cell. 2000 Apr; 5(4): 729-35. [PubMed]
  83. Coller HA, Grandori C, Tamayo P, Colbert T, Lander ES, Eisenman RN, Golub TR. Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3260-5. [PubMed][pdf]
  84. Sudarsanam P, Iyer VR, Brown PO, Winston F. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae.  Proc Natl Acad Sci U S A. 2000 Mar 28; 97(7): 3364-9 [PubMed][pdf]
  85. Voehringer DW, Hirschberg DL, Xiao J, Lu Q, Roederer M, Lock CB, Herzenberg LA, Steinman L,  Herzenberg LA.  Gene microarray identification of redox and mitochondrial elements that control resistance or sensitivity to apoptosis.  Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2680-5. [PubMed][pdf]
  86. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000 Mar;24(3):227-35. [PubMed][pdf][web supplement]
  87. Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science. 2000 Feb 4;287(5454):873-80. [PubMed]
  88. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000 Feb 3;403(6769):503-11. [PubMed][web supplement]
  89. Berns A. Gene expression in diagnosis. Nature. 2000. Feb 3;403(6770):491-492. [PubMed][pdf]
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  94. Hines RS. Molecular analysis of implantation.  Semin Reprod Med. 2000;18(1):91-6. Review. [PubMed]
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Genetic analysis

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  4. Kerstin Lindblad-Toh, David M. Tanenbaum, Mark J. Daly, Ellen Winchester, Weng-Onn Lui, Anuradha Villapakkam, Sasha E. Stanton, Catharina Larsson, Thomas J. Hudson, Bruce E. Johnson, Eric S. Lander & Matthew Meyerson. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nature Biotech. 2000 Sep 1;18 (9):1001-1005.[PubMed]
  5. Mei R, Galipeau PC, Prass C, Berno A, Ghandour G, Patil N, Wolff RK, Chee MS, Reid BJ, Lockhart DJ. Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays. Genome Res. 2000 Aug;10(8):1126-1137. [PubMed]
  6. Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10209-13. [PubMed][pdf]
  7. Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen L, Syvanen AC. A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays.  Genome Res. 2000 Jul;10(7):1031-42. [PubMed]
  8. Anderson RC, Su X, Bogdan GJ, Fenton J. A miniature integrated device for automated multistep genetic assays. Nucleic Acids Res. 2000 Jun 15;28(12):E60.[PubMed]
  9. Favis R, Day JP, Gerry NP, Phelan C, Narod S, Barany F.  Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2. Nat Biotechnol. 2000 May;18(5):561-4. [PubMed]
  10. Radtkey R, Feng L, Muralhidar M, Duhon M, Canter D, DiPierro D, Fallon S, Tu E, McElfresh K, Nerenberg M,Sosnowski R. Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip. Nucleic Acids Res. 2000 Apr 1;28(7):E17. [PubMed]
  11. Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette JP, Ardlie K, Reich DE, Robinson E,  Sklar P, Shah N, Thomas D, Fan JB, Gingeras T, Warrington J, Patil N, Hudson TJ, Lander ES.  Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse.  Nat Genet. 2000 Apr;24(4):381-6. [PubMed]
  12. Stomakhin AA, Vasiliskov VA, Timofeev E, Schulga D, Cotter RJ, Mirzabekov AD. DNA sequence analysis by hybridization with oligonucleotide microchips: MALDI mass spectrometry identification of 5mers contiguously stacked to microchip oligonucleotides. Nucleic Acids Res. 2000 Mar 1;28(5):1193-8. [PubMed]

Disease screening and clinical practice

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  4. Burczynski ME, McMillian M, Ciervo J, Li L, Parker JB, Dunn RT 2nd, Hicken S, Farr S, Johnson MD. Toxicogenomics-Based Discrimination of Toxic Mechanism in HepG2 Human Hepatoma Cells.Toxicol Sci. 2000 Dec;58(2):399-415. [PubMed]
  5. Shiffman D, Porter JG. Gene expression profiling of cardiovascular disease models.  Curr Opin Biotechnol. 2000 Dec 1;11(6):598-601. [PubMed]
  6. Xiong M, Jin L, Li W, Boerwinkle E.  Computational methods for gene expression-based tumor classification.  Biotechniques. 2000 Dec;29(6):1264-8, 1270. [PubMed]
  7. Snijders AM, Meijer GA, Brakenhoff RH, van den Brule AJ, van Diest PJ. Microarray techniques in pathology: tool or toy?  Mol Pathol. 2000 Dec;53(6):289-94. [PubMed]
  8. Rudert F. Genomics and proteomics tools for the clinic.  Curr Opin Mol Ther. 2000 Dec;2(6):633-42. [PubMed]
  9. Dieckgraefe BK, Stenson WF, Korzenik JR, Swanson PE, Harrington CA. Analysis of mucosal gene expression in inflammatory bowel disease by parallel oligonucleotide arrays. Physiol Genomics. 2000 Nov; 4:1-11 [link to journal]
  10. Ben-Dor A, Bruhn L, Friedman N, Nachman I, Schummer M, Yakhini Z. Tissue Classification with Gene Expression Profiles.  J Comput Biol. 2000 Nov;7(3):559-583. [PubMed]
  11. Mirnics K, Middleton FA, Marquez A, Lewis DA, Levitt P. Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex. Neuron. 2000. Oct; 28:53-67
  12. Wikman FP, Lu ML, Thykjaer T, Olesen SH, Andersen LD, Cordon-Cardo C, Orntoft TF. Evaluation of the Performance of a p53 Sequencing Microarray Chip Using 140 Previously Sequenced Bladder Tumor Samples. Clin Chem. 2000 Oct;46(10):1555-1561. [PubMed]
  13. Diamandis EP. Sequencing with Microarray Technology-A Powerful New Tool For Molecular Diagnostics. Clin Chem. 2000 Oct;46(10):1523-1525. [PubMed]
  14. Liotta L, Petricoin E. Molecular profiling of human cancer. Nature reviews genetics. 2000 Oct; 1:48-56.
  15. Jean Marx. DNA Arrays Reveal Cancer in Its Many Forms. Science 2000 Sep8; 289(5485):1670-1672. [link to journal][PubMed]
  16. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D.  Molecular portraits of human breast tumours. Nature. 2000 Aug 17;406(6797):747-52. [PubMed][pdf][web supplement]
  17. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A, Sampas N, Dougherty E, Wang E, Marincola F, Gooden C, Lueders J, Glatfelter A, Pollock P, Carpten J,Gillanders E, Leja D, Dietrich K, Beaudry C, Berens M, Alberts D, Sondak V. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000 Aug 3;406(6795):536-40. [PubMed][pdf]
  18. Clark EA, Golub TR, Lander ES, Hynes RO.  Genomic analysis of metastasis reveals an essential role for RhoC.  Nature. 2000 Aug 3;406(6795):532-5. [PubMed][pdf]
  19. Ridley A. Molecular switches in metastasis. Nature. 2000 Aug 3;406(6795):466-7. [PubMed][pdf]
  20. Wooster R. Cancer classification with DNA microarrays is less more? Trends Genet. 2000 Aug;16(8):327-9. [PubMed]
  21. Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10209-13. [PubMed][pdf]
  22. Takahashi Y, Nagata T, Asai S, Shintaku K, Eguchi T, Ishii Y, Fujii M, Ishikawa K. Detection of aberrations of 17p and p53 gene in gastrointestinal cancers by dual (two-color) fluorescence in situ hybridization and GeneChip p53 assay. Cancer Genet Cytogenet. 2000 Aug;121(1):38-43.
  23. Perrone EE, Theoharis C, Mucci NR, Hayasaka S, Taylor JM, Cooney KA, Rubin MA. Tissue microarray assessment of prostate cancer tumor proliferation in African- American and white men. J Natl Cancer Inst. 2000 Jun 7;92(11):937-9. [PubMed]
  24. Friddle CJ, Koga T, Rubin EM, Bristow J. Expression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6745-50. [PubMed][pdf]
  25. Stanton LW, Garrard LJ, Damm D, Garrick BL, Lam A, Kapoun AM, Zheng Q, Protter AA, Schreiner GF, White RT. Altered patterns of gene expression in response to myocardial infarction. Circ Res. 2000 May 12;86(9):939-45. [PubMed]
  26. Eckmann L, Smith JR, Housley MP, Dwinell MB, Kagnoff MF. Analysis by high density cDNA arrays of altered gene expression in human intestinal epithelial cells in response to infection with the invasive enteric bacteria Salmonella. J Biol Chem. 2000 May 12;275(19):14084-94. [PubMed]
  27. Diehn M, Alizadeh AA, Brown PO. Examining the living genome in health and disease with DNA microarrays.  JAMA. 2000 May 3; 283(17): 2298-9. [PubMed]
  28. Favis R, Day JP, Gerry NP, Phelan C, Narod S, Barany F.  Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2. Nat Biotechnol. 2000 May;18(5):561-4. [PubMed]
  29. Carlisle AJ, Prabhu VV, Elkahloun A, Hudson J, Trent JM, Linehan WM, Williams ED, Emmert-Buck MR, Liotta LA, Munson PJ, Krizman DB. Development of a prostate cDNA microarray and statistical gene expression analysis package. Mol Carcinog. 2000 May;28(1):12-22. [PubMed]
  30. Masters JR, Lakhani SR. How diagnosis with microarrays can help cancer patients. Nature. 2000 Apr 27;404(6781):921. [PubMed]
  31. Heiskanen MA, Bittner ML, Chen Y, Khan J, Adler KE, Trent JM, Meltzer PS. Detection of gene amplification by genomic hybridization to cDNA microarrays. Cancer Res. 2000 Feb 15;60(4):799-802. [PubMed]
  32. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000 Feb 3;403(6769):503-11. [PubMed][pdf][web supplement]
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  35. Kitchens WH, Byrne MC, Strominger JL, Wilson SB. Using DNA chips to unravel the genetics of type 1 diabetes. Diabetes Technol Ther. 2000 Summer;2(2):249-58. [PubMed]
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Pharmacogenomics and pharmacogenetics

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  2. Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN. A gene expression database for the molecular pharmacology of cancer. Nat Genet. 2000 Mar;24(3):236-44. [PubMed][pdf]

Technical development

  1. Waddell E, Wang Y, Stryjewski W, McWhorter S, Henry AC, Evans D, McCarley RL, Soper SA.  High-resolution near-infrared imaging of DNA microarrays with time-resolved acquisition of fluorescence lifetimes. Anal Chem. 2000 Dec 15;72(24):5907-17. [PubMed]
  2. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol. 2000 Dec;18(12):1262-1268. [PubMed]
  3. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 2000 Nov 15;28(22):4552-4557. [PubMed]
  4. Souteyrand E, Chen C, Cloarec JP, Nesme X, Simonet P, Navarro I, Martin JR.  Comparison between electrochemical and optoelectrochemical impedance measurements for detection of DNA hybridization. Appl Biochem Biotechnol. 2000 Nov-Dec;89(2-3):195-207. [PubMed]
  5. Adessi C, Matton G, Ayala G, Turcatti G, Mermod JJ, Mayer P, Kawashima E. Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res. 2000 Oct 15;28(20):E87. [PubMed]
  6. Moller R, Csaki A, Kohler JM, Fritzsche W. DNA probes on chip surfaces studied by scanning force microscopy using specific binding of colloidal gold. Nucleic Acids Res. 2000 Oct 15;28(20):E91. [PubMed]
  7. Diamandis EP. Sequencing with Microarray Technology-A Powerful New Tool For Molecular Diagnostics. Clin Chem. 2000 Oct;46(10):1523-1525. [PubMed]
  8. Taton TA, Mirkin CA, Letsinger RL. Scanometric DNA Array Detection with Nanoparticle Probes. Science. 2000 Sep 8;289(5485):1757-1760. [PubMed]
  9. Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen L, Syvanen AC. A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays.  Genome Res. 2000 Jul;10(7):1031-42. [PubMed]
  10. Afanassiev V, Hanemann V, Wolfl S. Preparation of DNA and protein micro arrays on glass slides coated with an agarose film. Nucleic Acids Res. 2000 Jun 15;28(12):E66. [PubMed]
  11. Anderson RC, Su X, Bogdan GJ, Fenton J. A miniature integrated device for automated multistep genetic assays. Nucleic Acids Res. 2000 Jun 15;28(12):E60.[PubMed]
  12. Schuchhardt J, Beule D, Malik A, Wolski E, Eickhoff H, Lehrach H, Herzel H. Normalization strategies for cDNA microarrays. Nucleic Acids Res. 2000 May 15;28(10):E47. [PubMed]
  13. Radtkey R, Feng L, Muralhidar M, Duhon M, Canter D, DiPierro D, Fallon S, Tu E, McElfresh K, Nerenberg M,Sosnowski R. Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip. Nucleic Acids Res. 2000 Apr 1;28(7):E17. [PubMed]
  14. Stomakhin AA, Vasiliskov VA, Timofeev E, Schulga D, Cotter RJ, Mirzabekov AD. DNA sequence analysis by hybridization with oligonucleotide microchips: MALDI mass spectrometry identification of 5mers contiguously stacked to microchip oligonucleotides. Nucleic Acids Res. 2000 Mar 1;28(5):1193-8. [PubMed]
  15. Beier M, Hoheisel JD.  Production by quantitative photolithographic synthesis of individually quality checked DNA microarrays. Nucleic Acids Res. 2000 Feb 15;28(4):E11. [PubMed]

    16.  

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

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  2. Ohyama H, Zhang X, Kohno Y, Alevizos I, Posner M, Wong DT, Todd R. Laser capture microdissection-generated target sample for high-density oligonucleotide array hybridization.  Biotechniques. 2000 Sep;29(3):530-6. [PubMed]
  3. Lee ML, Kuo FC, Whitmore GA, Sklar J. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9834-9839. [PubMed][pdf]
  4. Vernon SD, Unger ER, Rajeevan M, Dimulescu IM, Nisenbaum R, Campbell CE. Reproducibility of alternative probe synthesis approaches for gene expression profiling with arrays.  J Mol Diagn. 2000 Aug;2(3):124-7. [PubMed]
  5. Talaat AM, Hunter P, Johnston SA.  Genome-directed primers for selective labeling of bacterial transcripts for DNA microarray analysis. Nat Biotechnol. 2000 Jun;18(6):679-82. [PubMed]
  6. Krylov SN, Arriaga E, Zhang Z, Chan NW, Palcic MM, Dovichi NJ. Single-cell analysis avoids sample processing bias.  J Chromatogr B Biomed Sci Appl. 2000 Apr 28;741(1):31-5. [PubMed]
  7. Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM. High-fidelity mRNA amplification for gene profiling. Nat Biotechnol. 2000 Apr;18(4):457-9. [PubMed]
  8. Bashiardes S, Lovett M. cDNA detection and analysis. Curr Opin Chem Biol. 2001 Feb;5(1):15-20. Review. [PubMed]
Data analysis
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  5. Klevecz RR. Dynamic architecture of the yeast cell cycle uncovered by wavelet decomposition of expression microarray data. Funct Integr Genomics 2000. 1:186-192 [PubMed]
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  38. Dudoit S, Fridlyand J, Speed TP.  Comparison of Discrimination Methods for the  Classification of Tumors Using Gene Expression Data. June 2000. Technical report #576 [abstract][pdf][ps]
  39. Stanton LW, Garrard LJ, Damm D, Garrick BL, Lam A, Kapoun AM, Zheng Q, Protter AA, Schreiner GF, White RT. Altered patterns of gene expression in response to myocardial infarction. Circ Res. 2000 May 12;86(9):939-45. [PubMed]
  40. Carlisle AJ, Prabhu VV, Elkahloun A, Hudson J, Trent JM, Linehan WM, Williams ED, Emmert-Buck MR, Liotta LA, Munson PJ, Krizman DB. Development of a prostate cDNA microarray and statistical gene expression analysis package. Mol Carcinog. 2000 May;28(1):12-22. [PubMed]
  41. Rogge L, Bianchi E, Biffi M, Bono E, Chang SY, Alexander H, Santini C, Ferrari G, Sinigaglia L, Seiler M, Neeb M,Mous J, Sinigaglia F, Certa U. Transcript imaging of the development of human T helper cells using oligonucleotide arrays. Nat Genet. 2000 May;25(1):96-101. [PubMed]
  42. Zhao R, Gish K, Murphy M, Yin Y, Notterman D, Hoffman WH, Tom E, Mack DH, Levine AJ. Analysis of p53-regulated gene expression patterns using oligonucleotide arrays. Genes Dev. 2000 Apr 15;14(8):981-93. [PubMed]
  43. Coller HA, Grandori C, Tamayo P, Colbert T, Lander ES, Eisenman RN, Golub TR. Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3260-5. [PubMed][pdf]
  44. Gaasterland T, Bekiranov S. Making the most of microarray data. Nat Genet. 2000 Mar;24(3):204-6. [PubMed]
  45. Sherlock G. Analysis of large-scale gene expression data. Curr Opin Immunol. 2000 Apr;12(2):201-5. Review. [PubMed]
  46. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000 Feb 3;403(6769):503-11. [PubMed]
  47. Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):262-7. [PubMed][pdf][web supplement]
  48. Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK.  Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria.  Mol Microbiol. 2000 Jan;35(1):6-14. [PubMed]
  49. Raychaudhuri S, Stuart JM, Altman RB. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput. 2000;:455-66. [PubMed][pdf][web]
  50. Zhu, J. and Zhang, M. Q. (2000) Cluster, function and promoter analysis of the yeast expression array. Pac. Symp. Biocomp. 2000, 479-490. [PubMed][pdf]
  51. Kuklin A, Shams S, Shah S.  High throughput screening of gene expression signatures.  Genetica. 2000;108(1):41-6. [PubMed]
  52. Kerr MK, Martin M, Churchill GA.  Analysis of variance for gene expression microarray data.  J Comput Biol. 2000;7(6):819-37. [PubMed][pdf]
  53. Kerr and Churchill. Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments. 2000. [pdf]
  54. Ideker T, Thorsson V, Siegel AF, Hood LE.  Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data.  J Comput Biol. 2000;7(6):805-17. [PubMed]
  55. Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data.  J Comput Biol. 2000;7(3-4):601-20. [PubMed][pdf]
  56. Kishino H, Waddell PJ. Correspondence analysis of genes and tissue types and finding genetic links from microarray data. Genome Inform Ser Workshop Genome Inform. 2000;11:83-95. [PubMed][pdf]
  57. Kato M, Tsunoda T, Takagi T. Inferring genetic networks from DNA microarray data by multiple regression analysis. Genome Inform Ser Workshop Genome Inform. 2000;11:118-28. [PubMed][pdf]
  58. Waddell PJ, Kishino H. Cluster Inference Methods and Graphical Models Evaluated on NCI60 Microarray Gene Expression Data. Genome Inform Ser Workshop Genome Inform. 2000;11:129-40. [PubMed][pdf]
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Database

  1. Christopher M.L.S. Bouton and Jonathan Pevsner.  DRAGON: Database Referencing of Array Genes Online.  Bioinformatics 2000 16: 1038-1039. [Abstract][PubMed]

Tissue microarray

  1. Camp RL, Charette LA, Rimm DL.  Validation of tissue microarray technology in breast carcinoma. Lab Invest. 2000 Dec;80(12):1943-9. [PubMed]
  2. Perrone EE, Theoharis C, Mucci NR, Hayasaka S, Taylor JM, Cooney KA, Rubin MA. Tissue microarray assessment of prostate cancer tumor proliferation in African- American and white men. J Natl Cancer Inst. 2000 Jun 7;92(11):937-9. [PubMed]

Protein array

  1. Wiltshire S, O'Malley S, Lambert J, Kukanskis K, Edgar D, Kingsmore SF, Schweitzer B. Detection of Multiple Allergen-specific IgEs on Microarrays by Immunoassay with Rolling Circle Amplification. Clin Chem. 2000 Dec;46(12):1990-1993. [PubMed]
  2. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M. Analysis of yeast protein kinases using protein chips. Nat Genet. 2000 Nov;26(3):283-289. [PubMed]
  3. von Eggeling F, Davies H, Lomas L, Fiedler W, Junker K, Claussen U, Ernst G. Tissue-specific microdissection coupled with ProteinChip array technologies: applications in cancer research. Biotechniques. 2000 Nov;29(5):1066-70. [PubMed]
  4. Luo LY, Diamandis EP. Preliminary examination of time-resolved fluorometry for protein array applications. Luminescence. 2000 Nov;15(6):409-413. [PubMed]
  5. Weinberger SR, Morris TS, Pawlak M.  Recent trends in protein biochip technology.  Pharmacogenomics. 2000 Nov;1(4):395-416. [PubMed]
  6. Robert F. Service. Protein Arrays Step Out of DNA's Shadow. Science Sep 8; 289(5485):1673. [link to journal][PubMed]
  7. MacBeath G, Schreiber SL. Printing Proteins as Microarrays for High-Throughput Function Determination. Science. 2000 Sep 8;289(5485):1760-1763. [PubMed]
  8. Robert A. Irving & Peter J. Hudson Proteins emerge from disarray.  Nature Biotech. 2000 Sep 1;18 (9): 932 - 933 [PubMed]
  9. Ruud M. T. de Wildt, Chris R. Mundy, Barbara D. Gorick & Ian M. Tomlinson. Antibody arrays for high-throughput screening of antibody-antigen interactions.  Nature Biotech. 2000 Sep 1;18 (9): 989 - 994 [PubMed]
  10. Rubin RB, Merchant M. A rapid protein profiling system that speeds study of cancer and other diseases. Am Clin Lab. 2000 Sep;19(8):28-9. [PubMed]
  11. Schweitzer B, Wiltshire S, Lambert J, O'Malley S, Kukanskis K, Zhu Z, Kingsmore SF, Lizardi PM, Ward DC. Inaugural article: immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10113-9. [PubMed][pdf][web supplement]
  12. Walter G, Bussow K, Cahill D, Lueking A, Lehrach H.  Protein arrays for gene expression and molecular interaction screening.  Curr Opin Microbiol. 2000 Jun;3(3):298-302. Review. [PubMed]
  13. Emili AQ, Cagney G. Large-scale functional analysis using peptide or protein arrays. Nat Biotechnol. 2000 Apr;18(4):393-7. [PubMed]
  14. Arenkov P, Kukhtin A, Gemmell A, Voloshchuk S, Chupeeva V, Mirzabekov A. Protein microchips: use for immunoassay and enzymatic reactions. Anal Biochem. 2000 Feb 15;278(2):123-31. [PubMed]
  15. Ge H. UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA,protein-RNA and protein-ligand interactions. Nucleic Acids Res. 2000 Jan 15;28(2):e3. [PubMed]
  16. Cagney G, Uetz P, Fields S. High-throughput screening for protein-protein interactions using two-hybrid assay. Methods Enzymol. 2000;328:3-14. [PubMed]
  17. Kido H, Maquieira A, Hammock BD. Disc-based immunoassay microarrays. Anal Chim Acta. 2000 441:1-11

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

  1. Sundberg SA, Chow A, Nikiforov T, Wada HG.  Microchip-based systems for target validation and HTS.  Drug Discov Today. 2000 Dec 1;5(12 Suppl 1):92-103. [PubMed]
  2. Rudert F. Genomics and proteomics tools for the clinic.  Curr Opin Mol Ther. 2000 Dec;2(6):633-42. [PubMed]
  3. Wang J. SURVEY AND SUMMARY: From DNA biosensors to gene chips. Nucleic Acids Res. 2000 Aug 15;28(16):3011-3016.[PubMed]
  4. Jain KK.  Applications of biochip and microarray systems in pharmacogenomics.  Pharmacogenomics. 2000 Aug;1(3):289-307. [PubMed]
  5. Anderson RC, Su X, Bogdan GJ, Fenton J. A miniature integrated device for automated multistep genetic assays. Nucleic Acids Res. 2000 Jun 15;28(12):E60.[PubMed]
  6. Liu S, Ren H, Gao Q, Roach DJ, Loder RT Jr, Armstrong TM, Mao Q, Blaga I, Barker DL, Jovanovich SB. Automated parallel DNA sequencing on multiple channel microchips.  Proc Natl Acad Sci U S A. 2000 May 9;97(10):5369-74. [PubMed][pdf]
  7. Sanders GHW, Manz A. Chip-based microsystems for genomic and proteomic analysis. Trends in analytical chemistry. 2000 19(6):364-378

Alternative array

  1. Ferguson JA, Steemers FJ, Walt DR. High-density fiber-optic DNA random microsphere array. Anal Chem. 2000 Nov 15;72(22):5618-24. [PubMed]
  2. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R,  George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J,  Fearon K, Mao J, Corcoran K. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol. 2000 Jun;18(6):630-4. [PubMed]
  3. Radtkey R, Feng L, Muralhidar M, Duhon M, Canter D, DiPierro D, Fallon S, Tu E, McElfresh K, Nerenberg M,Sosnowski R. Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip. Nucleic Acids Res. 2000 Apr 1;28(7):E17. [PubMed]
  4. Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C, Mao JI, Luo S,Kirchner JJ, Eletr S, DuBridge RB, Burcham T, Albrecht G. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1665-70. [PubMed][pdf]
  5. Walt DR.  Techview: molecular biology. Bead-based fiber-optic arrays.  Science. 2000 Jan 21;287(5452):451-2. [PubMed]
  6. Steemers FJ, Ferguson JA, Walt DR.  Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nat Biotechnol. 2000 Jan;18(1):91-4. [PubMed]
  7. Sakakibara Y, Suyama A. Intelligent DNA chips: logical operation of gene expression profiles on DNA computers. Genome Inform Ser Workshop Genome Inform. 2000;11:33-42 [PubMed][pdf]

last updated: 25 Nov 2001
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