My microarray journal watch - year 2001 Jan-Jun  [ 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
Human disease studies
   Disease screening, profiling and classification
   Diagnosis and clinical application
   In vitro and animal model study
Basic science studies
   Human
   Animal
   Plant
   Microbiology
Genome scale studies
Genetic analysis
   ArrayCGH
Pharmacogenomics and pharmacogenetics
Toxicogenomics
Technical development
Other related technical issue; microdissection;  linear amplification of RNA (aRNA)
Data analysis
   Image analysis
   Normalization
   Pattern recognition, classification & data mining by unsupervised methods
   Pattern recognition, classification & data mining by supervised methods
   Network/pathway reconstruction and analysis
   Statistical significance of analysis
   Software
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 2001in my site? 
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General

  1. Devaux F, Marc P, Jacq C. Transcriptomes, transcription activators and microarrays. FEBS Lett. 2001 Jun 8;498(2-3):140-4. [PubMed]
  2. Ruth L. Microarray standards adopted. Anal Chem. 2001 Jun 1;73(11):309A. [PubMed]
  3. Meltzer PS. Spotting the target: microarrays for disease gene discovery. Curr Opin Genet Dev. 2001 Jun; 11: 258-263. [PubMed]
  4. Graham D. Biochips to bavarian cows. Trends Biotechnol. 2001 Jun; 19:199-200 [PubMed]
  5. Mirnics K. OPINION Microarrays in brain research: the good, the bad and the ugly. Nat Rev Neurosci. 2001 Jun;2(6):444-7. [PubMed]
  6. Kurella M, Hsiao LL, Yoshida T, Randall JD, Chow G, Sarang SS, Jensen RV, Gullans SR. DNA Microarray Analysis of Complex Biologic Processes. J Am Soc Nephrol. 2001 May;12(5):1072-1078. [PubMed]
  7. Heinrichs A. Microarray consortium. Trends Mol Med. 2001 May;7(5):200. [PubMed]
  8. Williams DM, Cole PA. Kinase chips hit the proteomics era.  Trends Biochem Sci. 2001 May;26(5):271-3. [PubMed]
  9. Kricka LJ. Microchips, microarrays, biochips and nanochips: personal laboratories for the 21st century.  Clin Chim Acta. 2001 May;307(1-2):219-223. [PubMed]
  10. Saito H, Nakajima T, Matsumoto K. Human mast cell transcriptome project. Int Arch Allergy Immunol. 2001 May;125(1):1-8. Review. [PubMed]
  11. Free and public expression. Nature. 2001 Apr 19;410(6831):851. [PubMed]
  12. Knight J. Cancer comes under scrutiny in fresh genomics initiative. Nature. 2001 Apr 19;410(6831):855. [PubMed]
  13. Knight J. When the chips are down. Nature. 2001 Apr 19;410(6831):860-1. [PubMed]
  14. Pugh BF, Gilmour DS. Genome-wide analysis of protein-DNA interactions in living cells. Genome Biol 2001. Apr 4; 2(4): reviews 1013.1-3 [PubMed][pdf]
  15. Yue H. et.al. An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acid Res. 2001. Apr; 29:e41. [PubMed]
  16. Burgess JK. Gene expression studies using microarrays. Clin Exp Pharmacol Physiol. 2001 Apr;28(4):321-8. [PubMed]
  17. Baba Y. Development of novel biomedicine based on genome science.  Eur J Pharm Sci. 2001 Apr;13(1):3-4. [PubMed]
  18. Luo Z, Geschwind DH. Microarray applications in neuroscience. Neurobiol Dis. 2001 Apr;8(2):183-93. [PubMed]
  19. Paulsen IT, Chen J, Nelson KE, Saier MH Jr. Comparative genomics of microbial drug efflux systems.  J Mol Microbiol Biotechnol. 2001 Apr;3(2):145-50. [PubMed]
  20. Kumar A, Snyder M. Emerging technologies in yeast genomics. Nat Rev Genet. 2001 Apr;2(4):302-12. Review. [PubMed]
  21. Rimm DL. Impact of microarray technologies on cytopathology. Overview of technologies and commentary on current and future implications for pathologists and cytopathologists. Acta Cytol. 2001 Mar-Apr;45(2):111-4. [PubMed]
  22. Heinrich-Hirsch B, Madle S, Oberemm A, Gundert-Remy U. The use of toxicodynamics in risk assessment. Toxicol Lett. 2001 Mar 31;120(1-3):131-41. [PubMed]
  23. Pennie WD, Woodyatt NJ, Aldridge TC, Orphanides G. Application of genomics to the definition of the molecular basis for toxicity. Toxicol Lett. 2001 Mar 31;120(1-3):353-8. [PubMed]
  24. Strogatz SH. Exploring complex networks. Nature 2001. Mar 8; 410:268-276. [PubMed]
  25. Ruth L. Connecting the dots: standards for DNA analysis. Anal Chem. 2001 Mar 1;73(5):130A-131A. [PubMed]
  26. Bertucci F, Loriod B, Tagett R, Granjeaud S, Birnbaum D, Nguyen C, Houlgatte R. DNA arrays: technological aspects and applications  Bull Cancer. 2001 Mar;88(3):243-52. [PubMed]
  27. Kallioniemi OP. Biochip technologies in cancer research. Ann Med. 2001 Mar;33(2):142-7. [PubMed]
  28. Miller RA, Galecki A, Shmookler-Reis RJ. Interpretation, design, and analysis of gene array expression experiments. J Gerontol A Biol Sci Med Sci. 2001 Feb;56(2):B52-7. [PubMed]
  29. Jain KK.  Cambridge Healthtech Institute's Third Annual Conference on Lab-on-a-Chip and Microarrays. 22-24 January 2001, Zurich, Switzerland. Pharmacogenomics. 2001 Feb;2(1):73-7. [PubMed]
  30. Human Genome Project Publications:
  31. Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G, Wu LF, Altschuler SJ, Edwards S, King J, Tsang JS, Schimmack G, Schelter JM, Koch J, Ziman M, Marton MJ, Li B, Cundiff P, Ward T, Castle J, Krolewski M, Meyer MR, Mao M, Burchard J, Kidd MJ, Dai H, Phillips JW, Linsley PS, Stoughton R, Scherer S, Boguski MS. Experimental annotation of the human genome using microarray technology. Nature 2001. Feb 15; 409:922-927. [PubMed][pdf]
  32. Siedow JN. Making sense of microarrays. Genome Biol. 2001 Feb 7;2(2):REPORTS4003. [PubMed]
  33. Diehn M, Relman DA. Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions.  Curr Opin Microbiol. 2001 Feb 1;4(1):95-101. [PubMed]
  34. Hughes TR, Shoemaker DD. DNA microarrays for expression profiling.  Curr Opin Chem Biol. 2001 Feb 1;5(1):21-25. [PubMed]
  35. Blohm DH, Guiseppi-Elie A. New developments in microarray technology. Curr Opin Biotechnol. 2001 Feb 12(1): 41-47 [PubMed]
  36. van Berkum NL, Holstege FCP. DNA microarrays: raising the profile. Curr Opin Biotechnol. 2001 Feb 12(1): 48-52 [PubMed]
  37. Wildsmith SE, Elcock FJ. Microarrays under the microscope.  Mol Pathol. 2001 Feb;54(1):8-16. [PubMed]
  38. Casci T. Technology. ChIP on chips.  Nat Rev Genet. 2001 Feb;2(2):88 [PubMed]
  39. Triendl R. Chinese gov't chips in to industry. Nat Biotechnol. 2001 Jan;19(1):12-13. [PubMed]
  40. Brenton JD, Aparicio SA, Caldas C. Molecular profiling of breast cancer: portraits but not physiognomy.  Breast Cancer Res. 2001;3(2):77-80. [PubMed]
  41. Rubenstein KE.  Business aspects of biochip technologies. Methods Mol Biol. 2001;170:247-56. [PubMed]
  42. Thibault C, Wang L, Zhang L, Miles MF. DNA arrays and functional genomics in neurobiology. Int Rev Neurobiol. 2001;48:219-53. [PubMed]
  43. Gabig M, Wegrzyn G. An introduction to DNA chips: principles, technology, applications and analysis. Acta Biochim Pol. 2001;48(3):615-22. [PubMed]

Human disease studies

  1. Meltzer PS. Spotting the target: microarrays for disease gene discovery. Curr Opin Genet Dev. 2001 Jun; 11: 258-263. [PubMed]
  2. Williams ED, Brooks JD.  New molecular approaches for identifying novel targets, mechanisms, and biomarkers for prostate cancer chemopreventive agents. Urology. 2001 Apr;57(4 Suppl 1):100-102. [PubMed]
  3. Geraci MW, Gao B, Hoshikawa Y, Yeager ME, Tuder RM, Voelkel NF. Genomic approaches to research in pulmonary hypertension.  Respir Res. 2001;2(4):210-215. [PubMed]
  4. Chan WC, Huang JZ.  Gene expression analysis in aggressive NHL. Ann Hematol. 2001;80 Suppl 3:B38-41. [PubMed]
  5. Marciano P, Eberwine JH, Raghupathi R, McIntosh TK. The assessment of genomic alterations using DNA arrays following traumatic brain injury: a review.  Restor Neurol Neurosci. 2001;18(2,3):105-113. [PubMed]
  6. Cooper CS. Applications of microarray technology in breast cancer research. Breast Cancer Res. 2001;3(3):158-175. [PubMed]
  7. Buchholz M, Boeck W, Fensterer H, Muller F, Wenger C, Michl P, Adler G, Gress TM. Use of DNA arrays/microarrays in pancreatic research. Pancreatology. 2001;1(6):581-6. [PubMed]

Disease screening, profiling and classification

  1. Hata R, Masumura M, Akatsu H, Li F, Fujita H, Nagai Y, Yamamoto T, Okada H, Kosaka K, Sakanaka M, Sawada T. Up-Regulation of Calcineurin Abeta mRNA in the Alzheimer's Disease Brain: Assessment by cDNA Microarray. Biochem Biophys Res Commun. 2001 Jun 8;284(2):310-6. [PubMed]
  2. Bull JH, Ellison G, Patel A, Muir G, Walker M, Underwood M, Khan F, Paskins L.  Identification of potential diagnostic markers of prostate cancer and prostatic intraepithelial neoplasia using cDNA microarray.  Br J Cancer. 2001 Jun;84(11):1512-9. [PubMed]
  3. Granger JP, Alexander BT, Bennett WA, Khalil RA.  Pathophysiology of pregnancy-induced hypertension.  Am J Hypertens. 2001 Jun;14(6 Pt 2):178S-185S. [PubMed]
  4. Houghton RL, Dillon DC, Molesh DA, Zehentner BK, Xu J, Jiang J, Schmidt C, Frudakis A, Repasky E, Filho AM, Nolasco M, Badaro R, Zhang X, Roche PC, Persing DH,  Reed SG.  Transcriptional complementarity in breast cancer: Application to detection of circulating tumor cells. Mol Diagn. 2001 Jun;6(2):79-91. [PubMed]
  5. Monni O, Barlund M, Mousses S, Kononen J, Sauter G, Heiskanen M, Paavola P, Avela K, Chen Y, Bittner ML, Kallioniemi A.  Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc Natl Acad Sci U S A. 2001 May 8;98(10):5711-5716. [PubMed][pdf][web supplement]
  6. Kitahara O, Furukawa Y, Tanaka T, Kihara C, Ono K, Yanagawa R, Nita ME, Takagi T, Nakamura Y, Tsunoda T. Alterations of Gene Expression during Colorectal Carcinogenesis Revealed by cDNA Microarrays after Laser-Capture Microdissection of Tumor Tissues and Normal Epithelia. Cancer Res. 2001 May 1;61(9):3544-3549. [PubMed]
  7. Chetcuti A, Margan S, Mann S, Russell P, Handelsman D, Rogers J, Dong Q. Identification of differentially expressed genes in organ-confined prostate cancer by gene expression array. Prostate. 2001 May 1;47(2):132-40. [PubMed]
  8. Hwang JJ, Dzau VJ, Liew CC. Genomics and the Pathophysiology of Heart Failure. Curr Cardiol Rep. 2001 May;3(3):198-207. [PubMed]
  9. El-Rifai W, Frierson HF Jr, Harper JC, Powell SM, Knuutila S. Expression profiling of gastric adenocarcinoma using cDNA array. Int J Cancer 2001. May 93:832-838. [PubMed]
  10. Mirnics K, Middleton FA, Stanwood GD, Lewis DA, Levitt P. Disease-specific changes in regulator of G-protein signaling 4 (RGS4) expression in schizophrenia. Mol Psychiatry. 2001 May;6(3):293-301. [PubMed]
  11. Zhou M, Rubin MA. Molecular markers for renal cell carcinoma: impact on diagnosis and treatment.  Semin Urol Oncol. 2001 May;19(2):80-7. [PubMed]
  12. Hakak Y, Walker JR, Li C, Wong WH, Davis KL, Buxbaum JD, Haroutunian V, Fienberg AA.  Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia.  Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4746-4751. [PubMed][pdf][web supplement]
  13. Lukas J, Gao DQ, Keshmeshian M, Wen WH, Tsao-Wei D, Rosenberg S, Press MF.  Alternative and Aberrant Messenger RNA Splicing of the mdm2 Oncogene in Invasive Breast Cancer .Cancer Res. 2001 Apr 1;61(7):3212-3219. [PubMed]
  14. Xu L, Hui L, Wang S, Gong J, Jin Y, Wang Y, Ji Y, Wu X, Han Z, Hu G. Expression profiling suggested a regulatory role of liver-enriched transcription factors in human hepatocellular carcinoma. Cancer Res. 2001 Apr 1;61(7):3176-81. [PubMed]
  15. Notterman DA, Alon U, Sierk AJ, Levine AJ. Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays.  Cancer Res. 2001 Apr 1;61(7):3124-30. [PubMed]
  16. Lakhani SR, O'Hare MJ, Ashworth A. Profiling familial breast cancer.  Nat Med. 2001 Apr;7(4):408-410. [PubMed]
  17. Shirota Y, Kaneko S, Honda M, Kawai HF, Kobayashi K.  Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. Hepatology. 2001 Apr;33(4):832-840. [PubMed]
  18. Li S, Ross DT, Kadin ME, Brown PO, Wasik MA. Comparative Genome-Scale Analysis of Gene Expression Profiles in T Cell Lymphoma Cells during Malignant Progression Using a Complementary DNA Microarray.  Am J Pathol. 2001 Apr;158(4):1231-1237. [PubMed]
  19. Vlahou A, Schellhammer PF, Mendrinos S, Patel K, Kondylis FI, Gong L, Nasim S, Wright Jr GL Jr. Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am J Pathol. 2001 Apr;158(4):1491-502. [PubMed]
  20. Lassus H, Laitinen MP, Anttonen M, Heikinheimo M, Aaltonen LA, Ritvos O, Butzow R.  Comparison of Serous and Mucinous Ovarian Carcinomas: Distinct Pattern of Allelic Loss at Distal 8p and Expression of Transcription Factor GATA-4. Lab Invest. 2001 Apr;81(4):517-26. [PubMed]
  21. Feske S, Giltnane J, Dolmetsch R, Staudt LM, Rao A. Gene regulation mediated by calcium signals in T lymphocytes. Nat Immunol. 2001 Apr;2(4):316-324. [PubMed]
  22. Geraci MW, Moore M, Gesell T, Yeager ME, Alger L, Golpon H, Gao B, Loyd JE, Tuder RM, Voelkel NF.  Gene Expression Patterns in the Lungs of Patients With Primary Pulmonary Hypertension : A Gene Microarray Analysis.  Circ Res. 2001 Mar 30;88(6):555-562. [PubMed]
  23. Chaib H, Rubin MA, Mucci NR, Li L, Taylor JMG, Day ML, Rhim JS, Macoska JA. Activated in prostate cancer: a PDZ domain-containing protein highly expressed in human primary prostate tumors.  Cancer Res. 2001 Mar 15;61(6):2390-4. [PubMed]
  24. Thykjaer T, Workman C, Kruhoffer M, Demtroder K, Wolf H, Andersen LD, Frederiksen CM, Knudsen S, Orntoft TF. Identification of gene expression patterns in superficial and invasive human bladder cancer.  Cancer Res. 2001 Mar 15;61(6):2492-9. [PubMed]
  25. Hanna E, Shrieve DC, Ratanatharathorn V, Xia X, Breau R, Suen J, Li S. A novel alternative approach for prediction of radiation response of squamous cell carcinoma of head and neck.  Cancer Res. 2001 Mar 15;61(6):2376-80. [PubMed]
  26. Chow ML, Moler EJ, Mian IS. Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiol Genomics. 2001 Mar 8;5(2):99-111. [PubMed]
  27. Lawrance IC, Fiocchi C, Chakravarti S. Ulcerative colitis and Crohn's disease: distinctive gene expression profiles and novel susceptibility candidate genes. Hum Mol Genet. 2001 Mar 1;10(5):445-456. [PubMed]
  28. Okabe H, Satoh S, Kato T, Kitahara O, Yanagawa R, Yamaoka Y, Tsunoda T, Furukawa Y, Nakamura Y.  Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: identification of genes involved in viral carcinogenesis and tumor progression.  Cancer Res. 2001 Mar 1;61(5):2129-37. [PubMed]
  29. Watson MA, Perry A, Budhjara V, Hicks C, Shannon WD, Rich KM. Gene expression profiling with oligonucleotide microarrays distinguishes World Health Organization grade of oligodendrogliomas. Cancer Res. 2001 Mar 1;61(5):1825-9. [PubMed]
  30. Lawrance IC, Fiocchi C, Chakravarti S. Ulcerative colitis and Crohn's disease: distinctive gene expression profiles and novel susceptibility candidate genes. Hum Mol Genet. 2001 Mar 1;10(5):445-456. [PubMed]
  31. Golpon HA, Geraci MW, Moore MD, Miller HL, Miller GJ, Tuder RM, Voelkel NF. HOX Genes in Human Lung : Altered Expression in Primary Pulmonary Hypertension and Emphysema. Am J Pathol. 2001 Mar;158(3):955-966. [PubMed]
  32. Honda M, Kaneko S, Kawai H, Shirota Y, Kobayashi K.  Differential Gene Expression Between Chronic Hepatitis B and C Hepatic Lesion. Gastroenterology. 2001 Mar;120(4):955-966. [PubMed]
  33. Chen CC, Shieh B, Jin YT, Liau YE, Huang CH, Liou JT, Wu LW, Huang W, Young KC, Lai MD, Liu HS, Li C.  Microarray Profiling of Gene Expression Patterns in Bladder Tumor Cells Treated with Genistein.   J Biomed Sci. 2001 Mar;8(2):214-222. [PubMed]
  34. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, Wilfond B, Borg A, Trent J. Gene expression profiles in hereditary breast cancer. New Engl J Med 2001. Feb 22. 344:539-548. [PubMed]
  35. Rozovskaia T, Feinstein E, Mor O, Foa R, Blechman J, Nakamura T, Croce CM, Cimino G, Canaani E. Upregulation of Meis1 and HoxA9 in acute lymphocytic leukemias with the t(4 : 11) abnormality. Oncogene. 2001 Feb 15;20(7):874-8. [PubMed]
  36. Stratowa C, Loffler G, Lichter P, Stilgenbauer S, Haberl P, Schweifer N, Dohner H, Wilgenbus KK. cDNA microarray gene expression analysis of b-cell chronic lymphocytic leukemia proposes potential new prognostic markers involved in lymphocyte trafficking. Int. J. Cancer 2001. Feb 15; 91:474-480. [PubMed]
  37. Xu J, Kalos M, Stolk JA, Zasloff EJ, Zhang X, Houghton RL, Filho AM, Nolasco M, Badaro R, Reed SG.  Identification and characterization of prostein, a novel prostate-specific protein.  Cancer Res. 2001 Feb 15;61(4):1563-8. [PubMed]
  38. Ho L, Guo Y, Spielman L, Petrescu O, Haroutunian V, Purohit D, Czernik A, Yemul S, Aisen PS, Mohs R, Pasinetti GM. Altered expression of a-type but not b-type synapsin isoform in the brain of patients at high risk for Alzheimer's disease assessed by DNA  microarray technique.  Neurosci Lett. 2001 Feb 9;298(3):191-194. [PubMed]
  39. Barrans JD, Stamatiou D, Liew C. Construction of a human cardiovascular cDNA microarray: Portrait of the failing heart. Biochem Biophys Res Com. 2001 Feb; 280(4):964-969 [PubMed]
  40. Dales JP, Plumas J, Palmerini F, Devilard E, Defrance T, Lajmanovich A, Pradel V, Birg F, Xerri L.  Correlation between apoptosis microarray gene expression profiling and histopathological lymph node lesions.  Mol Pathol. 2001 Feb;54(1):17-23. [PubMed]
  41. Barrans JD, Stamatiou D, Liew CC. Construction of a human cardiovascular cDNA microarray: Portrait of the failing heart. Biochem Biophys Res Com. 2001 Feb; 280(4):964-969 [PubMed]
  42. Dales JP, Plumas J, Palmerini F, Devilard E, Defrance T, Lajmanovich A, Pradel V, Birg F, Xerri L.  Correlation between apoptosis microarray gene expression profiling and histopathological lymph node lesions.  Mol Pathol. 2001 Feb;54(1):17-23. [PubMed]
  43. Chaib H, Cockrell EK, Rubin MA, Macoska JA. Profiling and Verification of Gene Expression Patterns in Normal and Malignant Human Prostate Tissues by cDNA Microarray Analysis. Neoplasia. 2001 Jan-Feb;3(1):43-52. [PubMed]
  44. Tsunoda T, Nakamura T, Ishimoto K, Yamaue H, Tanimura H, Saijo N, Nishio K. Upregulated expression of angiogenesis genes and down regulation of cell cycle genes in human colorectal cancer tissue determined by cDNA macroarray. Anticancer Res. 2001 Jan-Feb;21(1A):137-43. [PubMed]
  45. Kato T, Satoh S, Okabe H, Kitahara O, Ono K, Kihara C, Tanaka T, Tsunoda T, Yamaoka Y, Nakamura Y, Furukawa Y. Isolation of a novel human gene, markl1, homologous to mark3 and its involvement in hepatocellular carcinogenesis. Neoplasia. 2001 Jan-Feb;3(1):4-9. [PubMed]
  46. Welsh JB, Zarrinkar PP, Sapinoso LM, Kern SG, Behling CA, Monk BJ, Lockhart DJ, Burger RA, Hampton GM. Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci U S A. 2001 Jan 30; 98(3): 1176-1181[PubMed][pdf]
  47. Ma C, Staudt LM.  Molecular definition of the germinal centre stage of B-cell differentiation. Philos Trans R Soc Lond B Biol Sci. 2001 Jan 29;356(1405):83-9. [PubMed]
  48. Storz M, Zepter K, Kamarashev J, Dummer R, Burg G, Haffner AC.  Coexpression of CD40 and CD40 ligand in cutaneous T-cell lymphoma (mycosis fungoides).  Cancer Res. 2001 Jan 15;61(2):452-4. [PubMed]
  49. Lu T, Liu J, LeCluyse EL, Zhou YS, Cheng ML, Waalkes MP. Application of cDNA Microarray to the Study of Arsenic-Induced Liver Diseases in the Population of Guizhou, China. Toxicol Sci. 2001 Jan;59(1):185-192. [PubMed]
  50. Brenton JD, Aparicio SA, Caldas C. Molecular profiling of breast cancer: portraits but not physiognomy.  Breast Cancer Res. 2001;3(2):77-80. [PubMed]
  51. Unger MA, Rishi M, Clemmer VB, Hartman JL, Keiper EA, Greshock JD, Chodosh LA, Liebman MN, Weber BL. Characterization of adjacent breast tumors using oligonucleotide microarrays. Breast Cancer Res. 2001;3(5):336-41. [PubMed]
  52. Stevenson FK, Sahota SS, Ottensmeier CH, Zhu D, Forconi F, Hamblin TJ. The occurrence and significance of V gene mutations in B cell-derived human malignancy. Adv Cancer Res. 2001;83:81-116. [PubMed]
  53. Amundson SA, Fornace AJ Jr. Gene expression profiles for monitoring radiation exposure. Radiat Prot Dosimetry. 2001;97(1):11-6. [PubMed]
  54. Dressman M A, Walz T M, Lavedan C, Barnes L, Buchholtz S, Kwon I, Ellis M J, Polymeropoulos M H. Genes that co-cluster with estrogen receptor alpha in microarray analysis of breast biopsies. Pharmacogenomics J. 2001;1(2):135-41. [PubMed]
  55. Oestreicher JL, Walters IB, Kikuchi T, Gilleaudeau P, Surette J, Schwertschlag U, Dorner AJ, Krueger JG, Trepicchio WL. Molecular classification of psoriasis disease-associated genes through pharmacogenomic expression profiling. Pharmacogenomics J. 2001;1(4):272-87. [PubMed]

Diagnosis and clinical application

  1. Cuzin M. DNA chips: a new tool for genetic analysis and diagnostics. Transfus Clin Biol. 2001 Jun;8(3):291-6. [PubMed]
  2. He YD, Friend SH. Microarrays--the 21st century divining rod? Nat Med. 2001 Jun;7(6):658-9. [PubMed]
  3. Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schwab M, Antonescu CR, Peterson C, Meltzer PS. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med. 2001 Jun;7(6):673-9. [PubMed]
  4. Xu B, Sakkas LI, Slachta CA, Goldman BI, Jeevanandam V, Oleszak EL, Platsoucas CD. Apoptosis in chronic rejection of human cardiac allografts. Transplantation. 2001 Apr 27;71(8):1137-46. [PubMed]
  5. Hakenbeck R, Balmelle N, Weber B, Gardes C, Keck W, de Saizieu A. Mosaic Genes and Mosaic Chromosomes: Intra- and Interspecies Genomic Variation of Streptococcus pneumoniae. Infect Immun. 2001 Apr;69(4):2477-86. [PubMed]
  6. Chow ML, Moler EJ, Mian IS. Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiol Genomics. 2001 Mar 8;5(2):99-111. [PubMed]
  7. Eyster KM, Lindahl R. Molecular medicine: a primer for clinicians. Part XII: DNA microarrays and their application to clinical medicine.  S D J Med. 2001 Feb;54(2):57-61. [PubMed]
  8. Dales JP, Plumas J, Palmerini F, Devilard E, Defrance T, Lajmanovich A, Pradel V, Birg F, Xerri L.  Correlation between apoptosis microarray gene expression profiling and histopathological lymph node lesions.  Mol Pathol. 2001 Feb;54(1):17-23. [PubMed]
  9. Magee JT, Fox JD, Stubbs SL.  Cashing in your chips: speculation on the future of diagnostic laboratories in the era of DNA chips. J Med Microbiol. 2001 Feb;50(2):111-5. [PubMed]
  10. Stern LE, Erwin CR, Falcone RA, Huang FS, Kemp CJ, Williams JL, Warner BW.  cDNA microarray analysis of adapting bowel after intestinal resection  J Pediatr Surg. 2001 Jan;36(1):190-5. [PubMed]
  11. Petrik J.  Microarray technology: the future of blood testing? Vox Sang. 2001 Jan;80(1):1-11. [PubMed]
  12. Harris NL, Stein H, Coupland SE, Hummel M, Favera RD, Pasqualucci L, Chan WC. New approaches to lymphoma diagnosis. Hematology (Am Soc Hematol Educ Program). 2001 Jan;:194-220. [PubMed]
  13. Habeck M. DNA microarray technology to revolutionise cancer treatment. Lancet Oncol. 2001 Jan;2(1):5. [PubMed]
  14. Miller JC, Butler EB, Teh BS, Haab BB. The application of protein microarrays to serum diagnostics: prostate cancer as a test case. Dis Markers. 2001;17(4):225-34. [PubMed]
  15. Pasinetti GM, Ho L. From cDNA microarrays to high-throughput proteomics. Implications in the search for preventive initiatives to slow the clinical progression of Alzheimer's disease dementia. Restor Neurol Neurosci. 2001;18(2,3):137-142. [PubMed]

In vitro and animal model study

  1. Blader IJ, Manger ID, Boothroyd JC. Microarray Analysis Reveals Previously Unknown Changes in Toxoplasma gondii-infected Human Cells. J Biol Chem. 2001 Jun 29;276(26):24223-31. [PubMed]
  2. Ying G, Huang C, Jing N, Zhou C. Identification of differentially expressed genes in the denervated rat hippocampus by cDNA arrays. Neurosci Lett. 2001 Jun 22; 306:121-125. [PubMed]
  3. Wu CG, Salvay DM, Forgues M, Valerie K, Farnsworth J, Markin RS, Wang XW. Distinctive gene expression profiles associated with Hepatitis B virus x protein.  Oncogene. 2001 Jun 21;20(28):3674-82. [PubMed]
  4. Dong G, Loukinova E, Chen Z, Gangi L, Chanturita TI, Liu ET, Van Waes C.Molecular Profiling of Transformed and Metastatic Murine Squamous Carcinoma Cells by Differential Display and cDNA Microarray Reveals Altered Expression of Multiple Genes Related to Growth, Apoptosis, Angiogenesis, and the NF-kappaB Signal Pathway. Cancer Res. 2001 Jun 15;61(12):4797-4808. [PubMed]
  5. Narravula S, Colgan SP. Hypoxia-Inducible Factor 1-Mediated Inhibition of Peroxisome Proliferator-Activated Receptor alpha Expression During Hypoxia.  J Immunol. 2001 Jun 15;166(12):7543-8. [PubMed]
  6. Maeda S, Otsuka M, Hirata Y, Mitsuno Y, Yoshida H, Shiratori Y, Masuho Y, Muramatsu Ma, Seki N, Omata M. cDNA Microarray Analysis of Helicobacter pylori-Mediated Alteration of Gene Expression in Gastric Cancer Cells. Biochem Biophys Res Commun. 2001 Jun 8;284(2):443-9. [PubMed]
  7. Kannan K, Kaminski N, Rechavi G, Jakob-Hirsch J, Amariglio N, Givol D.DNA microarray analysis of genes involved in p53 mediated apoptosis: activation of Apaf-1.  Oncogene. 2001 Jun 7;20(26):3449-55. [PubMed]
  8. Aronow BJ, Toyokawa T, Canning A, Haghighi K, Delling U, Kranias E, Molkentin JD, Dorn GW 2nd. Divergent transcriptional responses to independent genetic causes of cardiac hypertrophy. Physiol Genomics. 2001 Jun 6;6(1):19-28. [PubMed]
  9. Glueck SB, Dzau VJ, Lee R, Pratt RE. Challenges of comparative expression profiling studies of complex diseases: mouse models of myocardial hypertrophy Focus on "Divergent transcriptional responses to independent genetic causes of cardiac hypertrophy". Physiol Genomics. 2001 Jun 6;6(1):1-2. [PubMed]
  10. Kagnoff MF, Eckmann L. Analysis of host responses to microbial infection using gene expression profiling. Curr Opin Microbiol. 2001. Jun; 4:246-250. [PubMed]
  11. Simmons A, Aluvihare V, McMichael A. Nef triggers a transcriptional program in t cells imitating single-signal t cell activation and inducing hiv virulence mediators. Immunity. 2001 Jun;14(6):763-77. [PubMed]
  12. Willers J, Haffner A, Zepter K, Storz M, Urosevic M, Burg G, Dummer R. The Interferon Inhibiting Cytokine IK is Overexpressed in Cutaneous T Cell Lymphoma Derived Tumor Cells That Fail to Upregulate Major Histocompatibility Complex Class II Upon Interferon-gamma Stimulation.  J Invest Dermatol. 2001 Jun;116(6):874-879. [PubMed]
  13. Mariani L, Beaudry C, McDonough WS, Hoelzinger DB, Demuth T, Ross KR, Berens T, Coons SW, Watts G, Trent JM, Wei JS, Giese A, Berens ME. Glioma cell motility is associated with reduced transcription of proapoptotic and proliferation genes: a cDNA microarray analysis. J Neurooncol. 2001 Jun;53(2):161-76. [PubMed]
  14. Neiman PE, Ruddell A, Jasoni C, Loring G, Thomas SJ, Brandvold KA, Lee Rm R, Burnside J, Delrow J. Analysis of gene expression during myc oncogene-induced lymphomagenesis in the bursa of Fabricius. Proc Natl Acad Sci U S A. 2001 May 22;98(11):6378-6383.[PubMed][pdf][web supplement]
  15. Manos EJ, Kim ML, Kassis J, Chang PY, Wells A, Jones DA. Dolichol-phosphate-mannose-3 (DPM3)/prostin-1 is a novel phospholipase C-gamma regulated gene negatively associated with prostate tumor  invasion.  Oncogene. 2001 May 17;20(22):2781-90. [PubMed]
  16. Hishikawa K, Oemar BS, Nakaki T.  Static pressure regulates connective tissue growth factor expression in human mesangial cells.  J Biol Chem. 2001 May 18;276(20):16797-16803. [PubMed]
  17. Brem R, Certa U, Neeb M, Nair AP, Moroni C. Global analysis of differential gene expression after transformation with the v-H-ras oncogene in a murine tumor model.  Oncogene. 2001 May 17;20(22):2854-8. [PubMed]
  18. Graveel CR, Jatkoe T, Madore SJ, Holt AL, Farnham PJ. Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene. 2001 May 10;20(21):2704-12. [PubMed]
  19. Detweiler CS, Cunanan DB, Falkow S. Host microarray analysis reveals a role for the Salmonella response regulator phoP in human macrophage cell death. Proc Natl Acad Sci U S A. 2001 May 8;98(10):5850-5. [PubMed][pdf][web supplement]
  20. Khanna C, Khan J, Nguyen P, Prehn J, Caylor J, Yeung C, Trepel J, Meltzer P, Helman L. Metastasis-associated differences in gene expression in a murine model of osteosarcoma. Cancer Res. 2001 May 1;61(9):3750-9. [PubMed]
  21. Nagarajan R, Svaren J, Le N, Araki T, Watson M, Milbrandt J. Egr2 mutations in inherited neuropathies dominant-negatively inhibit myelin gene expression. Neuron. 2001 May;30(2):355-68. [PubMed]
  22. Detera-Wadleigh SD.  Lithium-related genetics of bipolar disorder.  Ann Med. 2001 May;33(4):272-85. [PubMed]
  23. Cardozo AK, Kruhoffer M, Leeman R, Orntoft T, Eizirik DL.  Identification of novel cytokine-induced genes in pancreatic beta-cells by high-density oligonucleotide arrays. Diabetes. 2001 May;50(5):909-20. [PubMed]
  24. Zhang S, Day IN, Ye S. Microarray analysis of nicotine-induced changes in gene expression in endothelial cells. Physiol Genomics. 2001 Apr 27;5(4):187-92. [PubMed]
  25. Nishizuka S, Winokur ST, Simon M, Martin J, Tsujimoto H, Stanbridge EJ. Oligonucleotide microarray expression analysis of genes whose expression is correlated with tumorigenic and non-tumorigenic phenotype of HeLaxhuman fibroblast hybrid cells.  Cancer Lett. 2001 Apr 26;165(2):201-209. [PubMed]
  26. Kang D, Jiang H, Wu Q, Pestka S, Fisher PB. Cloning and characterization of human ubiquitin-processing protease-43 from terminally differentiated human melanoma cells using a rapid subtraction hybridization protocol RaSH. Gene. 2001 Apr 18;267(2):233-42. [PubMed]
  27. Lee H, Greeley GH, Englander EW.  Age-associated changes in gene expression patterns in the duodenum and colon of rats.  Mech Ageing Dev. 2001 Apr 15;122(4):355-371. [PubMed]
  28. Park WY, Hwang CI, Kang MJ, Seo JY, Chung JH, Kim YS, Lee JH, Kim H, Kim KA, Yoo HJ, Seo JS. Gene Profile of Replicative Senescence Is Different from Progeria or Elderly Donor. Biochem Biophys Res Commun. 2001 Apr 13;282(4):934-9. [PubMed]
  29. Saban MR, Hellmich H, Nguyen NB, Winston J, Hammond TG, Saban R. Time course of LPS-induced gene expression in a mouse model of genitourinary inflammation.  Physiol Genomics. 2001 Apr 2;5(3):147-160. [PubMed]
  30. Komatani H, Kotani H, Hara Y, Nakagawa R, Matsumoto M, Arakawa H, Nishimura S. Identification of Breast Cancer Resistant Protein/Mitoxantrone Resistance/Placenta-Specific, ATP-binding Cassette Transporter as a Transporter of  NB-506 and J-107088, Topoisomerase I Inhibitors with an Indolocarbazole Structure. Cancer Res. 2001 Apr 1;61(7):2827-2832. [PubMed]
  31. Resor L, Bowen TJ, Wynshaw-Boris A. Unraveling human cancer in the mouse: recent refinements to modeling and analysis. Hum Mol Genet. 2001 Apr 1;10(7):669-75. [PubMed]
  32. Brenner V, Lindauer K, Parkar A, Fordham J, Hayes I, Stow M, Gama R, Pollock K, Jupp R.  Analysis of cellular adhesion by microarray expression profiling. J Immunol Methods. 2001 Apr 1;250(1-2):15-28. [PubMed]
  33. Mathiassen S, Lauemoller SL, Ruhwald M, Claesson MH, Buus S. Tumor-associated antigens identified by mRNA expression profiling induce protective anti-tumor immunity. Eur J Immunol. 2001 Apr;31(4):1239-1246. [PubMed]
  34. Wells DB, Tighe PJ, Wooldridge KG, Robinson K, Ala' Aldeen DA. Differential gene expression during meningeal-meningococcal interaction: evidence for self-defense and early release of cytokines and chemokines.  Infect Immun. 2001 Apr;69(4):2718-22. [PubMed]
  35. Choi D, Whittier PS, Oshima J, Funk WD. Telomerase expression prevents replicative senescence but does not fully reset mRNA expression patterns in Werner syndrome cell strains.  FASEB J. 2001 Apr;15(6):1014-20. [PubMed]
  36. Meinhold-Heerlein I, Stenner-Liewen F, Liewen H, Kitada S, Krajewska M, Krajewski S, Zapata JM, Monks A, Scudiero DA, Bauknecht T, Reed JC. Expression and potential role of fas-associated phosphatase-1 in ovarian cancer.  Am J Pathol. 2001 Apr;158(4):1335-44. [PubMed]
  37. Li S, Ross DT, Kadin ME, Brown PO, Wasik MA. Comparative Genome-Scale Analysis of Gene Expression Profiles in T Cell Lymphoma Cells during Malignant Progression Using a Complementary DNA Microarray.  Am J Pathol. 2001 Apr;158(4):1231-1237. [PubMed]
  38. Lomri A, Lemonnier J, Delannoy P, Marie PJ. Increased expression of protein kinase Calpha, interleukin-1alpha, and RhoA guanosine 5'-triphosphatase in osteoblasts expressing the Ser252Trp fibroblast growth factor 2 Apert mutation: identification by analysis of complementary DNA microarray.  J Bone Miner Res. 2001 Apr;16(4):705-12. [PubMed]
  39. Nagai M, Tanaka S, Tsuda M, Endo S, Kato H, Sonobe H, Minami A, Hiraga H, Nishihara H, Sawa H, Nagashima K.  Analysis of transforming activity of human synovial sarcoma-associated chimeric protein SYT-SSX1 bound to chromatin remodeling factor  hBRM/hSNF2alpha.  Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3843-3848. [PubMed][pdf]
  40. Huang Y, Uchiyama Y, Fujimura T, Kanamori H, Doi T, Takamizawa A, Hamakubo T, Kodama T.  A Human Hepatoma Cell Line Expressing Hepatitis C Virus Nonstructural Proteins Tightly Regulated by Tetracycline.  Biochem Biophys Res Commun. 2001 Mar 2;281(3):732-740. [PubMed]
  41. Israel DA, Salama N, Arnold CN, Moss SF, Ando T, Wirth HP, Tham KT, Camorlinga M, Blaser MJ, Falkow S, Peek RM.  Helicobacter pylori strain-specific differences in genetic content, identified by microarray, influence host  inflammatory responses.  J Clin Invest. 2001 Mar 1;107(5):611-620. [PubMed]
  42. Tonko M, Ausserlechner MJ, Bernhard D, Helmberg A, Kofler R. Gene expression profiles of proliferating vs. G1/G0 arrested human leukemia cells suggest a mechanism for glucocorticoid-induced apoptosis. FASEB J. 2001 Mar;15(3):693-9. [PubMed]
  43. Kawai HF, Kaneko S, Honda M, Shirota Y, Kobayashi K.alpha-fetoprotein-producing hepatoma cell lines share common expression profiles of genes in various categories demonstrated by cDNA microarray analysis. Hepatology. 2001 Mar;33(3):676-691.[PubMed]
  44. Wong KK, Cheng RS, Mok SC. Identification of differentially expressed genes from ovarian cancer cells by MICROMAX cDNA microarray system. Biotechniques. 2001 Mar;30(3):670-5. [PubMed]
  45. Chiang LW, Grenier JM, Ettwiller L, Jenkins LP, Ficenec D, Martin J, Jin F, DiStefano PS, Wood A.  An orchestrated gene expression component of neuronal programmed cell death revealed by cDNA array analysis.  Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2814-2819. [PubMed][pdf][Supplemental Data]
  46. Chun HS, Gibson GE, DeGiorgio LA, Zhang H, Kidd VJ, Son JH.  Dopaminergic cell death induced by MPP(+), oxidant and specific neurotoxicants shares the common  molecular mechanism.  J Neurochem. 2001 Feb 15;76(4 Part 4):1010-1021. [PubMed]
  47. Lin B, White JT, Ferguson C, Wang S, Vessella R, Bumgarner R, True LD, Hood L, Nelson PS.  Prostate short-chain dehydrogenase reductase 1 (PSDR1): a new member of the short-chain steroid dehydrogenase/reductase family highly expressed  in normal and neoplastic prostate epithelium. Cancer Res. 2001 Feb 15;61(4):1611-8. [PubMed]
  48. Kettunen E, Nissen AM, Ollikainen T, Taavitsainen M, Tapper J, Mattson K, Linnainmaa K, Knuutila S, El-Rifai W. Gene expression profiling of malignant mesothelioma cell lines: cDNA array study. Int. J. Cancer 2001. Feb 15; 91:492-496. [PubMed]
  49. Hippo Y, Yashiro M, Ishii M, Taniguchi H, Tsutsumi S, Hirakawa K, Kodama T, Aburatani H. Differential gene expression profiles of scirrhous gastric cancer cells with high metastatic potential to peritoneum or lymph nodes.  Cancer Res. 2001 Feb 1;61(3):889-95. [PubMed]
  50. Calaluce R, Kunkel MW, Watts GS, Schmelz M, Hao J, Barrera J, Gleason-Guzman M, Isett R, Fitchmun M, Bowden GT, Cress AE, Futscher BW, Nagle RB.  Laminin-5-mediated gene expression in human prostate carcinoma cells.  Mol Carcinog. 2001 Feb;30(2):119-129. [PubMed]
  51. Chen H, Liu J, Merrick BA, Waalkes MP.  Genetic events associated with arsenic-induced malignant transformation: applications of cDNA microarray technology.  Mol Carcinog. 2001 Feb;30(2):79-87. [PubMed]
  52. Storz M, Zepter K, Kamarashev J, Dummer R, Burg G, Haffner AC.  Coexpression of CD40 and CD40 ligand in cutaneous T-cell lymphoma (mycosis fungoides).  Cancer Res. 2001 Jan 15;61(2):452-4. [PubMed]
  53. Renne R, Barry C, Dittmer D, Compitello N, Brown PO, Ganem D. Modulation of cellular and viral gene expression by the latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus.  J Virol. 2001 Jan; 75(1): 458-68. [PubMed]
  54. Lanford RE, Bigger C, Bassett S, Klimpel G. The chimpanzee model of hepatitis c virus infections. ILAR J. 2001;42(2):117-26. [PubMed]
  55. Vincenti MP, Brinckerhoff CE. Early response genes induced in chondrocytes stimulated with the inflammatory cytokine interleukin-1beta. Arthritis Res. 2001;3(6):381-8. [PubMed]
  56. Pereira M, Simpson-Haidaris PJ.  Fibrinogen modulates gene expression in wounded fibroblasts.  Ann N Y Acad Sci. 2001;936:438-43. Review. [PubMed]
  57. Huang W, Sher YP, Delgado-West D, Wu JT, Peck K, Fung YC. Tissue remodeling of rat pulmonary artery in hypoxic breathing. I. Changes of morphology, zero-stress state, and gene expression. Ann Biomed Eng. 2001;29(7):535-51. [PubMed]
  58. Ueda K.  Detection of the retinoic acid-regulated genes in a RTBM1 neuroblastoma cell line using cDNA microarray. Kurume Med J. 2001;48(2):159-64. [PubMed]
  59. Cherkaoui-Malki M, Meyer K, Cao WQ, Latruffe N, Yeldandi AV, Rao MS, Bradfield CA, Reddy JK. Identification of novel peroxisome proliferator-activated receptor alpha (PPARalpha) target genes in mouse liver using cDNA microarray analysis. Gene Expr. 2001;9(6):291-304. [PubMed]
  60. Leikauf GD, McDowell SA, Bachurski CJ, Aronow BJ, Gammon K, Wesselkamper SC, Hardie W, Wiest JS, Leikauf JE, Korfhagen TR, Prows DR. Functional genomics of oxidant-induced lung injury. Adv Exp Med Biol. 2001;500:479-87. [PubMed]
  61. Chang YE, Laimins LA. Interferon-inducible genes are major targets of human papillomavirus type 31: Insights from microarray analysis. Dis Markers. 2001;17(3):139-42. [PubMed]
  62. Mikovits J, Ruscetti F, Zhu W, Bagni R, Dorjsuren D, Shoemaker R. Potential cellular signatures of viral infections in human hematopoietic cells. Dis Markers. 2001;17(3):173-8. [PubMed]
  63. Katsuma S, Shiojima S, Hirasawa A, Suzuki Y, Takagaki K, Murai M, Kaminishi Y, Hada Y, Koba M, Muso E, Miyawaki S, Ohgi T, Yano J, Tsujimoto G. Genomic analysis of a mouse model of immunoglobulin A nephropathy reveals an enhanced PDGF-EDG5 cascade. Pharmacogenomics J. 2001;1(3):211-7. [PubMed]
  64. Andersson T, Borang S, Larsson M, Wirta V, Wennborg A, Lundeberg J, Odeberg J. Novel candidate genes for atherosclerosis are identified by representational difference analysis-based transcript profiling of cholesterol-loaded macrophages. Pathobiology. 2001;69(6):304-14. [PubMed]

Basic science studies

  1. Fan M, Goodwin ME, Birrer MJ, Chambers TC. The c-Jun NH(2)-terminal Protein Kinase/AP-1 Pathway Is Required for Efficient Apoptosis Induced by Vinblastine.  Cancer Res. 2001 Jun 1;61(11):4450-4458. [PubMed]
  2. de Veer MJ, Holko M, Frevel M, Walker E, Der S, Paranjape JM, Silverman RH, Williams BR.  Functional classification of interferon-stimulated genes identified using microarrays.  J Leukoc Biol. 2001 Jun;69(6):912-20. [PubMed]
  3. Verrecchia F, Chu ML, Mauviel A.  Identification of novel TGF-beta/Smad gene targets in dermal fibroblasts using a combined cDNA microarray/promoter transactivation approach.  J Biol Chem. 2001 May 18;276(20):17058-17062. [PubMed]
  4. Shen X, Li J, Hu PP, Waddell D, Zhang J, Wang XF. The activity of guanine exchange factor Net1 is essential for TGF-beta mediated stress fiber formation. J Biol Chem. 2001 May 4;276(18):15362-8 [PubMed]
  5. Xynos ID, Edgar AJ, Buttery LD, Hench LL, Polak JM.  Gene-expression profiling of human osteoblasts following treatment with the ionic products of Bioglass(R) 45S5 dissolution.  J Biomed Mater Res. 2001 May;55(2):151-7. [PubMed]
  6. Kannan K, Amariglio N, Rechavi G, Jakob-Hirsch J, Kela I, Kaminski N, Getz G, Domany E, Givol D.  DNA microarrays identification of primary and secondary target genes regulated by p53.  Oncogene. 2001 Apr 26;20(18):2225-34. [PubMed]
  7. Ortaldo JR, Bere EW, Hodge D, Young HA. Activating ly-49 nk receptors: central role in cytokine and chemokine production.  J Immunol. 2001 Apr 15;166(8):4994-9. [PubMed]
  8. Kalma Y, Marash L, Lamed Y, Ginsberg D.  Expression analysis using DNA microarrays demonstrates that E2F-1 up-regulates expression of DNA replication genes including replication protein  A2.  Oncogene. 2001 Mar 15;20(11):1379-87. [PubMed]
  9. Presti RM, Popkin DL, Connick M, Paetzold S, Virgin HW.  Novel Cell Type-specific Antiviral Mechanism of Interferon gamma Action in Macrophages.  J Exp Med. 2001 Feb 19;193(4):483-496. [PubMed]
  10. Khaoustov VI, Risin D, Pellis NR, Yoffe B. Microarray analysis of genes differentially expressed in HepG2 cells cultured in simulated microgravity: preliminary report. In Vitro Cell Dev Biol Anim. 2001 Feb;37(2):84-8. [PubMed]
  11. Cohen SB, Waha A, Gelman IH, Vogt PK. Expression of a down-regulated target, SSeCKS, reverses v-Jun-induced transformation of 10T1/2 murine fibroblasts. Oncogene. 2001 Jan 11;20(2):141-6. [PubMed]
  12. Habets GG, Knepper M, Sumortin J, Choi YJ, Sasazuki T, Shirasawa S, Bollag G. cDNA array analyses of K-ras-induced gene transcription. Methods Enzymol. 2001;332:245-60. [PubMed]

Human

  1. Soref CM, Di YP, Hayden L, Zhao YH, Satre MA, Wu R. Characterization of A novel airway epithelial cell-specific short chain alcohol dehydrogenase/reductase gene whose expression is up-regulated by  retinoids and is involved in the metabolism of retinol. J Biol Chem. 2001 2001 Jun 29;276(26):24194-202. [PubMed]
  2. Liu Tj, Lai Hc, Wu W, Chinn S, Wang PH. Developing a strategy to define the effects of insulin-like growth factor-1 on gene expression profile in cardiomyocytes. Circ Res. 2001 Jun 22;88(12):1231-8. [PubMed]
  3. Hamalainen H, Zhou H, Chou W, Hashizume H, Heller R, Lahesmaa R. Distinct gene expression profiles of human type 1 and type 2 T helper cells. Genome Biol. 2001 Jun 21;2(7):RESEARCH0022. [PubMed]
  4. Becker B, Vogt T, Landthaler M, Stolz W. Detection of differentially regulated genes in keratinocytes by cDNA array hybridization: Hsp27 and other novel players in response to artificial ultraviolet radiation.  J Invest Dermatol. 2001 Jun;116(6):983-8. [PubMed]
  5. Chen J, Zhong Q, Wang J, Cameron RS, Borke JL, Isales CM, Bollag RJ. Microarray analysis of Tbx2-directed gene expression: a possible role in osteogenesis.  Mol Cell Endocrinol. 2001 May 25;177(1-2):43-54. [PubMed]
  6. Le Naour F, Hohenkirk L, Grolleau A, Misek DE, Lescure P, Geiger JD, Hanash SM, Beretta L.  Profiling changes in gene expression during differentiation and maturation of monocyte-derived dendritic cells using both oligonucleotide microarrays and proteomics. J Biol Chem. 2001 May 25;276(21):17920-31. [PubMed]
  7. Catani MV, Rossi A, Costanzo A, Sabatini S, Levrero M, Melino G, Avigliano L. Induction of gene expression via activator protein-1 in the ascorbate protection against UV-induced damage. Biochem J. 2001 May 15;356(Pt 1):77-85. [PubMed]
  8. Riewald M, Kravchenko VV, Petrovan RJ, O'Brien PJ, Brass LF, Ulevitch RJ, Ruf W. Gene induction by coagulation factor Xa is mediated by activation of protease-activated receptor 1. Blood. 2001 May 15;97(10):3109-16. [PubMed]
  9. Ellisen LW, Palmer RE, Maki RG, Truong VB, Tamayo P, Oliner JD, Haber DA. Cascades of transcriptional induction during human lymphocyte activation. Eur J Cell Biol. 2001 May;80(5):321-8. [PubMed]
  10. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad Sci. 2001 Apr 24;98(9):5116-21. [PubMed][pdf]
  11. Welle S, Brooks A, Thornton CA.  Senescence-related changes in gene expression in muscle: similarities and differences between mice and  men. Physiol Genomics. 2001 Mar 8;5(2):67-73. [PubMed]
  12. Webb GC, Akbar MS, Zhao C, Steiner DF. Expression profiling of pancreatic beta-cells: glucose regulation of secretory and metabolic pathway genes. Diabetes. 2001 Feb;50 Suppl 1:S135-6. [PubMed]
  13. Ma C, Staudt LM.  Molecular definition of the germinal centre stage of B-cell differentiation. Philos Trans R Soc Lond B Biol Sci. 2001 Jan 29;356(1405):83-9. [PubMed]
  14. Lockhart DJ, Barlow C. Expressing what's on your mind: DNA arrays and the brain. Nat Rev Neurosci. 2001 Jan;2(1):63-8. Review. [PubMed]
  15. Husbeck B, Berggren MI, Powis G. DNA microarray reveals increased expression of thioredoxin peroxidase in thioredoxin-1 transfected cells and its functional consequences. Adv Exp Med Biol. 2001;500:157-68. [PubMed]
  16. Kornblum H, Geschwind D. The use of representational difference analysis and cDNA microarrays in neural repair research. Restor Neurol Neurosci. 2001;18(2,3):89-94. [PubMed]
  17. Abe M, Sato Y. cDNA microarray analysis of the gene expression profile of VEGF-activated human umbilical vein endothelial cells. Angiogenesis. 2001;4(4):289-98. [PubMed]

Animal

  1. Dolznig H, Boulme F, Stangl K, Deiner EM, Mikulits W, Beug H, Mullner EW. Establishment of normal, terminally differentiating mouse erythroid progenitors: molecular characterization by cDNA arrays. FASEB J. 2001 Jun;15(8):1442-4. [PubMed]
  2. Xu Y, Ehringer M, Yang F, Sikela JM. Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array  hybridization. Alcohol Clin Exp Res. 2001 Jun;25(6):810-8. [PubMed]
  3. Li W, Liang X, Leu JI, Kovalovich K, Ciliberto G, Taub R.  Global changes in interleukin-6-dependent gene expression patterns in mouse livers after partial hepatectomy. Hepatology. 2001 Jun;33(6):1377-86. [PubMed]
  4. Stuart RO, Bush KT, Nigam SK. Changes in global gene expression patterns during development and maturation of the rat kidney. Proc Natl Acad Sci U S A. 2001 May 8;98(10):5649-54. [PubMed][pdf]
  5. Feng X, Jiang Y, Meltzer P, Yen PM.  Transgenic targeting of a dominant negative corepressor to liver blocks basal repression by thyroid hormone receptor and increases cell proliferation. J Biol Chem. 2001 May 4;276(18):15066-72. [PubMed]
  6. Liu H, He Z, Rosenwaks Z. Application of complementary DNA microarray (DNA chip) technology in the study of gene expression profiles during folliculogenesis. Fertil Steril. 2001 May;75(5):947-55. [PubMed]
  7. Cavallaro S, Schreurs BG, Zhao W, D'Agata V, Alkon DL. Gene expression profiles during long-term memory consolidation. Eur J Neurosci. 2001 May;13(9):1809-1815. [PubMed]
  8. Zirlinger M, Kreiman G, Anderson DJ.  Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei. Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5270-5275. [PubMed][pdf]
  9. Leemans R, Loop T, Egger B, He H, Kammermeier L, Hartmann B, Certa U, Reichert H, Hirth F. Identification of candidate downstream genes for the homeodomain transcription factor Labial in Drosophila through oligonucleotide-array transcript imaging. Genome Biology. 2001. Apr 24; 2(5):research0015.1-015.9 [PubMed][pdf]
  10. Mziaut H, Korza G, Elkahloun AG, Ozols J. Induction of stearoyl CoA desaturase is associated with high-level induction of emerin RNA. Biochem Biophys Res Commun. 2001 Apr 13;282(4):910-5. [PubMed]
  11. Lichtlen P, Wang Y, Belser T, Georgiev O, Certa U, Sack R, Schaffner W. Target gene search for the metal-responsive transcription factor MTF-1.  Nucleic Acids Res. 2001 Apr 1;29(7):1514-23. [PubMed]
  12. Campbell WG, Gordon SE, Carlson CJ, Pattison JS, Hamilton MT, Booth FW. Differential global gene expression in red and white skeletal muscle.  Am J Physiol Cell Physiol. 2001 Apr;280(4):C763-C768. [PubMed]
  13. Welle S, Brooks A, Thornton CA.  Senescence-related changes in gene expression in muscle: similarities and differences between mice and  men. Physiol Genomics. 2001 Mar 8;5(2):67-73. [PubMed]
  14. Huang W, Carlsen B, Rudkin GH, Shah N, Chung C, Ishida K, Yamaguchi DT, Miller TA. Effect of serial passage on gene expression in MC3T3-E1 preosteoblastic cells: a microarray study. Biochem Biophys Res Comm. 2001. Mar; 281:1120-1126 [PubMed]
  15. Weindruch R, Kayo T, Lee CK, Prolla TA. Microarray Profiling of Gene Expression in Aging and Its Alteration by Caloric Restriction in Mice.  J Nutr. 2001 Mar;131(3):918S-923S. [PubMed]
  16. Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y,  Kikuchi N, Ishii Y, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Satomi S, Yoshiki A, Kusakabe M, DeRisi JL, Eisen MB, Iyer VR,  Brown PO, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y.  Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of  18,816 full-length enriched mouse cDNA arrays.  Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2199-2204. [PubMed][pdf][Supplemental Figures]
  17. Presti RM, Popkin DL, Connick M, Paetzold S, Virgin HW.  Novel Cell Type-specific Antiviral Mechanism of Interferon gamma Action in Macrophages.  J Exp Med. 2001 Feb 19;193(4):483-496. [PubMed]
  18. Dozmorov I, Bartke A, Miller RA. Array-based expression analysis of mouse liver genes: effect of age and of the longevity mutant Prop1df.  J Gerontol A Biol Sci Med Sci. 2001 Feb;56(2):B72-80. [PubMed]
  19. Cohen SB, Waha A, Gelman IH, Vogt PK. Expression of a down-regulated target, SSeCKS, reverses v-Jun-induced transformation of 10T1/2 murine fibroblasts. Oncogene. 2001 Jan 11;20(2):141-6. [PubMed]
  20. Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, Kim SK. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):218-223. [PubMed][pdf]
  21. Zhou FC, Duguid JR, Edenberg HJ, McClintick J, Young P, Nelson P. DNA microarray analysis of differential gene expression of 6-year-old rat neural striatal progenitor cells during early differentiation. Restor Neurol Neurosci. 2001;18(2,3):95-104. [PubMed]
  22. Burton JL, Madsen SA, Yao J, Sipkovsky SS, Coussens PM. An immunogenomics approach to understanding periparturient immunosuppression and mastitis susceptibility in dairy cows. Acta Vet Scand. 2001;42(3):407-24. [PubMed]

Plant

  1. Breyne P, Zabeau M. Genome-wide expression analysis of plant cell cycle modulated genes.  Curr Opin Plant Biol. 2001. Apr 4:136-142. [PubMed]
  2. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ.  Gene Expression Profiles during the Initial Phase of Salt Stress in Rice.  Plant Cell. 2001 Apr;13(4):889-906. [PubMed]
  3. Hihara Y, Kamei A, Kanehisa M, Kaplan A, Ikeuchi M.  DNA Microarray Analysis of Cyanobacterial Gene Expression during Acclimation to High Light.  Plant Cell. 2001 Apr;13(4):793-806. [PubMed]
  4. Dong Y, Glasner JD, Blattner FR, Triplett EW.  Genomic Interspecies Microarray Hybridization: Rapid Discovery of Three Thousand Genes in the Maize Endophyte, Klebsiella pneumoniae 342, by  Microarray Hybridization with Escherichia coli K-12 Open Reading Frames.  Appl Environ Microbiol. 2001 Apr;67(4):1911-1921. [PubMed]
  5. Rowland O, Jones JDG. Unraveling regulatory networks in plant defense using microarrays. Genome Biology Jan 3; 2001 2(1): reviews1001.1-1001.3 [link to article][pdf]
  6. Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Carninci P, Hayashizaki Y, Shinozaki K.  Monitoring the Expression Pattern of 1300 Arabidopsis Genes under Drought and Cold Stresses by Using a  Full-Length cDNA Microarray.  Plant Cell. 2001 Jan;13(1):61-72. [PubMed]
  7. Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, Wisman E.  Microarray Analysis of Diurnal and Circadian-Regulated Genes in Arabidopsis.  Plant Cell. 2001 Jan;13(1):113-123. [PubMed]

Microbiology

  1. Sherman DR, Voskuil M, Schnappinger D, Liao R, Harrell MI, Schoolnik GK. Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding alpha -crystallin. Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7534-9. [PubMed][pdf]
  2. Krylov AS, Zasedateleva OA, Prokopenko DV, Rouviere-Yaniv J, Mirzabekov AD. Massive parallel analysis of the binding specificity of histone-like protein HU to single- and  double-stranded DNA with generic oligodeoxyribonucleotide microchips. Nucleic Acids Res. 2001 Jun 15;29(12):2654-60. [PubMed]
  3. Alexandre H, Ansanay-Galeote V, Dequin S, Blondin B. Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Lett. 2001 Jun 1;498(1):98-103. [PubMed]
  4. Paustian ML, May BJ, Kapur V. Pasteurella multocida Gene Expression in Response to Iron Limitation. Infect Immun. 2001 Jun;69(6):4109-15. [PubMed]
  5. De Backer MD, Ilyina T, Ma XJ, Vandoninck S, Luyten WH, Vanden Bossche H. Genomic Profiling of the Response of Candida albicans to Itraconazole Treatment Using a DNA Microarray. Antimicrob Agents Chemother. 2001 Jun;45(6):1660-70. [PubMed]
  6. Shtrichman R, Samuel CE. The role of gamma interferon in antimicrobial immunity. Curr Opin Microbiol. 2001 Jun;4(3):251-9. [PubMed]
  7. Yale J, Bohnert HJ. Transcript Expression in Saccharomyces cerevisiae at high salinty.  J Biol Chem. 2001 May 11;276(19):15996-6007. [PubMed]
  8. Paulose-Murphy M, Ha NK, Xiang C, Chen Y, Gillim L, Yarchoan R, Meltzer P, Bittner M, Trent J, Zeichner S. Transcription program of human herpesvirus 8 (kaposi's sarcoma-associated herpesvirus).  J Virol. 2001 May;75(10):4843-53. [PubMed]
  9. Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli.  Genetics. 2001 May; 158(1): 41-64. [PubMed][web supplement]
  10. Hellauer K, Sirard E, Turcotte B.  Decreased expression of specific genes in yeast cells lacking histone H1.  J Biol Chem. 2001 Apr 27;276(17):13587-13592.[PubMed]
  11. Wei Y, Lee JM, Smulski DR, LaRossa RA.  Global Impact of sdiA Amplification Revealed by Comprehensive Gene Expression Profiling of Escherichia coli.  J Bacteriol. 2001 Apr 1;183(7):2265-2272. [PubMed]
  12. Hakenbeck R, Balmelle N, Weber B, Gardes C, Keck W, de Saizieu A. Mosaic Genes and Mosaic Chromosomes: Intra- and Interspecies Genomic Variation of Streptococcus pneumoniae. Infect Immun. 2001 Apr;69(4):2477-86. [PubMed]
  13. Suzuki I, Kanesaki Y, Mikami K, Kanehisa M, Murata N. Cold-regulated genes under control of the cold sensor Hik33 in Synechocystis. Mol Microbiol. 2001 Apr;40(1):235-244. [PubMed]
  14. Angus-Hill ML, Schlichter A, Roberts D, Erdjument-Bromage H, Tempst P, Cairns BR.  A rsc3/rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler rsc in gene expression and cell cycle control. Mol Cell. 2001 Apr;7(4):741-51. [PubMed]
  15. Wendisch VF, Zimmer DP, Khodursky A, Peter B, Cozzarelli N, Kustu S. Isolation of Escherichia coli mRNA and Comparison of Expression Using mRNA and Total RNA on DNA Microarrays.  Anal Biochem. 2001 Mar 15;290(2):205-213. [PubMed]
  16. May BJ, Zhang Q, Li LL, Paustian ML, Whittam TS, Kapur V.  Complete genomic sequence of Pasteurella multocida,Pm70.  Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3460-3465. [PubMed][pdf]
  17. Israel DA, Salama N, Arnold CN, Moss SF, Ando T, Wirth HP, Tham KT, Camorlinga M, Blaser MJ, Falkow S, Peek RM.  Helicobacter pylori strain-specific differences in genetic content, identified by microarray, influence host  inflammatory responses.  J Clin Invest. 2001 Mar 1;107(5):611-620. [PubMed]
  18. Martienssen R. Chipping away at chromatin. Nat Genet 2001. Mar; 27:240-241 [PubMed]
  19. van Steensel B, Delrow J, Henikoff S. Chromatin profiling using targeted DNA adenine methyltransferase.  Nat Genet. 2001 Mar;27(3):304-8. [PubMed][web supplement]
  20. Diehn M, Relman DA. Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions.  Curr Opin Microbiol. 2001 Feb 1;4(1):95-101. [PubMed]
  21. Yoshida Ki K, Kobayashi K, Miwa Y, Kang CM, Matsunaga M, Yamaguchi H, Tojo S, Yamamoto M, Nishi R, Ogasawara N, Nakayama T, Fujita Y.  Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res. 2001 Feb 1;29(3):683-692. [PubMed]
  22. Kuhn KM, DeRisi JL, Brown PO, Sarnow P.  Global and Specific Translational Regulation in the Genomic Response of Saccharomyces cerevisiae to a Rapid Transfer from a Fermentable to a Nonfermentable Carbon Source.  Mol Cell Biol. 2001 Feb 1;21(3):916-927. [PubMed]
  23. Li J, Chen S, Evans DH. Typing and Subtyping Influenza Virus Using DNA Microarrays and Multiplex Reverse Transcriptase PCR. J Clin Microbiol. 2001 Feb;39(2):696-704. [PubMed]
  24. Carmel-Harel O, Stearman R, Gasch AP, Botstein D, Brown PO, Storz G. Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae. Mol Microbiol. 2001 Feb; 39(3): 595-605. [PubMed][web supplement]
  25. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, Jan 25; 409:533-538 [PubMed]
  26. Palzkill T. Impending Doom: Antibiotic exposure and bacterial gene expression. Genome Res. 2001 Jan; 11: 1-2 [PubMed]
  27. Gmuender H, Kuratli K, di Padova K, Gray CP. Keck W, Evers S. Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis. Genome Res. 2001 Jan; 11: 28-42. [PubMed]
  28. Wei Y, Lee JM, Richmond C, Blattner FR, Rafalski JA, LaRossa RA. High-density microarray-mediated gene expression profiling of escherichia coli. J Bacteriol. 2001 Jan;183(2):545-56. [PubMed]
  29. Kapteyn JC, Ter Riet B , Vink E, Blad S, De Nobel H , Van Den Ende H , Klis FM.  Low external pH induces HOG1-dependent changes in the organization of the Saccharomyces cerevisiae cell wall.  Mol Microbiol. 2001 Jan;39(2):469-480. [PubMed]
  30. Mamoun CB, Gluzman IY, Hott C, MacMillan SK, Amarakone AS, Anderson DL, Carlton JM, Dame JB, Chakrabarti D, Martin RK, Brownstein BH, Goldberg DE.  Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum  revealed by microarray analysis.  Mol Microbiol. 2001 Jan;39(1):26-36. [PubMed]
  31. Schoolnik GK, Voskuil MI, Schnappinger D, Yildiz FH, Meibom K, Dolganov NA, Wilson MA, Chong KH. Whole genome DNA microarray expression analysis of biofilm development by Vibrio cholerae O1 E1 Tor.  Methods Enzymol. 2001;336:3-18. [PubMed]
  32. Deng M, Abrahamsen M S. Microarray-based expression analysis of human epithelial cell response to Cryptosporidium parvum infection. J Eukaryot Microbiol. 2001;Suppl:42S-43S. [PubMed]

Genome scale studies

  1. Bulyk ML, Huang X, Choo Y, Church GM.  Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.  Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7158-63. [PubMed][pdf][web supplement]
  2. Devaux F, Marc P, Bouchoux C, Delaveau T, Hikkel I, Potier MC, Jacq C. An artificial transcription activator mimics the genome-wide properties of the yeast Pdr1 transcription factor. EMBO Rep. 2001 Jun 1;2(6):493-498. [PubMed]
  3. De Backer MD, Ilyina T, Ma XJ, Vandoninck S, Luyten WH, Vanden Bossche H. Genomic Profiling of the Response of Candida albicans to Itraconazole Treatment Using a DNA Microarray. Antimicrob Agents Chemother. 2001 Jun;45(6):1660-70. [PubMed]
  4. Monni O, Barlund M, Mousses S, Kononen J, Sauter G, Heiskanen M, Paavola P, Avela K, Chen Y, Bittner ML, Kallioniemi A.  Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc Natl Acad Sci U S A. 2001 May 8;98(10):5711-5716. [PubMed][pdf][web supplement]
  5. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network.  Science. 2001 May 4;292(5518):929-934. [PubMed][web supplement]
  6. Hakenbeck R, Balmelle N, Weber B, Gardes C, Keck W, de Saizieu A. Mosaic Genes and Mosaic Chromosomes: Intra- and Interspecies Genomic Variation of Streptococcus pneumoniae. Infect Immun. 2001 Apr;69(4):2477-86. [PubMed]
  7. May BJ, Zhang Q, Li LL, Paustian ML, Whittam TS, Kapur V.  Complete genomic sequence of Pasteurella multocida,Pm70.  Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3460-3465. [PubMed][pdf]
  8. Van Dyk TK, Wei Y, Hanafey MK, Dolan M, Reeve MJ, Rafalski JA, Rothman-Denes LB, LaRossa RA.  A genomic approach to gene fusion technology.  Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2555-2560. [PubMed][pdf]
  9. Martienssen R. Chipping away at chromatin. Nat Genet 2001. Mar; 27:240-241 [PubMed]
  10. van Steensel B, Delrow J, Henikoff S. Chromatin profiling using targeted DNA adenine methyltransferase.  Nat Genet. 2001 Mar;27(3):304-8. [PubMed][web supplement]
  11. Tang CM, Moxon ER. The impact of microbial genomics on antimicrobial drug development.  Annu Rev Genomics Hum Genet. 2001;2:259-69. [PubMed]
  12. Jackson-Grusby L, Beard C, Possemato R, Tudor M, Fambrough D, Csankovszki G, Dausman J, Lee P, Wilson C, Lander E, Jaenisch R. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat Genet. 2001 Jan;27(1):31-39. [PubMed]

Genetic analysis

  1. Mahalingam R, Fedoroff N.  Screening insertion libraries for mutations in many genes simultaneously using DNA microarrays. Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7420-5. [PubMed][pdf]
  2. Cuzin M. DNA chips: a new tool for genetic analysis and diagnostics. Transfus Clin Biol. 2001 Jun;8(3):291-6. [PubMed]
  3. Tillib SV, Strizhkov BN, Mirzabekov AD. Integration of Multiple PCR Amplifications and DNA Mutation Analyses by Using Oligonucleotide Microchip. Anal Biochem. 2001 May 1;292(1):155-160. [PubMed]
  4. Loos A, Glanemann C, Willis LB, O'Brien XM, Lessard PA, Gerstmeir R, Guillouet S, Sinskey AJ. Development and Validation of Corynebacterium DNA Microarrays. Appl Environ Microbiol. 2001 May;67(5):2310-2318. [PubMed]
  5. Daigo Y, Chin SF, Gorringe KL, Bobrow LG, Ponder BA, Pharoah PD, Caldas C. Degenerate Oligonucleotide Primed-Polymerase Chain Reaction-Based Array Comparative Genomic Hybridization for Extensive Amplicon Profiling of Breast Cancers : A New Approach for the Molecular Analysis of Paraffin-Embedded Cancer Tissue. Am J Pathol. 2001 May;158(5):1623-1631. [PubMed]
  6. Lo AW, Magliano DJ, Sibson MC, Kalitsis P, Craig JM, Choo KH. A novel chromatin immunoprecipitation and array (CIA) analysis identifies a 460-kb CENP-A-bing neocentromere DNA. Genome Res 2001. Mar; 11:448-457. [PubMed]
  7. Raitio M, Lindroos K, Laukkanen M, Pastinen T, Sistonen P, Sajantila A, Syvanen AC. Y-Chromosomal SNPs in Finno-Ugric-Speaking populations analyzed by minisequencing on microarrays. Genome Res 2001. Mar; 11:471-482. [PubMed]
  8. Tian H, Brody LC, Fan S, Huang Z, Landers JP. Capillary and microchip electrophoresis for rapid detection of known mutations by combining allele-specific DNA amplification with heteroduplex analysis. Clin Chem 2001 Feb; 47(2):173-185 [PubMed]
  9. Bruder CE, Hirvela C, Tapia-Paez I, Fransson I, Segraves R, Hamilton G, Zhang XX, Evans DG, Wallace AJ, Baser ME, Zucman-Rossi J, Hergersberg M, Boltshauser E, Papi  L, Rouleau GA, Poptodorov G, Jordanova A, Rask-Andersen H, Kluwe L, Mautner V, Sainio M, Hung G, Mathiesen T, Moller C, Pulst SM, Harder H, Heiberg A, Honda M,  Niimura M, Sahlen S, Blennow E, Albertson DG, Pinkel D, Dumanski JP. High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH.  Hum Mol Genet. 2001 Feb 1;10(3):271-282. [PubMed]
  10. Lopez-Crapez E, Livache T, Marchand J, Grenier J. K-ras mutation detection by hybridization to a polypyrrole DNA chip. Anal Biochem 2001 Feb; 47(2):186-194 [PubMed]
  11. Jaccoud D, Peng K, Feinstein D, Kilian A. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acid Res. 2001 Feb; 29(4):e25 [PubMed]
  12. Li J, Chen S, Evans DH. Typing and Subtyping Influenza Virus Using DNA Microarrays and Multiplex Reverse Transcriptase PCR. J Clin Microbiol. 2001 Feb;39(2):696-704. [PubMed]
  13. Tillib SV, Mirzabekov AD. Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology. Curr Opin Biotechnol. 2001 Feb 12(1): 53-58 [PubMed]
  14. Nouzova M, Neumann P, Navratilova A, Galbraith DW, Macas J. Microarray-based survey of repetitive genomic sequences in Vicia spp. Plant Mol Biol. 2001 Jan;45(2):229-44. [PubMed]
  15. Cooper CS. Applications of microarray technology in breast cancer research. Breast Cancer Res. 2001;3(3):158-175. [PubMed]
  16. Haddock SH, Quartararo C, Cooley P, Dao DD. Low-resolution typing of HLA-DQA1 using DNA microarray. Methods Mol Biol. 2001;170:201-10. [PubMed]
  17. Chen JN, Li Y, Li YL, Qin HY, Li RY, Cao HM, Xie Y, Mao YM. [Investigation of genotyping HLA DRB1 gene using oligoneucleotide arrays].Yi Chuan Xue Bao. 2001;28(10):887-94. [PubMed]

ArrayCGH

  1. Watanabe CM, Wolffram S, Ader P, Rimbach G, Packer L, Maguire JJ, Schultz PG, Gohil K. The in vivo neuromodulatory effects of the herbal medicine ginkgo biloba.  Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6577-80. [PubMed][pdf]
  2. Daigo Y, Chin SF, Gorringe KL, Bobrow LG, Ponder BA, Pharoah PD, Caldas C. Degenerate Oligonucleotide Primed-Polymerase Chain Reaction-Based Array Comparative Genomic Hybridization for Extensive Amplicon Profiling of Breast Cancers : A New Approach for the Molecular Analysis of Paraffin-Embedded Cancer Tissue. Am J Pathol. 2001 May;158(5):1623-1631. [PubMed]
  3. Hui AB, Lo KW, Yin XL, Poon WS, Ng HK. Detection of multiple gene amplifications in glioblastoma multiforme using array-based comparative genomic hybridization. Lab Invest. 2001 May;81(5):717-23. [PubMed]
  4. Heiskanen M, Kononen J, Barlund M, Torhorst J, Sauter G, Kallioniemi A, Kallioniemi O.  CGH, cDNA and tissue microarray analyses implicate FGFR2 amplification in a small subset of breast tumors.  Anal Cell Pathol. 2001;22(4):229-34. [PubMed]

Pharmacogenomics and pharmacogenetics

  1. Makino K, Yu D, Hung MC. Transcriptional upregulation and activation of p55Cdc via p34(cdc2) in Taxol-induced apoptosis. Oncogene. 2001 May 3;20(20):2537-43. [PubMed]
  2. Yamada M, Yamada M, Yamazaki S, Takahashi K, Nara K, Ozawa H, Yamada S, Kiuchi Y, Oguchi K, Kamijima K, Higuchi T, Momose K. Induction of cysteine string protein after chronic antidepressant treatment in rat frontal cortex.  Neurosci Lett. 2001 Apr 6;301(3):183-6. [PubMed]
  3. Cronin MT, Pho M, Dutta D, Frueh F, Schwarcz L, Brennan T. Utilization of New Technologies in Drug Trials and Discovery.  Drug Metab Dispos. 2001 Apr 1;29(4 Pt 2):586-590. [PubMed]
  4. Komatani H, Kotani H, Hara Y, Nakagawa R, Matsumoto M, Arakawa H, Nishimura S. Identification of Breast Cancer Resistant Protein/Mitoxantrone Resistance/Placenta-Specific, ATP-binding Cassette Transporter as a Transporter of  NB-506 and J-107088, Topoisomerase I Inhibitors with an Indolocarbazole Structure. Cancer Res. 2001 Apr 1;61(7):2827-2832. [PubMed]
  5. Dong Y, Lisk D, Block E, Ip C. Characterization of the biological activity of gamma-glutamyl-Se-methylselenocysteine: a novel, naturally occurring anticancer agent from garlic. Cancer Res. 2001 Apr 1;61(7):2923-8. [PubMed]
  6. Bibb JA, Chen J, Taylor JR, Svenningsson P, Nishi A, Snyder GL, Yan Z, Sagawa ZK, Ouimet CC, Nairn AC, Nestler EJ, Greengard P. Effects of chronic exposure to cocaine are regulated by the neuronal protein Cdk5. Nature. 2001 Mar 15;410(6826):376-80 [PubMed]
  7. Chen CC, Shieh B, Jin YT, Liau YE, Huang CH, Liou JT, Wu LW, Huang W, Young KC, Lai MD, Liu HS, Li C.  Microarray Profiling of Gene Expression Patterns in Bladder Tumor Cells Treated with Genistein.   J Biomed Sci. 2001 Mar;8(2):214-222. [PubMed]
  8. Weinstein JN. Searching for pharmacogenomic markers: The synergy between omic and hypothesis-driven research. Dis Markers. 2001;17(2):77-88. [PubMed]
  9. Rockett JC. Chipping away at the mystery of drug responses. Pharmacogenomics J. 2001;1(3):161-3. [PubMed]

Toxicogenomics

  1. Bulera SJ, Eddy SM, Ferguson E, Jatkoe TA, Reindel JF, Bleavins MR, De La Iglesia FA. RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays. Hepatology. 2001 May;33(5):1239-58. [PubMed]
  2. Gerhold D, Lu M, Xu J, Austin C, Caskey CT, Rushmore T. Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays. Physiol Genomics. 2001 Apr 27;5(4):161-70. [PubMed]
  3. Waring JF, Ciurlionis R, Jolly RA, Heindel M, Ulrich RG. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett. 2001 Mar 31;120(1-3):359-68. [PubMed]
  4. Rockett JC, Christopher Luft J, Brian Garges J, Krawetz SA, Hughes MR, Hee Kirn K, Oudes AJ, Dix DJ. Development of a 950-gene DNA array for examining gene expression patterns in mouse testis. Genome Biol. 2001. Mar 22; 2(4) research0014.1-9 [