My microarray journal watch - year 2001 Jul-Dec [ 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
   Oligo design for array manufacturing
   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. Ghazizadeh M, Kawanami O, Araki T. Assessment of Gene Expression Profile by cDNA Microarray Analysis. J Nippon Med Sch. 2001 Dec 15;68(6):460-461. [PubMed]
  2. Nakanishi T, Oka T, Akagi T. Recent advances in DNA microarrays. Acta Med Okayama. 2001 Dec;55(6):319-28. [PubMed]
  3. Spellman PT. The future of publishing microarray data. Brief Bioinform. 2001 Dec;2(4):316-8. [PubMed]
  4. Knight J. Geneticists' work in disarray as DNA-chip producer pulls the plug. Nature. 2001 Nov 8;414(6860):135-6. [PubMed]
  5. Sutcliffe JG. Open-system approaches to gene expression in the cns.  J Neurosci. 2001 Nov 1;21(21):8306-9. [PubMed]
  6. Leung YF, Pang CP. All aboard the chip! Trends Biotechnol. 2001 Nov;19(11):430-1. [PubMed]
  7. Jiang L, Tsubakihara M, Heinke MY, Yao M, Dunn MJ, Phillips W, Remedios CG, Nosworthy NJ. Heart failure and apoptosis: Electrophoretic methods support data from micro- and macro-arrays. A critical review of genomics and proteomics. Proteomics. 2001 Nov;1(12):1481-1488. [PubMed]
  8. Brahmachari SK. Keynote: Functional genomics and DNA chips. Appl Biochem Biotechnol. 2001 Oct-Dec;96(1-3):9-12. [PubMed]
  9. Jain KK. Biochips for gene spotting. Science. 2001 Oct 19; 294:621-623. [PubMed]
  10. Ghazal P.  DNA microarray technology and integrative viral genomics. Drug Discov Today. 2001 Oct 15;6(20):1046. [PubMed]
  11. Huang JX, Mehrens D, Wiese R, Lee S, Tam SW, Daniel S, Gilmore J, Shi M, Lashkari D.  High-throughput genomic and proteomic analysis using microarray technology.  Clin Chem. 2001 Oct;47(10):1912-6. [PubMed]
  12. Dempsey AA, Dzau VJ, Liew CC.  Cardiovascular genomics: estimating the total number of genes expressed in the human cardiovascular system.  J Mol Cell Cardiol. 2001 Oct;33(10):1879-86. [PubMed]
  13. Kellam P. Post-genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions.  Rev Med Virol. 2001 Sep-Oct;11(5):313-29. [PubMed]
  14. Maughan NJ, Lewis FA, Smith V. An introduction to arrays. J Pathol 2001 Sep; 195: 3-6 [PubMed]
  15. Fernandez Zapico ME, Ahmad US, Urrutia R.  DNA microarrays: revolutionary insight into the living genome.  Surgery. 2001 Sep;130(3):403-7. Review. [PubMed]
  16. Schulze A, Downward J. Navigating gene expression using microarrays - a technology review.  Nat Cell Biol. 2001 Aug;3(8):E190-5. [PubMed]
  17. Brockman JA, Tamminga CA. The human genome: microarray expression analysis. Am J Psychiatry. 2001 Aug;158(8):1199. [PubMed]
  18. Moreno-Aliaga MJ, Marti A, Garcia-Foncillas J, Alfredo Martinez J. DNA hybridization arrays: a powerful technology for nutritional and obesity research. Br J Nutr. 2001 Aug;86(2):119-22. Review. [PubMed]
  19. Kricka LJ, Fortina P. Microarray technology and applications: an all-language literature survey including books and patents.  Clin Chem. 2001 Aug;47(8):1479-82. [PubMed]

Human disease studies

  1. Israel DA, Salama N, Krishna U, Rieger UM, Atherton JC, Falkow S, Peek RM Jr. Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc Natl Acad Sci U S A 2001 Dec 4;98(25):14625-14630 [PubMed]
  2. Kontoyiannis DP, May GS. Identification of azole-responsive genes by microarray technology: why are we missing the efflux transporter genes? Antimicrob Agents Chemother. 2001 Dec;45(12):3674-6. [PubMed]
  3. Hanash SM.  Global profiling of gene expression in cancer using genomics and proteomics. Curr Opin Mol Ther. 2001 Dec;3(6):538-45. [PubMed]
  4. Cristillo AD, Bierer BE. Identification of novel targets of immunosuppressive agents by cDNA-based microarray analysis. J Biol Chem. 2001 Nov 1 [epub ahead of print] [PubMed]
  5. Nestler EJ. Psychogenomics: opportunities for understanding addiction. J Neurosci. 2001 Nov 1;21(21):8324-7. [PubMed]
  6. Clarke PA, te Poele R, Wooster R, Workman P. Gene expression microarray analysis in cancer biology, pharmacology, and drug development: progress and potential. Biochem Pharm. 2001 Nov [PubMed]
  7. Kato-Maeda M, Gao Q, Small PM. Microarray analysis of pathogens and their interaction with hosts. Cell Microbiol. 2001 Nov;3(11):713-9. [PubMed]
  8. Fitzgerald JR, Musser JM. Evolutionary genomics of pathogenic bacteria. Trends Microbiol. 2001 Nov;9(11):547-53. [PubMed]
  9. Rifai A, Dworkin LD, Chen A. Genomic approaches to elucidating the pathophysiology of renal diseases. Zhonghua Yi Xue Za Zhi (Taipei). 2001 Oct;64(10):555-62. [PubMed]
  10. Mills GB, Bast RC Jr, Srivastava S.  Future for ovarian cancer screening: novel markers from emerging technologies of transcriptional profiling and proteomics.   J Natl Cancer Inst. 2001 Oct 3;93(19):1437-9. [PubMed]
  11. Monni O, Hyman E, Mousses S, Barlund M, Kallioniemi A, Kallioniemi OP. From chromosomal alterations to target genes for therapy: integrating cytogenetic and functional genomic views of the breast cancer genome.  Semin Cancer Biol. 2001 Oct;11(5):395-401. [PubMed]
  12. Raetz EA, Moos PJ, Szabo A, Carroll WL. Gene expression profiling. Methods and clinical applications in oncology. Hematol Oncol Clin North Am. 2001 Oct;15(5):911-30, ix. [PubMed]
  13. Greenberg SA. DNA microarray gene expression analysis technology and its application to neurological disorders. Neurology. 2001 Sep 11;57(5):755-61. [PubMed]
  14. Meltzer SJ. Tumor Genomics vs. Tumor Genetics: A Paradigm Shift? Gastroenterology. 2001 Sep;121(3):726-9. [PubMed]
  15. Rubin MA. Use of laser capture microdissection, cDNA microarrays, and tissue microarrays in advancing our understanding of prostate cancer. J Pathol 2001 Sep; 195:80-86 [PubMed]
  16. Strausberg RL. The Cancer Genome Anatomy Project:new resources for reading the molecular signatures of cancer. J Pathol 2001 Sep; 195: 31-40 [PubMed]
  17. Hoffman EP, Dressman D. Molecular pathophysiology and targeted therapeutics for muscular dystrophy. Trends Pharmacol Sci. 2001 Sep;22(9):465-70. [PubMed]
  18. Peale FV Jr, Gerritsen ME. Gene profiling techniques and their application in angiogenesis and vascular development. J Pathol 2001 Sep; 195: 7-19 [PubMed]
  19. Lobenhofer EK, Bushel PR, Afshari CA, Hamadeh HK. Progress in the application of dna microarrays. Environ Health Perspect. 2001 Sep;109(9):881-92. [PubMed]
  20. Marcotte ER, Srivastava LK, Quirion R. DNA microarrays in neuropsychopharmacology. Trends Pharmacol Sci. 2001 Aug; 22: 426-436 [PubMed]
  21. Price CP. Microarrays: the reincarnation of multiplexing in laboratory medicine, but now more relevant? Clin Chem. 2001 Aug;47(8):1345-6. [PubMed]
  22. Nadler ST, Attie AD. Please Pass the Chips: Genomic Insights into Obesity and Diabetes. J Nutr. 2001 Aug;131(8):2078-81. [PubMed]
  23. Zhang W, Laborde PM, Coombes KR, Berry DA, Hamilton SR.  Cancer Genomics: Promises and Complexities.  Clin Cancer Res. 2001 Aug;7(8):2159-2167. [PubMed]
  24. Rew DA. DNA microarray technology in cancer research. Eur J Surg Oncol. 2001 Aug;27(5):504-8. [PubMed]
  25. Lersch RA, Fung J, Hsieh HB, Smida J, Weier HU. Monitoring Signal Transduction in Cancer. From chips to fish.  J Histochem Cytochem. 2001 Jul;49(7):925-6. [PubMed]
  26. Helmberg A. DNA-microarrays: novel techniques to study aging and guide gerontologic medicine. Exp Gerontol. 2001 Jul;36(7):1189-98. [PubMed]
  27. Balmain A. Cancer genetics: from Boveri and Mendel to microarrays. Nature Rev Cancer. 2001 Oct;1(1):77-82. [PubMed]

Disease screening, profiling and classification

  1. Xu XR, Huang J, Xu ZG, Qian BZ, Zhu ZD, Yan Q, Cai T, Zhang X, Xiao HS, Qu J, Liu F, Huang QH, Cheng ZH, Li NG, Du JJ, Hu W, Shen KT, Lu G, Fu G, Zhong M, Xu SH, Gu WY, Huang W, Zhao XT, Hu GX, Gu JR, Chen Z, Han ZG. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Proc Natl Acad Sci. 2001 Dec 18; 98:15089-15094. [PubMed][pdf][web supplement]
  2. Huang Y, Prasad M, Lemon WJ, Hampel H, Wright FA, Kornacker K, LiVolsi V, Frankel W, Kloos RT, Eng C, Pellegata NS, de la Chapelle A. Gene expression in papillary thyroid carcinoma reveals highly consistent profiles. Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15044-9. [PubMed][pdf]
  3. Nacht M, Dracheva T, Gao Y, Fujii T, Chen Y, Player A, Akmaev V, Cook B, Dufault M, Zhang M, Zhang W, Guo M, Curran J, Han S, Sidransky D, Buetow K, Madden  SL, Jen J.  Molecular characteristics of non-small cell lung cancer. Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15203-8. [PubMed][pdf]
  4. Allander SV, Nupponen NN, Ringner M, Hostetter G, Maher GW, Goldberger N, Chen Y, Carpten J, Elkahloun AG, Meltzer PS. Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile. Cancer Res. 2001 Dec 15;61(24):8624-8. [PubMed]
  5. Ohmine K, Ota J, Ueda M, Ueno Si S, Yoshida K, Yamashita Y, Kirito K, Imagawa S, Nakamura Y, Saito K, Akutsu M, Mitani K, Kano Y, Komatsu N, Ozawa K, Mano H. Characterization of stage progression in chronic myeloid leukemia by DNA microarray with purified hematopoietic stem cells.  Oncogene. 2001 Dec 13;20(57):8249-57. [PubMed]
  6. Zhao B, Bepler G. Transcript map and complete genomic sequence for the 310 kb region of minimal allele loss on chromosome segment 11p15.5 in non-small-cell lung cancer. Oncogene. 2001 Dec 6;20(56):8154-64. [PubMed]
  7. Klein U, Tu Y, Stolovitzky GA, Mattioli M, Cattoretti G, Husson H, Freedman A, Inghirami G, Cro L, Baldini L, Neri A, Califano A, Dalla-Favera R. Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells. J Exp Med. 2001 Dec 3;194(11):1625-38. [PubMed]
  8. Rosenwald A, Alizadeh AA, Widhopf G, Simon R, Davis RE, Yu X, Yang L, Pickeral OK, Rassenti LZ, Powell J, Botstein D, Byrd JC, Grever MR, Cheson BD, Chiorazzi N, Wilson WH, Kipps TJ, Brown PO, Staudt LM. Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia.  J Exp Med. 2001 Dec 3; 194(11): 1639-47. [PubMed]
  9. Yan PS, Chen CM, Shi H, Rahmatpanah F, Wei SH, Caldwell CW, Huang TH. Dissecting Complex Epigenetic Alterations in Breast Cancer Using CpG Island Microarrays. Cancer Res. 2001 Dec 1;61(23):8375-8380. [PubMed]
  10. Wang T, Hopkins DA, Fan L, Fanger GR, Houghton R, Vedvick TS, Repasky E, Reed SG. A p53 homologue and a novel serine proteinase inhibitor are over-expressed in lung squamous cell carcinoma. Lung Cancer. 2001 Dec;34(3):363-74. [PubMed]
  11. Johnston MV, Jeon OH, Pevsner J, Blue ME, Naidu S. Neurobiology of Rett syndrome: a genetic disorder of synapse development. Brain Dev. 2001 Dec;23 Suppl 1:S206-S213. [PubMed]
  12. Greenberg DA. Microarrays, markers of disease, and the myth of "nonhypothesis-driven" research. Ann Neurol 2001 Dec;50(6):695. [PubMed]
  13. Tang Y, Lu A, Aronow BJ, Sharp FR. Blood genomic responses differ after stroke, seizures, hypoglycemia, and hypoxia: blood genomic fingerprints of disease. Ann Neurol. 2001 Dec;50(6):699-707. [PubMed]
  14. Aigner T, Zien A, Gehrsitz A, Gebhard PM, McKenna L. Anabolic and catabolic gene expression pattern analysis in normal versus osteoarthritic cartilage using complementary DNA-array technology. Arthritis Rheum. 2001 Dec;44(12):2777-89. [PubMed]
  15. Tang Y, Lu A, Aronow BJ, Sharp FR. Blood genomic responses differ after stroke, seizures, hypoglycemia, and hypoxia: Blood genomic fingerprints of disease. Ann Neurol. 2001 Dec [epub ahead of print] [PubMed][pdf]
  16. Wang T, Fan L, Watanabe Y, McNeill P, Fanger GR, Persing DH, Reed SG. L552S, an alternatively spliced isoform of XAGE-1, is over-expressed in lung adenocarcinoma. Oncogene. 2001 Nov 22;20(53):7699-709. [PubMed]
  17. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.  Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13790-13795. [PubMed][pdf][web supplement]
  18. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van De Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I. Diversity of gene expression in adenocarcinoma of the lung.  Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13784-13789. [PubMed][pdf][web supplement]
  19. Brown V, Jin P, Ceman S, Darnell JC, O'Donnell WT, Tenenbaum SA, Jin X, Feng Y, Wilkinson KD, Keene JD, Darnell RB, Warren ST.  Microarray Identification of FMRP-Associated Brain mRNAs and Altered mRNA Translational Profiles in Fragile X Syndrome. Cell. 2001 Nov 16;107(4):477-87. [PubMed][web supplement]
  20. Purcell AE, Jeon OH, Zimmerman AW, Blue ME, Pevsner J. Postmortem brain abnormalities of the glutamate neurotransmitter system in autism. Neurology. 2001 Nov 13;57(9):1618-1628. [PubMed]
  21. Finlin BS, Gau CL, Murphy GA, Shao H, Kimel T, Seitz RS, Chiu YF, Botstein D, Brown PO, Der CJ, Tamanoi F, Andres DA, Perou CM.  Rerg is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer.  J Biol Chem 2001 Nov 9;276(45):42259-67 [PubMed]
  22. Hegde P, Qi R, Gaspard R, Abernathy K, Dharap S, Earle-Hughes J, Gay C, Nwokekeh NU, Chen T, Saeed AI, Sharov V, Lee NH, Yeatman TJ, Quackenbush J. Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray. Cancer Res. 2001 Nov 1;61(21):7792-7. [PubMed]
  23. Fujita M, Furukawa Y, Tsunoda T, Tanaka T, Ogawa M, Nakamura Y. Up-Regulation of the Ectodermal-Neural Cortex 1 (ENC1) Gene, a Downstream Target of the beta-Catenin/T-Cell Factor Complex, in Colorectal Carcinomas. Cancer Res. 2001 Nov 1;61(21):7722-6. [PubMed]
  24. Lakhani S R, Ashworth A. Microarray and histopathological analysis of tumours: the future and the past? Nat Rev Cancer 2001 Nov; 1: 151-157. [PubMed]
  25. Boer JM, Huber WK, Sultmann H, Wilmer F, von Heydebreck A, Haas S, Korn B, Gunawan B, Vente A, Fuzesi L, Vingron M, Poustka A.  Identification and Classification of Differentially Expressed Genes in Renal Cell Carcinoma by Expression Profiling on a Global Human 31,500-Element cDNA Array.  Genome Res. 2001 Nov;11(11):1861-1870. [PubMed][web supplement]
  26. Loring JF, Wen X, Lee JM, Seilhamer J, Somogyi R. A gene expression profile of Alzheimer's disease. DNA Cell Biol. 2001 Nov;20(11):683-95. [PubMed]
  27. Connor JR, Kumar S, Sathe G, Mooney J, O'Brien SP, Mui P, Murdock PR, Gowen M, Lark MW. Clusterin expression in adult human normal and osteoarthritic articular cartilage. Osteoarthritis Cartilage. 2001 Nov;9(8):727-37. [PubMed]
  28. Pinheiro NA, Caballero OL, Soares F, Reis LF, Simpson AJ. Significant overexpression of oligophrenin-1 in colorectal tumors detected by cDNA microarray analysis. Cancer Lett. 2001 Oct 22; 172:67-73 [PubMed]
  29. Ahr A, Holtrich U, Solbach C, Scharl A, Strebhardt K, Karn T, Kaufmann M. Molecular classification of breast cancer patients by gene expression profiling. J Pathol. 2001 Oct; 195:312-320 [PubMed]
  30. Pavelic K, Gall-Troselj K. Recent advances in molecular genetics of breast cancer. J Mol Med. 2001 Oct;79(10):566-73. [PubMed]
  31. Eszlinger M, Krohn K, Paschke R. Complementary DNA expression array analysis suggests a lower expression of signal transduction proteins and receptors in cold and hot thyroid nodules. J Clin Endocrinol Metab. 2001 Oct;86(10):4834-42. [PubMed]
  32. Goodwin LO, Mason JM, Hajdu SI. Gene expression patterns of paired bronchioloalveolar carcinoma and benign lung tissue. Ann Clin Lab Sci. 2001 Oct;31(4):369-75. [PubMed]
  33. Baelde HJ, Cleton-Jansen AM, van Beerendonk H, Namba M, Bovee JV, Hogendoorn PC.  High quality RNA isolation from tumours with low cellularity and high extracellular matrix component for cDNA microarrays: application to chondrosarcoma.  J Clin Pathol. 2001 Oct;54(10):778-82. [PubMed]
  34. Colantuoni C, Jeon OH, Hyder K, Chenchik A, Khimani AH, Narayanan V, Hoffman EP, Kaufmann WE, Naidu S, Pevsner J.  Gene expression profiling in postmortem rett syndrome brain: differential gene expression and patient classification.  Neurobiol Dis. 2001 Oct;8(5):847-65. [PubMed]
  35. Cole J, Tsou R, Wallace K, Gibran N, Isik F. Early gene expression profile of human skin to injury using high-density cDNA microarrays. Wound Repair Regen. 2001 Sep-Oct;9(5):360-70. [PubMed]
  36. Alevizos I, Mahadevappa M, Zhang X, Ohyama H, Kohno Y, Posner M, Gallagher GT, Varvares M, Cohen D, Kim D, Kent R, Donoff RB, Todd R, Yung CM, Warrington JA, Wong DT.   Oral cancer in vivo gene expression profiling assisted by laser capture microdissection and microarray analysis.  Oncogene. 2001 Sep 27;20(43):6196-204. [PubMed]
  37. West M, Blanchette C, Dressman H, Huang E, Ishida S, Spang R, Zuzan H, Olson JA Jr, Marks JR, Nevins JR.  Predicting the clinical status of human breast cancer by using gene expression profiles.  Proc Natl Acad Sci U S A 2001 Sep 25;98(20):11462-7 [PubMed][pdf]
  38. Rickman DS, Bobek MP, Misek DE, Kuick R, Blaivas M, Kurnit DM, Taylor J, Hanash SM. Distinctive Molecular Profiles of High-Grade and Low-Grade Gliomas Based on Oligonucleotide Microarray Analysis.  Cancer Res. 2001 Sep 15;61(18):6885-6891. [PubMed]
  39. Pasinetti GM. Use of cDNA microarray in the search for molecular markers involved in the onset of Alzheimer's disease dementia. J Neurosci Res. 2001 Sep 15;65(6):471-6. [PubMed]
  40. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR. Chemosensitivity prediction by transcriptional profiling.  Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10787-10792. [PubMed][pdf]
  41. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D,  Eystein Lonning P, Borresen-Dale AL. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications.  Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74. [PubMed][pdf][web supplement]
  42. McCormack GW.  Subcellular micromolecular pharmacotherapy using computer-assisted microarray analysis.  J Natl Cancer Inst. 2001 Sep 5;93(17):1350-1. [PubMed]
  43. Lin YM, Ono K, Satoh S, Ishiguro H, Fujita M, Miwa N, Tanaka T, Tsunoda T, Yang KC, Nakamura Y, Furukawa Y. Identification of AF17 As a Downstream Gene of the beta-catenin/T-Cell Factor Pathway and Its Involvement in Colorectal Carcinogenesis. Cancer Res. 2001 Sep 1;61(17):6345-9. [PubMed]
  44. Kihara C, Tsunoda T, Tanaka T, Yamana H, Furukawa Y, Ono K, Kitahara O, Zembutsu H, Yanagawa R, Hirata K, Takagi T, Nakamura Y. Prediction of Sensitivity of Esophageal Tumors to Adjuvant Chemotherapy by cDNA Microarray Analysis of Gene-Expression Profiles.  Cancer Res. 2001 Sep 1;61(17):6474-9. [PubMed]
  45. Alizadeh AA, Ross DT, Perou CM, van De Rijn M. Towards a novel classification of human malignancies based on gene expression patterns. J Pathol 2001 Sep; 195:41-52 [PubMed]
  46. Siebert R, Rosenwald A, Staudt LM, Morris SW. Molecular features of B-cell lymphoma.  Curr Opin Oncol. 2001 Sep;13(5):316-24. [PubMed]
  47. Dolganov GM, Woodruff PG, Novikov AA, Zhang Y, Ferrando RE, Szubin R, Fahy JV.  A novel method of gene transcript profiling in airway biopsy homogenates reveals increased expression of a na(+)-k(+)-cl(-) cotransporter (nkcc1) in asthmatic subjects.  Genome Res. 2001 Sep;11(9):1473-83. [PubMed]
  48. Yanagawa R, Furukawa Y, Tsunoda T, Kitahara O, Kameyama M, Murata K, Ishikawa O, Nakamura Y. Genome-Wide Screening of Genes Showing Altered Expression in Liver Metastases of Human Colorectal Cancers by cDNA Microarray.  Neoplasia. 2001 Sep;3(5):395-401. [PubMed]
  49. Pasinetti GM. Use of cDNA microarray in the search for molecular markers involved in the onset of Alzheimer's disease dementia. J Neurosci Res. 2001 Sep; 65:471-476 [PubMed]
  50. Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM.  Delineation of prognostic biomarkers in prostate cancer. Nature. 2001 Aug 23;412(6849):822-6. [PubMed][web supplement]
  51. Schuldiner O, Benvenisty N.  A DNA microarray screen for genes involved in c-MYC and N-MYC oncogenesis in human tumors. Oncogene. 2001 Aug 16;20(36):4984-94. [PubMed]
  52. Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, Borg A, Ferno M, Peterson C, Meltzer PS. Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res. 2001 Aug 15;61(16):5979-84. [PubMed]
  53. Takahashi M, Rhodes DR, Furge KA, Kanayama Ho H, Kagawa S, Haab BB, Teh BT.  Gene expression profiling of clear cell renal cell carcinoma: Gene identification and prognostic classification. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9754-9. [PubMed][pdf][web supplement]
  54. Rutherford RM, Kehren J, Staedtler F, Chibout SD, Egan JJ, Tamm M, Gilmartin JJ, Brutsche MH. Functional genomics in sarcoidosis--reduced or increased apoptosis? Swiss Med Wkly. 2001 Aug 11;131(31-32):459-70. [PubMed]
  55. Takemasa I, Higuchi H, Yamamoto H, Sekimoto M, Tomita N, Nakamori S, Matoba R, Monden M, Matsubara K.  Construction of Preferential cDNA Microarray Specialized for Human Colorectal Carcinoma: Molecular Sketch of Colorectal Cancer. Biochem Biophys Res Commun. 2001 Aug 3;285(5):1244-9. [PubMed]
  56. Hofmann WK, de Vos S, Tsukasaki K, Wachsman W, Pinkus GS, Said JW, Koeffler HP. Altered apoptosis pathways in mantle cell lymphoma detected by oligonucleotide microarray.  Blood. 2001 Aug 1;98(3):787-94. [PubMed]
  57. Shridhar V, Lee J, Pandita A, Iturria S, Avula R, Staub J, Morrissey M, Calhoun E, Sen A, Kalli K, Keeney G, Roche P, Cliby W, Lu K, Schmandt R, Mills GB, Bast RC  Jr, James CD, Couch FJ, Hartmann LC, Lillie J, Smith DI. Genetic analysis of early- versus late-stage ovarian tumors.  Cancer Res. 2001 Aug 1;61(15):5895-904. [PubMed]
  58. Hsieh HB, Lersch RA, Callahan DE, Hayward S, Wong M, Clark OH, Weier HU. Monitoring Signal Transduction in Cancer. Cdna microarray for semiquantitative analysis.  J Histochem Cytochem. 2001 Aug;49(8):1057-8. [PubMed]
  59. Mirnics K, Middleton FA, Lewis DA, Levitt P. Analysis of complex brain disorders with gene expression microarrays: schizophrenia as a disease of the synapse. Trends Neurosci. 2001 Aug;24(8):479-86. [PubMed]
  60. Mariani L, Beaudry C, McDonough WS, Hoelzinger DB, Kaczmarek E, Ponce F, Coons SW, Giese A, Seiler RW, Berens ME. Death-associated protein 3 (dap-3) is overexpressed in invasive glioblastoma cells in vivo and in glioma cell lines with induced motility phenotype in vitro.  Clin Cancer Res. 2001 Aug;7(8):2480-9. [PubMed]
  61. Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T. Effects of ischemia on gene expression. J Surg Res. 2001 Aug;99(2):222-7. [PubMed]
  62. Lu YJ, Williamson D, Clark J, Wang R, Tiffin N, Skelton L, Gordon T, Williams R, Allan B, Jackman A, Cooper C, Pritchard-Jones K, Shipley J. Comparative expressed sequence hybridization to chromosomes for tumor classification and identification of genomic regions of differential gene expression. Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9197-9202. [PubMed][pdf][web supplement]
  63. Miyazato A, Ueno S, Ohmine K, Ueda M, Yoshida K, Yamashita Y, Kaneko T, Mori M, Kirito K, Toshima M, Nakamura Y, Saito K, Kano Y, Furusawa S, Ozawa K,  Mano H. Identification of myelodysplastic syndrome-specific genes by DNA microarray analysis with purified hematopoietic stem cell fraction. Blood. 2001 Jul 15;98(2):422-427. [PubMed]
  64. Cohen N, Rozenfeld-Granot G, Hardan I, Brok-Simoni F, Amariglio N, Rechavi G, Trakhtenbrot L.  Subgroup of patients with Philadelphia-positive chronic myelogenous leukemia characterized by a deletion of 9q proximal to ABL gene. expression profiling, resistance to interferon therapy, and poor prognosis. Cancer Genet Cytogenet. 2001 Jul 15;128(2):114-9. [PubMed]
  65. Ljubimova JY, Lakhter AJ, Loksh A, Yong WH, Riedinger MS, Miner JH, Sorokin LM, Ljubimov AV, Black KL. Overexpression of alpha4 chain-containing laminins in human glial tumors identified by gene microarray analysis.   Cancer Res. 2001 Jul 15;61(14):5601-10. [PubMed]
  66. Tackels-Horne D, David M, Williams AJ, Wilson DJ, Eskandari T, Vogt LM, Boland JF, Scherf U, Vockley JG. Identification of differentially expressed genes in hepatocellular carcinoma and metastatic liver tumors by oligonucleotide expression profiling. Cancer. 2001 Jul 15;92(2):395-405. [PubMed]
  67. Vawter MP, Barrett T, Cheadle C, Sokolov BP, Wood WH, Donovan DM, Webster M, Freed WJ, Becker KG. Application of cDNA microarrays to examine gene expression differences in schizophrenia. Brain Res Bulletin. 2001 Jul 15; 55:641-650. [PubMed]
  68. Tapper J, Kettunen E, El-Rifai W, Seppala M, Andersson LC, Knuutila S. Changes in gene expression during progression of ovarian carcinoma.  Cancer Genetics and Cytogenetics. 2001 Jul 1;128(1):1-6. [PubMed]
  69. Evans CO, Young AN, Brown MR, Brat DJ, Parks JS, Neish AS, Oyesiku NM. Novel Patterns of Gene Expression in Pituitary Adenomas Identified by Complementary Deoxyribonucleic Acid Microarrays and Quantitative Reverse Transcription-Polymerase Chain Reaction. J Clin Endocrinol Metab. 2001 Jul 1;86(7):3097-3107. [PubMed]
  70. Shaughnessy J Jr, Gabrea A, Qi Y, Brents L, Zhan F, Tian E, Sawyer J, Barlogie B, Bergsagel PL, Kuehl M. Cyclin D3 at 6p21 is dysregulated by recurrent chromosomal translocations to immunoglobulin loci in multiple myeloma. Blood. 2001 Jul 1;98(1):217-223. [PubMed]
  71. Klus GT, Rokaeus N, Bittner ML, Chen Y, Korz DM, Sukumar S, Schick A, Szallasi Z.  Down-regulation of the desmosomal cadherin desmocollin 3 in human breast cancer.  Int J Oncol. 2001 Jul;19(1):169-74. [PubMed]
  72. Xiong M, Li W, Zhao J, Jin L, Boerwinkle E. Feature (gene) selection in gene expression-based tumor classification. Mol Genet Metab. 2001 Jul;73(3):239-47. [PubMed]
  73. Bahn S, Augood SJ, Ryan M, Standaert DG, Starkey M, Emson PC. Gene expression profiling in the post-mortem human brain - no cause for dismay. J Chem Neuroanat. 2001 Jul;22(1-2):79-94. [PubMed]

Diagnosis and clinical application

  1. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15149-54 [PubMed][pdf]
  2. Gabrielson E, Berg K, Anbazhagan R. Functional Genomics, Gene Arrays, and the Future of Pathology. Mod Pathol. 2001 Dec;14(12):1294-1299. [PubMed]
  3. Hamels S, Gala JL, Dufour S, Vannuffel P, Zammatteo N, Remacle J. Consensus PCR and microarray for diagnosis of the genus Staphylococcus, species, and methicillin resistance. Biotechniques. 2001 Dec;31(6):1364-6, 1368, 1370-2. [PubMed]
  4. Reese J, Das SK, Paria BC, Lim H, Song H, Matsumoto HM, Knudtson KL, DuBois RN, Dey SK. Global gene expression analysis to identify molecular markers of uterine receptivity and embryo implantation.  J Biol Chem 2001 Nov 23;276(47):44137-44145 [PubMed]
  5. Lakhani S R, Ashworth A. Microarray and histopathological analysis of tumours: the future and the past? Nat Rev Cancer 2001 Nov; 1: 151-157. [PubMed]
  6. Jiang Z, Woda BA, Rock KL, Xu Y, Savas L, Khan A, Pihan G, Cai F, Babcook JS, Rathanaswami P, Reed SG, Xu J, Fanger GR.  P504S: A New Molecular Marker for the Detection of Prostate Carcinoma.  Am J Surg Pathol. 2001 Nov;25(11):1397-1404. [PubMed]
  7. Jun AS, Liu SH, Koo EH, Do DV, Stark WJ, Gottsch JD. Microarray Analysis of Gene Expression in Human Donor Corneas. Arch Ophthalmol. 2001 Nov;119(11):1629-1634. [PubMed]
  8. Katsuma S, Tsujimoto G. Genome medicine promised by microarray technology. Expert Rev Mol Diagn. 2001 Nov;1(4):377-82. [PubMed]
  9. Shi L. Arrays, molecular diagnostics, personalized therapy and informatics. Expert Rev Mol Diagn. 2001 Nov;1(4):363-5. [PubMed]
  10. Bertucci F, Houlgatte R, Nguyen C, Viens P, Jordan B R, Birnbaum D. Gene expression profiling of cancer by use of DNA arrays: how far from the clinic? Lancet Oncol. 2001 Nov;2(11):674-82. Review. [PubMed]
  11. Fluit AC, Visser MR, Schmitz FJ. Molecular detection of antimicrobial resistance. Clin Microbiol Rev. 2001 Oct;14(4):836-71. [PubMed]
  12. Raetz EA, Moos PJ, Szabo A, Carroll WL. Gene expression profiling. Methods and clinical applications in oncology. Hematol Oncol Clin North Am. 2001 Oct;15(5):911-30, ix. [PubMed]
  13. Aitman TJ.  DNA microarrays in medical practice. BMJ. 2001 Sep 15;323(7313):611-5 [PubMed]
  14. Akalin E, Hendrix RC, Polavarapu RG, Pearson TC, Neylan JF, Larsen CP, Lakkis FG.  Gene expression analysis in human renal allograft biopsy samples using high-density oligoarray technology. Transplantation. 2001 Sep 15;72(5):948-53. [PubMed]
  15. McCormack GW.  Subcellular micromolecular pharmacotherapy using computer-assisted microarray analysis.  J Natl Cancer Inst. 2001 Sep 5;93(17):1350-1. [PubMed]
  16. Lonning PE, Sorlie T, Perou CM, Brown PO, Botstein D, Borresen-Dale AL. Microarrays in primary breast cancer - lessons from chemotherapy studies.  Endocr Relat Cancer. 2001 Sep; 8(3): 259-63. [PubMed]
  17. Beaucage SL.  Strategies in the preparation of dna oligonucleotide arrays for diagnostic applications. Curr Med Chem. 2001 Aug;8(10):1213. [PubMed]
  18. Bubendorf L. High-throughput microarray technologies: from genomics to clinics. Eur Urol. 2001 Aug;40(2):231-8. [PubMed]

In vitro and animal model study

  1. Cardozo AK, Heimberg H, Heremans Y, Leeman R, Kutlu B, Kruhoffer M, Orntoft T, Eizirik DL. A comprehensive analysis of cytokine-induced and NF-kB dependent genes in primary rat pancreatic {beta}-cells.  J Biol Chem 2001 Dec 28;276(52):48879-86 [PubMed]
  2. Carmel JB, Galante A, Soteropoulos P, Tolias P, Recce M, Young W, Hart RP. Gene expression profiling of acute spinal cord injury reveals spreading inflammatory signals and neuron loss. Physiol Genomics. 2001 Dec 21;7(2):201-213. [PubMed][web supplement]
  3. Brar AK, Handwerger S, Kessler CA, Aronow BJ. Gene induction and categorical reprogramming during in vitro human endometrial fibroblast decidualization. Physiol Genomics. 2001 Dec 21;7(2):135-48. [PubMed]
  4. Yan D, Wiesmann M, Rohan M, Chan V, Jefferson AB, Guo L, Sakamoto D, Caothien RH, Fuller JH, Reinhard C, Garcia PD, Randazzo FM, Escobedo J, Fantl WJ, Williams LT. Elevated expression of axin2 and hnkd mRNA provides evidence that Wnt/beta -catenin signaling is activated in human colon tumors. Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14973-8. [PubMed][pdf]
  5. Zhou X, Tan FK, Xiong M, Milewicz DM, Feghali CA, Fritzler MJ, Reveille JD, Arnett FC. Systemic sclerosis (scleroderma): specific autoantigen genes are selectively overexpressed in scleroderma fibroblasts. J Immunol. 2001 Dec 15;167(12):7126-33. [PubMed]
  6. Otsuka M, Kato M, Yoshikawa T, Chen H, Brown EJ, Masuho Y, Omata M, Seki N. Differential Expression of the L-Plastin Gene in Human Colorectal Cancer Progression and Metastasis. Biochem Biophys Res Commun. 2001 Dec 14;289(4):876-881. [PubMed]
  7. Whitney LW, Ludwin SK, McFarland HF, Biddison WE. Microarray analysis of gene expression in multiple sclerosis and EAE identifies 5-lipoxygenase as a component of inflammatory lesions. J Neuroimmunol. 2001 Dec 3;121(1-2):40-8. [PubMed]
  8. Ehrlich M, Buchanan KL, Tsien F, Jiang G, Sun B, Uicker W, Weemaes CM, Smeets D, Sperling K, Belohradsky BH, Tommerup N, Misek DE, Rouillard JM, Kuick R, Hanash SM. DNA methyltransferase 3B mutations linked to the ICF syndrome cause dysregulation of lymphogenesis genes. Hum Mol Genet. 2001 Dec 1;10(25):2917-2931. [PubMed]
  9. Stone DH, Sivamurthy N, Contreras MA, Fitzgerald L, LoGerfo FW, Quist WC. Altered ubiquitin/proteasome expression in anastomotic intimal hyperplasia. J Vasc Surg. 2001 Dec;34(6):1016-1022. [PubMed]
  10. Takahashi M, Nishihira J, Shimpo M, Mizue Y, Ueno S, Mano H, Kobayashi E, Ikeda U, Shimada K. Macrophage migration inhibitory factor as a redox-sensitive cytokine in cardiac myocytes. Cardiovasc Res. 2001 Dec;52(3):438-445. [PubMed]
  11. Schlake T, Boehm T. Expression domains in the skin of genes affected by the nude mutation and identified by gene expression profiling. Mech Dev. 2001 Dec;109(2):419-22. [PubMed]
  12. Narayanan BA, Narayanan NK, Reddy BS. Docosahexaenoic acid regulated genes and transcription factors inducing apoptosis in human colon cancer cells. Int J Oncol. 2001 Dec;19(6):1255-62. [PubMed]
  13. Mullan PB, McWilliams S, Quinn J, Andrews H, Gilmore P, McCabe N, McKenna S, Harkin DP. Uncovering BRCA1-regulated signalling pathways by microarray-based expression profiling. Biochem Soc Trans. 2001 Dec;29(6):678-83. [PubMed]
  14. Hill JM, Lukiw WJ, Gebhardt BM, Higaki S, Loutsch JM, Myles ME, Thompson HW, Kwon BS, Bazan NG, Kaufman HE. Gene expression analyzed by microarrays in HSV-1 latent mouse trigeminal ganglion following heat stress.Virus Genes. 2001 Dec;23(3):273-80. [PubMed]
  15. Valery C, Grob JJ, Verrando P. Identification by cDNA microarray technology of genes modulated by artificial ultraviolet radiation in normal human melanocytes: relation to melanocarcinogenesis.  J Invest Dermatol. 2001 Dec;117(6):1471-82. [PubMed]
  16. Leikauf G D, McDowell S A, Wesselkamper S C, Miller C R, Hardie W D, Gammon K, Biswas P P, Korfhagen T R, Bachurski C J, Wiest J S, Willeke K, Bingham E, Leikauf J E, Aronow B J, Prows D R. Pathogenomic mechanisms for particulate matter induction of acute lung injury and inflammation in mice. Res Rep Health Eff Inst. 2001 Dec;(105):5-58; discussion 59-71. [PubMed]
  17. Irwin LN. Gene expression in the hippocampus of behaviorally stimulated rats: analysis by DNA microarray. Brain Res Mol Brain Res. 2001 Nov 30;96(1-2):163-9. [PubMed]
  18. Kato M, Seki N, Sugano S, Hashimoto K, Masuho Y, Muramatsu Ma MA, Kaibuchi K, Nakafuku M. Identification of sonic hedgehog-responsive genes using cDNA microarray. Biochem Biophys Res Commun. 2001 Nov 30;289(2):472-8. [PubMed]
  19. Janowski BA, Shan B, Russell DW. The Hypocholesterolemic Agent LY295427 Reverses Suppression of Sterol Regulatory Element-binding Protein Processing Mediated by Oxysterols. J Biol Chem 2001 Nov 30;276(48):45408-16 [PubMed]
  20. Seta KA, Kim R, Kim HW, Millhorn DE, Beitner-Johnson D. Hypoxia-induced Regulation of MAPK Phosphatase-1 as Identified by Subtractive Suppression Hybridization and cDNA Microarray Analysis. J Biol Chem 2001 Nov 30;276(48):44405-12 [PubMed]
  21. Tomasini R, Azizi Samir A, Vaccaro MI, Pebusque MJ, Dagorn JC, Iovanna JL, Dusetti NJ.  Molecular and Functional Characterization of the Stress-induced Protein (SIP) Gene and Its Two Transcripts Generated by Alternative Splicing. SIP INDUCED BY STRESS AND PROMOTES CELL DEATH. J Biol Chem 2001 Nov 23;276(47):44185-44192 [PubMed]
  22. Chabas D, Baranzini SE, Mitchell D, Bernard CC, Rittling SR, Denhardt DT, Sobel RA, Lock C, Karpuj M, Pedotti R, Heller R, Oksenberg JR, Steinman L. The influence of the proinflammatory cytokine, osteopontin, on autoimmune demyelinating disease.  Science. 2001 Nov 23;294(5547):1731-5. [PubMed][web supplement]
  23. Wang Y, Hu L, Yao R, Wang M, Crist KA, Grubbs CJ, Johanning GL, Lubet RA, You M. Altered gene expression profile in chemically induced rat mammary adenocarcinomas and its modulation by an aromatase inhibitor. Oncogene. 2001 Nov 22;20(53):7710-21. [PubMed]
  24. Richer JK, Jacobsen BM, Manning NG, Abel MG, Wolf DM, Horwitz KB. Differential gene regulation by the two progesterone receptor isoforms in human breast cancer cells. J Biol Chem. 2001 Nov 20 [epub ahead of print][PubMed]
  25. Blanchard RK, Moore JB, Green CL, Cousins RJ. Modulation of intestinal gene expression by dietary zinc status: Effectiveness of cDNA arrays for expression profiling of a single nutrient deficiency.  Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13507-13. [PubMed][pdf]
  26. Wolfgang CD, Essand M, Lee B, Pastan I. T-Cell Receptor gamma Chain Alternate Reading Frame Protein (TARP) Expression in Prostate Cancer Cells Leads to an Increased Growth Rate and Induction of Caveolins and Amphiregulin.  Cancer Res. 2001 Nov 15;61(22):8122-6. [PubMed]
  27. Phillips JL, Hayward SW, Wang Y, Vasselli J, Pavlovich C, Padilla-Nash H, Pezullo JR, Ghadimi BM, Grossfeld GD, Rivera A, Linehan WM, Cunha GR, Ried T. The consequences of chromosomal aneuploidy on gene expression profiles in a cell line model for prostate carcinogenesis. Cancer Res. 2001 Nov 15;61(22):8143-9. [PubMed]
  28. Kauraniemi P, Barlund M, Monni O, Kallioniemi A. New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Res. 2001 Nov 15;61(22):8235-40. [PubMed]
  29. Yoneda K, Peck K, Chang MM, Chmiel K, Sher YP, Chen J, Yang PC, Chen Y, Wu R. Development of High-density DNA Microarray Membrane for Profiling Smoke- and Hydrogen Peroxide-induced Genes in a Human Bronchial Epithelial Cell Line. Am J Respir Crit Care Med. 2001 Nov 15;164(10 Pt 2):S85-S89. [PubMed]
  30. Katsuma S, Nishi K, Tanigawara K, Ikawa H, Shiojima S, Takagaki K, Kaminishi Y, Suzuki Y, Hirasawa A, Ohgi T, Yano J, Murakami Y, Tsujimoto G. Molecular monitoring of bleomycin-induced pulmonary fibrosis by cDNA microarray-based gene expression profiling. Biochem Biophys Res Commun. 2001 Nov 9;288(4):747-51. [PubMed]
  31. Finlin BS, Gau CL, Murphy GA, Shao H, Kimel T, Seitz RS, Chiu YF, Botstein D, Brown PO, Der CJ, Tamanoi F, Andres DA, Perou CM. RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer. J Biol Chem. 2001 Nov 9; 276(45): 42259-42267. [PubMed]
  32. Yuan Rq RQ, Fan S, Achary M, Stewart DM, Goldberg ID, Rosen EM. Altered gene expression pattern in cultured human breast cancer cells treated with hepatocyte growth factor/scatter factor in the setting of DNA damage. Cancer Res. 2001 Nov 1;61(21):8022-31. [PubMed]
  33. Hegde P, Qi R, Gaspard R, Abernathy K, Dharap S, Earle-Hughes J, Gay C, Nwokekeh NU, Chen T, Saeed AI, Sharov V, Lee NH, Yeatman TJ, Quackenbush J. Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray. Cancer Res. 2001 Nov 1;61(21):7792-7. [PubMed]
  34. Fujita M, Furukawa Y, Tsunoda T, Tanaka T, Ogawa M, Nakamura Y. Up-Regulation of the Ectodermal-Neural Cortex 1 (ENC1) Gene, a Downstream Target of the beta-Catenin/T-Cell Factor Complex, in Colorectal Carcinomas. Cancer Res. 2001 Nov 1;61(21):7722-6. [PubMed]
  35. He LZ, Tolentino T, Grayson P, Zhong S, Warrell RP Jr, Rifkind RA, Marks PA, Richon VM, Pandolfi PP. Histone deacetylase inhibitors induce remission in transgenic models of therapy-resistant acute promyelocytic leukemia. J Clin Invest. 2001 Nov;108(9):1321-30. [PubMed]
  36. Watts GS, Futscher BW, Isett R, Gleason-Guzman M, Kunkel MW, Salmon SE. cDna microarray analysis of multidrug resistance: doxorubicin selection produces multiple defects in apoptosis signaling pathways. J Pharmacol Exp Ther. 2001 Nov;299(2):434-41. [PubMed]
  37. Hoffmann KF, McCarty TC, Segal DH, Chiaramonte M, Hesse M, Davis EM, Cheever AW, Meltzer PS, Morse III HC, Wynn TA. Disease fingerprinting with cDNA microarrays reveals distinct gene expression profiles in lethal type-1 and type-2 cytokine-mediated inflammatory reactions. FASEB J 2001 Nov;15(13):2545-2547[PubMed]
  38. Arendt CW, Littman DR. HIV: master of the host cell. Genome Biol. 2001 Nov;2(11):REVIEWS1030. [PubMed]
  39. Huang Q, Liu doN, Majewski P, Schulte leAC, Korn JM, Young RA, Lander ES, Hacohen N.  The plasticity of dendritic cell responses to pathogens and their components.  Science. 2001 Oct 26;294(5543):870-5. [PubMed][web supplement]
  40. Tobe K, Suzuki R, Aoyama M, Yamauchi T, Kamon J, Kubota N, Terauchi Y, Matsui J, Akanuma Y, Kimura S, Tanaka J, Abe M, Ohsumi J, Nagai R, Kadowaki T.  Increased expression of the sterol regulatory element-binding protein (SREBP)-1 gene in insulin receptor substrate-2-/- mouse liver.  J Biol Chem 2001 Oct 19;276(42):38337-40 [PubMed]
  41. Ehrt S, Schnappinger D, Bekiranov S, Drenkow J, Shi S, Gingeras TR, Gaasterland T, Schoolnik G, Nathan C.  Reprogramming of the Macrophage Transcriptome in Response to Interferon-gamma and Mycobacterium tuberculosis. Signaling roles of nitric oxide synthase-2 and phagocyte oxidase.  J Exp Med. 2001 Oct 15;194(8):1123-40. [PubMed]
  42. Kumar A, Soprano DR, Parekh HK.  Cross-resistance to the synthetic retinoid cd437 in a paclitaxel-resistant human ovarian carcinoma cell line is independent of the overexpression of retinoic acid receptor-gamma. Cancer Res. 2001 Oct 15;61(20):7552-5. [PubMed]
  43. Kiemer AK, Takeuchi K, Quinlan MP. Identification of genes involved in epithelial-mesenchymal transition and tumor progression. Oncogene. 2001 Oct 11;20(46):6679-88. [PubMed]
  44. Mousses S, Wagner U, Chen Y, Kim JW, Bubendorf L, Bittner M, Pretlow T, Elkahloun AG, Trepel JB, Kallioniemi OP. Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling. Oncogene. 2001 Oct 11;20(46):6718-23. [PubMed]
  45. Dinh HK, Zhao B, Schuschereba ST, Merrill G, Bowman PD.  Gene expression profiling of the response to thermal injury in human cells.  Physiol Genomics. 2001 Oct 10;7(1):3-13. [PubMed]
  46. Chen BP, Li YS, Zhao Y, Chen KD, Li S, Lao J, Yuan S, Shyy JY, Chien S. DNA microarray analysis of gene expression in endothelial cells in response to 24-h shear stress.  Physiol Genomics. 2001 Oct 10;7(1):55-63. [PubMed][web supplement]
  47. Sun Y, Huang PL, Li JJ, Huang YQ, Zhang L, Huang PL, Lee-Huang S. Anti-hiv agent map30 modulates the expression profile of viral and cellular genes for proliferation and apoptosis in aids-related lymphoma cells  infected with kaposi's sarcoma-associated virus. Biochem Biophys Res Commun. 2001 Oct 5;287(4):983-94. [PubMed]
  48. Tonin PN, Hudson TJ, Rodier F, Bossolasco M, Lee PD, Novak J, Manderson EN, Provencher D, Mes-Masson AM. Microarray analysis of gene expression mirrors the biology of an ovarian cancer model. Oncogene. 2001 Oct 4;20(45):6617-26. [PubMed]
  49. Mok SC, Chao J, Skates S, Wong Kk, Yiu GK, Muto MG, Berkowitz RS, Cramer DW.  Prostasin, a potential serum marker for ovarian cancer: identification through microarray technology.  J Natl Cancer Inst. 2001 Oct 3;93(19):1458-64. [PubMed]
  50. Murakami T, Fujimoto M, Ohtsuki M, Nakagawa H. Expression profiling of cancer-related genes in human keratinocytes following non-lethal ultraviolet B irradiation.  J Dermatol Sci. 2001 Oct;27(2):121-9. [PubMed]
  51. Suzuki J, Shen WJ, Nelson BD, Patel S, Veerkamp JH, Selwood SP, Murphy GM Jr, Reaven E, Kraemer FB.  Absence of cardiac lipid accumulation in transgenic mice with heart-specific HSL overexpression.  Am J Physiol Endocrinol Metab. 2001 Oct;281(4):E857-66. [PubMed]
  52. Hedberg JJ, Grafstrom RC, Vondracek M, Sarang Z, Warngard L, Hoog JO. Micro-array chip analysis of carbonyl-metabolising enzymes in normal, immortalised and malignant human oral keratinocytes. Cell Mol Life Sci. 2001 Oct;58(11):1719-26. [PubMed]
  53. Ibrahim SM, Mix E, Bottcher T, Koczan D, Gold R, Rolfs A, Thiesen HJ. Gene expression profiling of the nervous system in murine experimental autoimmune encephalomyelitis.  Brain. 2001 Oct;124(Pt 10):1927-38. [PubMed]
  54. Steinman L.  Gene microarrays and experimental demyelinating disease: a tool to enhance serendipity.   Brain. 2001 Oct;124(Pt 10):1897-9. [PubMed]
  55. Varedi M, Lee HM, Greeley GH Jr, Herndon DN, Englander EW.  Gene expression in intestinal epithelial cells, IEC-6, is altered by burn injury-induced circulating factors.  Shock. 2001 Oct;16(4):259-63. [PubMed]
  56. Oka T, Yoshino T, Hayashi K, Ohara N, Nakanishi T, Yamaai Y, Hiraki A, Sogawa CA, Kondo E, Teramoto N, Takahashi K, Tsuchiyama J, Akagi T. Reduction of Hematopoietic Cell-Specific Tyrosine Phosphatase SHP-1 Gene Expression in Natural Killer Cell Lymphoma and Various Types of  Lymphomas/Leukemias : Combination Analysis with cDNA Expression Array and Tissue Microarray.  Am J Pathol. 2001 Oct;159(4):1495-1505. [PubMed]
  57. Jones D, Amin M, Ordonez NG, Glassman AB, Hayes KJ, Jeffrey Medeiros L. Reticulum cell sarcoma of lymph node with mixed dendritic and fibroblastic features. Mod Pathol. 2001 Oct;14(10):1059-67.[PubMed]
  58. Ferrante AW, Thearle M, Liao T, Leibel RL.  Effects of leptin deficiency and short-term repletion on hepatic gene expression in genetically obese mice.  Diabetes. 2001 Oct;50(10):2268-78. [PubMed]
  59. Ohsaka Y, Ohgiya S, Hoshino T, Ishizaki K. Cold-stimulated increase in a regulatory subunit of cAMP-dependent protein kinase in human hepatoblastoma cells. DNA Cell Biol. 2001 Oct;20(10):667-73. [PubMed]
  60. Fan M, Mi R, Yew D T, Chan W Y. Analysis of gene expression following sciatic nerve crush and spinal cord hemisection in the mouse by microarray expression profiling. Cell Mol Neurobiol. 2001 Oct;21(5):497-508. [PubMed]
  61. Tarbe N, Evtimova V, Burtscher H, Jarsch M, Alves F, Weidle UH. Transcriptional profiling of cell lines derived from an orthotopic pancreatic tumor model reveals metastasis-associated genes. Anticancer Res. 2001 Sep-Oct;21(5):3221-8. [PubMed]
  62. Shih JY, Yang SC, Hong TM, Yuan A, Chen JJ, Yu CJ, Chang YL, Lee YC, Peck K, Wu CW, Yang PC.  Collapsin Response Mediator Protein-1 and the Invasion and Metastasis of Cancer Cells. J Natl Cancer Inst. 2001 Sep 19;93(18):1392-1400. [PubMed]
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  65. Yamanaka Y, Tamari M, Nakahata T, Nakamura Y.  Gene expression profiles of human small airway epithelial cells treated with low doses of 14- and 16-membered macrolides.  Biochem Biophys Res Commun. 2001 Sep 14;287(1):198-203. [PubMed]
  66. Sampson NS, Ryan ST, Enke DA, Cosgrove D, Koteliansky V, Gotwals P. Global gene expression analysis reveals a role for the {alpha}{sub1} integrin in renal pathogenesis. J Biol Chem. 2001 Sep 7;276(36):34182-8. [PubMed]
  67. Pan W, Zhang Q, Xi QS, Gan RB, Li TP.  Fup1, a gene associated with hepatocellular carcinoma, stimulates nih3t3 cell proliferation and tumor formation in nude mice.  Biochem Biophys Res Commun. 2001 Sep 7;286(5):1033-8. [PubMed]
  68. Ho L, Xiang Z, Mukherjee P, Zhang W, De Jesus N, Mirjany M, Yemul S, Pasinetti GM.  Gene expression profiling of the tau mutant (P301L) transgenic mouse brain.  Neurosci Lett. 2001 Sep 7;310(1):1-4. [PubMed]
  69. Seftor RE, Seftor EA, Koshikawa N, Meltzer PS, Gardner LM, Bilban M, Stetler-Stevenson WG, Quaranta V, Hendrix MJ. Cooperative Interactions of Laminin 5 gamma2 Chain, Matrix Metalloproteinase-2, and Membrane Type-1-Matrix/Metalloproteinase Are Required for Mimicry of Embryonic Vasculogenesis by Aggressive Melanoma.  Cancer Res. 2001 Sep 1;61(17):6322-7. [PubMed]
  70. Lieuallen K, Pennacchio LA, Park M, Myers RM, Lennon GG.  Cystatin B-deficient mice have increased expression of apoptosis and glial activation genes.  Hum Mol Genet. 2001 Sep 1;10(18):1867-1871. [PubMed]
  71. Zhao X, Demary K, Wong L, Vaziri C, McKenzie AB, Eberlein TJ, Spanjaard RA. Retinoic acid receptor-independent mechanism of apoptosis of melanoma cells by the retinoid CD437 (AHPN). Cell Death Differ. 2001 Sep;8(9):878-86. [PubMed]
  72. Joseph P, Muchnok T, Ong Tm. Gene expression profile in BALB/c-3T3 cells transformed with beryllium sulfate.  Mol Carcinog. 2001 Sep;32(1):28-35. [PubMed]
  73. Wandinger KP, Sturzebecher CS, Bielekova B, Detore G, Rosenwald A, Staudt LM, McFarland HF, Martin R.  Complex immunomodulatory effects of interferon-beta in multiple sclerosis include the upregulation of T helper 1-associated marker genes.  Ann Neurol. 2001 Sep;50(3):349-57. [PubMed]
  74. Ragno S, Romano M, Howell S, Pappin DJ, Jenner PJ, Colston MJ. Changes in gene expression in macrophages infected with Mycobacterium tuberculosis: a combined transcriptomic and proteomic approach.  Immunology. 2001 Sep;104(1):99-108. [PubMed]
  75. Kan T, Shimada Y, Sato F, Maeda M, Kawabe A, Kaganoi J, Itami A, Yamasaki S, Imamura M. Gene Expression Profiling in Human Esophageal Cancers Using cDNA Microarray. Biochem Biophys Res Commun. 2001 Aug 31;286(4):792-801. [PubMed]
  76. Ishiguro H, Tsunoda T, Tanaka T, Fujii Y, Nakamura Y, Furukawa Y. Identification of AXUD1, a novel human gene induced by AXIN1 and its reduced expression in human carcinomas of the lung, liver, colon and kidney. Oncogene. 2001 Aug 16;20(36):5062-5066. [PubMed]
  77. Keshelava N, Zuo JJ, Chen P, Waidyaratne SN, Luna MC, Gomer CJ, Triche TJ, Reynolds CP.  Loss of p53 function confers high-level multidrug resistance in neuroblastoma cell lines.  Cancer Res. 2001 Aug 15;61(16):6185-93. [PubMed]
  78. Gupta RA, Brockman JA, Sarraf P, Willson TM, DuBois RN. Target genes of peroxisome proliferator-activated receptor {gamma} in colorectal cancer cells.  J Biol Chem. 2001 Aug 10;276(32):29681-7. [PubMed]
  79. Medico E, Gentile A, Celso CL, Williams TA, Gambarotta G, Trusolino L, Comoglio PM. Osteopontin Is an Autocrine Mediator of Hepatocyte Growth Factor-induced Invasive Growth.  Cancer Res. 2001 Aug 1;61(15):5861-8. [PubMed]
  80. Bigger CB, Brasky KM, Lanford RE. Dna microarray analysis of chimpanzee liver during acute resolving hepatitis c virus infection.  J Virol. 2001 Aug;75(15):7059-66. [PubMed]
  81. Mariani L, Beaudry C, McDonough WS, Hoelzinger DB, Kaczmarek E, Ponce F, Coons SW, Giese A, Seiler RW, Berens ME. Death-associated protein 3 (dap-3) is overexpressed in invasive glioblastoma cells in vivo and in glioma cell lines with induced motility phenotype in vitro.  Clin Cancer Res. 2001 Aug;7(8):2480-9. [PubMed]
  82. Hu YC, Lam KY, Law S, Wong J, Srivastava G. Identification of Differentially Expressed Genes in Esophageal Squamous Cell Carcinoma (ESCC) by cDNA Expression Array: Overexpression of Fra-1, Neogenin, Id-1, and CDC25B Genes in ESCC. Clin Cancer Res. 2001 Aug;7(8):2213-21. [PubMed]
  83. Saiura A, Mataki C, Murakami T, Umetani M, Wada Y, Kohro T, Aburatani H, Harihara Y, Hamakubo T, Yamaguchi T, Hasegawa G, Naito M, Makuuchi M, Kodama T.  A comparison of gene expression in murine cardiac allografts and isografts by means dna microarray analysis. Transplantation. 2001 Jul 27;72(2):320-9. [PubMed]
  84. Prince LS, Karp PH, Moninger TO, Welsh MJ. KGF alters gene expression in human airway epithelia: potential regulation of the inflammatory response. Physiol Genomics. 2001 Jul 17;6(2):81-9. [PubMed]
  85. Yang J, Fizazi K, Peleg S, Sikes CR, Raymond AK, Jamal N, Hu M, Olive M, Martinez LA, Wood CG, Logothetis CJ, Karsenty G, Navone NM. Prostate cancer cells induce osteoblast differentiation through a Cbfa1-dependent pathway. Cancer Res. 2001 Jul 15;61(14):5652-9. [PubMed]
  86. Lin CS, Ho HC, Gholami S, Chen KC, Jad A, Lue TF. Gene Expression Profiling of an Arteriogenic Impotence Model. Biochem Biophys Res Commun. 2001 Jul 13;285(2):565-9. [PubMed]
  87. Frueh FW, Hayashibara KC, Brown PO, Whitlock JP Jr. Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expression. Toxicol Lett. 2001 Jul 6; 122(3): 189-203. [PubMed]
  88. Shi Y, Simmons MN, Seki T, Oh SP, Sugrue SP.  Change in gene expression subsequent to induction of Pnn/DRS/memA: increase in p21(cip1/waf1).  Oncogene. 2001 Jul 5;20(30):4007-18 [PubMed]
  89. Hendrix MJ, Seftor EA, Meltzer PS, Gardner LM, Hess AR, Kirschmann DA, Schatteman GC, Seftor RE.  Expression and functional significance of VE-cadherin in aggressive human melanoma cells: Role in vasculogenic mimicry. Proc Natl Acad Sci U S A 2001 Jul 3;98(14):8018-23 [PubMed][pdf]
  90. Grunblatt E, Mandel S, Maor G, Youdim MB. Gene expression analysis in N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine mice model of Parkinson's disease using cDNA microarray: effect of R-apomorphine. J Neurochem. 2001 Jul 1;78(1):1-12. [PubMed]
  91. Arvand A, Welford SM, Teitell MA, Denny CT. The COOH-Terminal Domain of FLI-1 Is Necessary for Full Tumorigenesis and Transcriptional Modulation by EWS/FLI-1. Cancer Res. 2001 Jul 1;61(13):5311-5317. [PubMed]
  92. Chen JJ, Peck K, Hong TM, Yang SC, Sher YP, Shih JY, Wu R, Cheng JL, Roffler SR, Wu CW, Yang PC. Global analysis of gene expression in invasion by a lung cancer model. Cancer Res. 2001 Jul 1;61(13):5223-30. [PubMed]
  93. Scandurro AB, Weldon CW, Figueroa YG, Alam J, Beckman BS.  Gene microarray analysis reveals a novel hypoxia signal transduction pathway in human hepatocellular carcinoma cells. Int J Oncol. 2001 Jul;19(1):129-35. [PubMed]
  94. Gail M, Gross U, Bohne W. Transcriptional profile of Toxoplasma gondii-infected human fibroblasts as revealed by gene-array hybridization.  Mol Genet Genomics. 2001 Jul;265(5):905-12. [PubMed]
  95. Flores-Morales A, Stahlberg N, Tollet-Egnell P, Lundeberg J, Malek RL, Quackenbush J, Lee NH, Norstedt G. Microarray analysis of the in vivo effects of hypophysectomy and growth hormone treatment on gene expression in the rat. Endocrinology. 2001 Jul;142(7):3163-76. [PubMed]
  96. Monti J, Gross V, Luft FC, Franca Milia A, Schulz H, Dietz R, Sharma AM, Hubner N. Expression analysis using oligonucleotide microarrays in mice lacking bradykinin type 2 receptors. Hypertension. 2001 Jul;38(1):E1-3. [PubMed]
  97. Jin K, Mao XO, Eshoo MW, Nagayama T, Minami M, Simon RP, Greenberg DA. Microarray analysis of hippocampal gene expression in global cerebral ischemia. Ann Neurol. 2001 Jul;50(1):93-103. [PubMed]

Basic science studies

  1. Stillman B. DNA replication. Genomic views of genome duplication. Science. 2001 Dec 14;294(5550):2301-4. [PubMed]
  2. Wu L, Thompson DK, Li G, Hurt RA, Tiedje JM, Zhou J. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol. 2001 Dec;67(12):5780-90. [PubMed]
  3. Cao Y, Dulac C. Profiling brain transcription: neurons learn a lesson from.  Curr Opin Neurobiol. 2001 Oct;11(5):615-20 [PubMed]
  4. Peale FV Jr, Gerritsen ME. Gene profiling techniques and their application in angiogenesis and vascular development. J Pathol 2001 Sep; 195: 7-19 [PubMed]
  5. White KP. Functional genomics and the study of development, variation and evolution.  Nat Rev Genet. 2001 Jul;2(7):528-37. [PubMed]
Human
  1. Mayanil CS, George D, Freilich L, Miljan EJ, Mania-Farnell B, McLone DG, Bremer EG. Microarray analysis detects novel Pax3 downstream target genes.  J Biol Chem 2001 Dec 28;276(52):49299-309 [PubMed]
  2. Butte AJ, Dzau VJ, Glueck SB. Further defining housekeeping, or “maintenance,” genes. Focus on “A compendium of gene expression in normal human tissues” Physiol. Genomics. 2001 Dec 21; 7:95-96. [PubMed]
  3. Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, Lee KF, Clark KE, Haverty P, Weng Z, Mutter GL, Frosch MP, Macdonald ME, Milford EL, Crum CP, Bueno R, Pratt RE, Mahadevappa M, Warrington JA, Stephanopoulos G, Stephanopoulos G, Gullans SR. A compendium of gene expression in normal human tissues. Physiol. Genomics. 2001 Dec 21; 7:97-104. [PubMed]
  4. Zhao X, Lein ES, He A, Smith SC, Aston C, Gage FH. Transcriptional profiling reveals strict boundaries between hippocampal subregions. J Comp Neurol. 2001 Dec 17;441(3):187-196. [PubMed]
  5. Grundschober C, Delaunay F, Puhlhofer A, Triqueneaux G, Laudet V, Bartfai T, Nef P. Circadian Regulation of Diverse Gene Products Revealed by mRNA Expression Profiling of Synchronized Fibroblasts. J Biol Chem. 2001 Dec 14;276(50):46751-46758. [PubMed][web supplement]
  6. Wurmbach E, Yuen T, Ebersole BJ, Sealfon SC. Gonadotropin-releasing Hormone Receptor-coupled Gene Network Organization. J Biol Chem. 2001 Dec 14;276(50):47195-47201. [PubMed][web supplement]
  7. Shi S, Robey PG, Gronthos S. Comparison of human dental pulp and bone marrow stromal stem cells by cDNA microarray analysis. Bone. 2001 Dec;29(6):532-9. [PubMed]
  8. Jean S, Bideau C, Bellon L, Halimi G, De Meo M, Orsiere T, Dumenil G, Berge-Lefranc JL, Botta A. The expression of genes induced in melanocytes by exposure to 365-nm UVA: study by cDNA arrays and real-time quantitative RT-PCR. Biochem Biophys Acta. 2001. Dec; 1522:89-96. [PubMed]
  9. Granucci F, Castagnoli PR, Rogge L, Sinigaglia F. Gene expression profiling in immune cells using microarray. Int Arch Allergy Immunol. 2001 Dec;126(4):257-66. [PubMed]
  10. Lebkowski JS, Gold J, Xu C, Funk W, Chiu CP, Carpenter MK. Human embryonic stem cells: culture, differentiation, and genetic modification for regenerative medicine applications. Cancer J. 2001 Nov-Dec;7 Suppl 2:S83-93. [PubMed]
  11. Neilsen PO, Zimmerman GA, McIntyre TM. Escherichia coli Braun Lipoprotein Induces a Lipopolysaccharide-Like Endotoxic Response from Primary Human Endothelial Cells.  J Immunol. 2001 Nov 1;167(9):5231-9. [PubMed]
  12. Wang L, Wu Q, Qiu P, Mirza A, McGuirk M, Kirschmeier P, Greene JR, Wang Y, Pickett CB, Liu S. Analyses of P53 target genes in the human genome by bioinformatic and microarray approaches.  J Biol Chem 2001 Nov 23;276(47):43604-10 [PubMed]
  13. Xiao J, Gregersen S, Kruhoffer M, Pedersen SB, Orntoft TF, Hermansen K. The effect of chronic exposure to fatty acids on gene expression in clonal insulin-producing cells: studies using high density oligonucleotide microarray. Endocrinology. 2001 Nov;142(11):4777-84. [PubMed]
  14. Zhao B, Bowden RA, Stavchansky SA, Bowman PD. Human endothelial cell response to gram-negative lipopolysaccharide assessed with cDNA microarrays.  Am J Physiol Cell Physiol 2001 Nov; 281: C1587-C1595. [PubMed]
  15. Amundson SA, Bittner M, Meltzer P, Trent J, Fornace AJ. Induction of gene expression as a monitor of exposure to ionizing radiation.  Radiat Res. 2001 Nov;156(5):657-61. [PubMed]
  16. Qian J, Ramroop K, McLeod A, Bandari P, Livingston DH, Harrison JS, Rameshwar P. Induction of hypoxia-inducible factor-1alpha and activation of caspase-3 in hypoxia-reoxygenated bone marrow stroma is negatively regulated by the delayed production of substance p. J Immunol. 2001 Oct 15;167(8):4600-8. [PubMed]
  17. Fortin A, Cregan SP, MacLaurin JG, Kushwaha N, Hickman ES, Thompson CS, Hakim A, Albert PR, Cecconi F, Helin K, Park DS, Slack RS.  APAF1 is a key transcriptional target for p53 in the regulation of neuronal cell death.   J Cell Biol 2001 Oct 15;155(2):207-16 [PubMed]
  18. Boeuf S, Klingenspor M, Van Hal NL, Schneider T, Keijer J, Klaus S. Differential gene expression in white and brown preadipocytes. Physiol Genomics. 2001 Oct 10;7(1):15-25. [PubMed]
  19. Bouton CM, Hossain MA, Frelin LP, Laterra J, Pevsner J. Microarray analysis of differential gene expression in lead-exposed astrocytes. Toxicol Appl Pharmacol. 2001 Oct 1;176(1):34-53. [PubMed]
  20. Cao Y, Dulac C. Profiling brain transcription: neurons learn a lesson from.  Curr Opin Neurobiol. 2001 Oct;11(5):615-20 [PubMed]
  21. Lu C, Kasik J, Stephan DA, Yang S, Sperling MA, Menon RK. Grtp1, a novel gene regulated by growth hormone.  Endocrinology. 2001 Oct;142(10):4568-71. [PubMed]
  22. Miller LD, Park KS, Guo QM, Alkharouf NW, Malek RL, Lee NH, Liu ET, Cheng SY. Silencing of Wnt signaling and activation of multiple metabolic pathways in response to thyroid hormone-stimulated cell  proliferation. Mol Cell Biol 2001 Oct;21(19):6626-39 [PubMed]
  23. Suciu-Foca Cortesini N, Piazza F, Ho E, Ciubotariu R, LeMaoult J, Dalla-Favera R, Cortesini R. Distinct mRNA microarray profiles of tolerogenic dendritic cells. Hum Immunol. 2001 Oct;62(10):1065-72. [PubMed]
  24. Sivamurthy N, Stone DH, Logerfo FW, Quist WC. Apolipoprotein J inhibits the migration, adhesion, and proliferation of vascular smooth muscle cells. J Vasc Surg. 2001 Oct;34(4):716-23. [PubMed]
  25. Kessler D, Dethlefsen S, Haase I, Plomann M, Hirche F, Krieg T, Eckes B. Fibroblasts in mechanically stressed collagen lattices assume a "synthetic" phenotype.   J Biol Chem 2001 Sep 28;276(39):36575-85 [PubMed]
  26. Robles AI, Bemmels NA, Foraker AB, Harris CC.  APAF-1 Is a Transcriptional Target of p53 in DNA Damage-induced Apoptosis.  Cancer Res. 2001 Sep 15;61(18):6660-4. [PubMed]
  27. Suzuki Y, Rahman M, Mitsuya H.  Diverse transcriptional response of CD4(+) T cells to stromal cell-derived factor (SDF)-1: cell survival promotion and priming effects of SDF-1 on CD4(+) T cells.  J Immunol. 2001 Sep 15;167(6):3064-73. [PubMed]
  28. Muhle RA, Pavlidis P, Grundy WN, Hirsch E. A high-throughput study of gene expression in preterm labor with a subtractive microarray approach.  Am J Obstet Gynecol. 2001 Sep;185(3):716-24. [PubMed]
  29. Shaffer AL, Rosenwald A, Hurt EM, Giltnane JM, Lam LT, Pickeral OK, Staudt LM.  Signatures of the immune response. Immunity. 2001 Sep;15(3):375-85. [PubMed]
  30. Sanchez-Ramos JR, Song S, Kamath SG, Zigova T, Willing A, Cardozo-Pelaez F, Stedeford T, Chopp M, Sanberg PR. Expression of neural markers in human umbilical cord blood. Exp Neurol. 2001 Sep;171(1):109-15. [PubMed]
  31. Zhang W, Bardwell PD, Woo CJ, Poltoratsky V, Scharff MD, Martin A.Clonal instability of V region hypermutation in the Ramos Burkitt's lymphoma cell line. Int Immunol. 2001 Sep;13(9):1175-84. [PubMed]
  32. Alcantara O, Kalidas M, Baltathakis I, Boldt DH. Expression of multiple genes regulating cell cycle and apoptosis in differentiating hematopoietic cells is dependent on iron. Exp Hematol. 2001 Sep;29(9):1060-9. [PubMed]
  33. Honda S, Farboud B, Hjelmeland LM, Handa JT. Induction of an Aging mRNA Retinal Pigment Epithelial Cell Phenotype by Matrix-Containing Advanced Glycation End Products In Vitro. Invest Ophthalmol Vis Sci. 2001 Sep;42(10):2419-25 [PubMed]
  34. Aberger F, Costa-Pereira AP, Schlaak JF, Williams TM, O'Shaughnessy RF, Hollaus G, Kerr IM, Frischauf AM. Analysis of Gene Expression Using High-Density and IFN-gamma-Specific Low-Density cDNA Arrays. Genomics. 2001 Sep;77(1/2):50-57. [PubMed]
  35. J Glynne R, R Watson S. The immune system and gene expression microarrays - new answers to old questions. J Pathol 2001 Sep; 195: 20-30 [PubMed]
  36. Teruyama K, Abe M, Nakano T, Takahashi S, Yamada S, Sato Y.  Neurophilin-1 is a downstream target of transcription factor Ets-1 in human umbilical vein endothelial cells.  FEBS Lett. 2001 Aug 24;504(1-2):1-4. [PubMed]
  37. Liu R, Liu H, Chen X, Kirby M, Brown PO, Zhao K. Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell. 2001 Aug 10;106(3):309-18. [PubMed]
  38. Devireddy LR, Teodoro JG, Richard FA, Green MR. Induction of apoptosis by a secreted lipocalin that is transcriptionally regulated by IL-3 deprivation.  Science. 2001 Aug 3;293(5531):829-34. [PubMed]
  39. Lewis ML, Cubano LA, Zhao B, Dinh HK, Pabalan JG, Piepmeier EH, Bowman PD. cDNA microarray reveals altered cytoskeletal gene expression in space-flown leukemic T lymphocytes (Jurkat). FASEB J. 2001 Aug;15(10):1783-1785. [PubMed]
  40. Dent GW, O'Dell DM, Eberwine JH. Gene expression profiling in the amygdala: An approach to examine the molecular substrates of mammalian behavior.  Physiol Behav. 2001 Aug;73(5):841-7. [PubMed]
  41. Bell SE, Mavila A, Salazar R, Bayless KJ, Kanagala S, Maxwell SA, Davis GE. Differential gene expression during capillary morphogenesis in 3D collagen matrices: regulated expression of genes involved in basement membrane matrix assembly, cell cycle progression, cellular differentiation and G-protein signaling. J Cell Sci. 2001 Aug;114(Pt 15):2755-73. [PubMed]
  42. McCormick SM, Eskin SG, McIntire LV, Teng CL, Lu CM, Russell CG, Chittur KK. DNA microarray reveals changes in gene expression of shear stressed human umbilical vein endothelial cells. Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):8955-8960. [PubMed][pdf]
  43. Lapteva N, Nieda M, Ando Y, Ide K, Hatta-Ohashi Y, Dymshits G, Ishikawa Y, Juji T, Tokunaga K. Expression of Renin-Angiotensin System Genes in Immature and Mature Dendritic Cells Identified Using Human cDNA Microarray. Biochem Biophys Res Commun. 2001 Jul 27;285(4):1059-65. [PubMed]
  44. Kerley JS, Olsen SL, Freemantle SJ, Spinella MJ. Transcriptional activation of the nuclear receptor corepressor rip140 by retinoic acid: a potential negative-feedback regulatory mechanism.  Biochem Biophys Res Commun. 2001 Jul 27;285(4):969-75. [PubMed]
  45. Reick M, Garcia JA, Dudley C, McKnight SL. NPAS2: an analog of clock operative in the mammalian forebrain. Science. 2001 Jul 20;293(5529):506-9. [PubMed]
  46. Aronow BJ, Richardson BD, Handwerger S. Microarray analysis of trophoblast differentiation: gene expression reprogramming in key gene function categories. Physiol Genomics. 2001 Jul 17;6(2):105-16. [PubMed]
  47. Terskikh AV, Easterday MC, Li L, Hood L, Kornblum HI, Geschwind DH, Weissman IL. From hematopoiesis to neuropoiesis: Evidence of overlapping genetic programs. Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7934-7939. [PubMed][pdf]
  48. Chu VT, Gage FH.  Chipping away at stem cells. Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7652-3. [PubMed][pdf]
  49. Ishida S, Huang E, Zuzan H, Spang R, Leone G, West M, Nevins JR. Role for e2f in control of both dna replication and mitotic functions as revealed from dna microarray analysis. Mol Cell Biol. 2001 Jul;21(14):4684-99. [PubMed]
  50. Lee JS, Liu JJ, Hong JW, Wilson SE. Differential expression analysis by gene array of cell cycle modulators in human corneal epithelial cells stimulated with epidermal growth factor (EGF), hepatocyte growth factor (HGF), or keratinocyte growth factor (KGF). Curr Eye Res. 2001 Jul;23(1):69-76. [PubMed]

Animal

  1. Liang CP, Tall AR. Transcriptional profiling reveals global defects in energy metabolism, lipoprotein and bile acid synthesis and transport with reversal by leptin treatment  in ob/ob mouse liver.  J Biol Chem 2001 Dec 28;276(52):49066-76 [PubMed]
  2. Weitzel JM, Radtke C, Seitz HJ. Two thyroid hormone-mediated gene expression patterns in vivo identified by cDNA expression arrays in rat. Nucleic Acid Res. 2001 Dec 15; 29:5148-5155 [PubMed]
  3. Mu X, Zhao S, Pershad R, Hsieh TF, Scarpa A, Wang SW, White RA, Beremand PD, Thomas TL, Gan L, Klein WH. Gene expression in the developing mouse retina by EST sequencing and microarray analysis. Nucleic Acid Res. 2001 Dec 15: 29:4983-4993. [PubMed]
  4. Holter JL, Humphries A, Crunelli V, Carter DA. Optimisation of methods for selecting candidate genes from cDNA array screens: application to rat brain punches and pineal. J Neurosci Methods. 2001 Dec 15;112(2):173-84. [PubMed]
  5. Irving P, Troxler L, Heuer TS, Belvin M, Kopczynski C, Reichhart JM, Hoffmann JA, Hetru C. A genome-wide analysis of immune responses in Drosophila. Proc Natl Acad Sci U S A. 2001 Dec 11 [epub ahead of print] [PubMed][pdf][web supplement]
  6. Linnarsson S, Mikaels A, Baudet C, Ernfors P. Activation by GDNF of a transcriptional program repressing neurite growth in dorsal root ganglia.  Proc Natl Acad Sci U S A 2001 Dec 4;98(25):14681-14686 [PubMed]
  7. Tong L, Shen H, Perreau VM, Balazs R, Cotman CW.  Effects of Exercise on Gene-Expression Profile in the Rat Hippocampus. Neurobiol Dis. 2001 Dec;8(6):1046-1056. [PubMed]
  8. Liu HC, Cheng HH, Tirunagaru V, Sofer L, Burnside J. A strategy to identify positional candidate genes conferring Marek's disease resistance by integrating DNA microarrays and genetic mapping. Anim Genet. 2001 Dec;32(6):351-359. [PubMed]
  9. Churchill GA, Oliver B. Sex, flies and microarrays. Nat Genet. 2001 Dec;29(4):355-6. [PubMed]
  10. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet. 2001 Dec;29(4):389-95. [PubMed][web supplement]
  11. Calame KL. Plasma cells: finding new light at the end of B cell development. Nat Immunol. 2001 Dec;2(12):1103-8. [PubMed]
  12. Custodia N, Won SJ, Novillo A, Wieland M, Li C, Callard IP. Caenorhabditis elegans as an environmental monitor using DNA microarray analysis. Ann N Y Acad Sci. 2001 Dec;948:32-42. [PubMed]
  13. Luo Y, Long J M, Spangler E L, Longo D L, Ingram D K, Weng N P. Identification of maze learning-associated genes in rat hippocampus by cDNA microarray. J Mol Neurosci. 2001 Dec;17(3):397-404. [PubMed]
  14. French PJ, O'Connor V, Voss K, Stean T, Hunt SP, Bliss TV. Seizure-induced gene expression in area CA1 of the mouse hippocampus. Eur J Neurosci. 2001 Dec;14(12):2037-2041. [PubMed]
  15. Chan JY, Chen LK, Chang JF, Ting HM, Goy C, Chen JL, Hwang JJ, Chen FD, Chen DJ, Ngo FQ. Differential gene expression in a DNA double-strand-break repair mutant XRS-5 defective in Ku80: analysis by cDNA microarray. J Radiat Res (Tokyo). 2001 Dec;42(4):371-85. [PubMed]
  16. McDonald MJ, Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell. 2001 Nov 30;107(5):567-78. [PubMed][web supplement]
  17. Hemberger M, Cross JC, Ropers HH, Lehrach H, Fundele R, Himmelbauer H. UniGene cDNA array-based monitoring of transcriptome changes during mouse placental development.  Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):13126-31. [PubMed][pdf][web supplement]
  18. Pritchard CC, Hsu L, Delrow J, Nelson PS.  Project normal: Defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):13266-71. [PubMed][pdf][web supplement]
  19. Stolarov J, Chang K, Reiner A, Rodgers L, Hannon GJ, Wigler MH, Mittal V.  Design of a retroviral-mediated ecdysone-inducible system and its application to the expression profiling of the PTEN tumor suppressor. Proc Natl Acad Sci U S A 2001 Nov 6;98(23):13043-8 [PubMed][pdf]
  20. Brenman JE, Gao FB, Jan LY, Jan YN. Sequoia, a tramtrack-related zinc finger protein, functions as a pan-neural regulator for dendrite and axon morphogenesis in Drosophila.  Dev Cell. 2001 Nov;1(5):667-77. [PubMed]
  21. Dupont J, Khan J, Qu BH, Metzler P, Helman L, LeRoith D. Insulin and IGF-1 Induce Different Patterns of Gene Expression in Mouse Fibroblast NIH-3T3 Cells: Identification by cDNA Microarray Analysis. Endocrinology. 2001 Nov;142(11):4969-75. [PubMed]
  22. Li QZ, Eckenrode S, Ruan QG, Wang CY, Shi JD, McIndoe RA, She JX. Rapid decrease of RNA level of a novel mouse mitochondria solute carrier protein (Mscp) gene at 4-5 weeks of age. Mamm Genome. 2001 Nov;12(11):830-6. [PubMed]
  23. De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays.  Pr