My microarray journal watch - year 2004 Jan-Mar  [ 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, prognosis and clinical applications
   Animal model studies
   In vitro studies
Basic science studies
   Gene product function
   General physiology
   Development & differentiation
   Neurobiology
   Signal transduction
   Apoptosis
   Human
   Animal
   Plant
   Microbiology
Genome scale studies
   Comparative Genomics
   Network/pathway reconstruction and analysis
Genetic analysis
   ArrayCGH

Pharmacogenomics and pharmacogenetics
Toxicogenomics
Technical development
Other related technical issue; microdissection; linear amplification of RNA (aRNA)
Experimental design, sample size & power
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)
Cell microarray
Other array platforms
Can't find the microarray article published in 2004 in my site? 
Try a Google search!
Google

General

  1. Check E. Geneticists chip away at unruly data. Nature. 2004 Jan 8;427(6970):91. [PubMed]
  2. Chen ZJ, Tew KD.  Amplified differential gene expression microarray. Methods Mol Biol. 2004;258:95-106. [PubMed]

Human disease studies

  1. Grant GM, Fortney A, Gorreta F, Estep M, Del Giacco L, Van Meter A, Christensen A, Appalla L, Naouar C, Jamison C, Al-Timimi A, Donovan J, Cooper J, Garrett C, Chandhoke V. Microarrays in cancer research. Anticancer Res. 2004 Mar-Apr;24(2A):441-8. [PubMed]
  2. Cleator S, Ashworth A. Molecular profiling of breast cancer: clinical implications. Br J Cancer. 2004 Mar 22;90(6):1120-4. [PubMed]
  3. Glanzer JG, Eberwine JH. Expression profiling of small cellular samples in cancer: less is more. Br J Cancer. 2004 Mar 22;90(6):1111-4. [PubMed]
  4. Li JZ, Vawter MP, Walsh DM, Tomita H, Evans SJ, Choudary PV, Lopez JF, Avelar A, Shokoohi V, Chung T, Mesarwi O, Jones EG, Watson SJ, Akil H, Bunney WE Jr, Myers RM. Systematic changes in gene expression in postmortem human brains associated with tissue pH and terminal medical conditions. Hum Mol Genet. 2004 Mar 15;13(6):609-16. [PubMed]
  5. Dahlberg PS, Ferrin LF, Grindle SM, Nelson CM, Hoang CD, Jacobson B. Gene expression profiles in esophageal adenocarcinoma. Ann Thorac Surg. 2004 Mar;77(3):1008-15. [PubMed]
  6. Hoffman EP, Awad T, Palma J, Webster T, Hubbell E, Warrington JA, Spira A, Wright G, Buckley J, Triche T, Davis R, Tibshirani R, Xiao W, Jones W, Tompkins R, West M. Guidelines: Expression profiling - best practices for data generation and interpretation in clinical trials. Nat Rev Genet. 2004 Mar;5(3):229-37. [PubMed]
  7. Van De Rijn M, Gilks CB. Applications of microarrays to histopathology. Histopathology. 2004 Feb;44(2):97-108. [PubMed]
  8. Huppi K, Chandramouli GV. Molecular profiling of prostate cancer. Curr Urol Rep. 2004 Feb; 5(1): 45-51. [PubMed]
  9. Warner GC, Reis PP, Makitie AA, Sukhai MA, Arora S, Jurisica I, Wells RA, Gullane P, Irish J, Kamel-Reid S. Current applications of microarrays in head and neck cancer research. Laryngoscope. 2004 Feb;114(2):241-8. [PubMed]
  10. Bryant PA, Venter D, Robins-Browne R, Curtis N. Chips with everything: DNA microarrays in infectious diseases. Lancet Infect Dis. 2004 Feb;4(2):100-11. [PubMed]
  11. Grutzmann R, Saeger HD, Luttges J, Schackert HK, Kalthoff H, Kloppel G, Pilarsky C. Microarray-based gene expression profiling in pancreatic ductal carcinoma: status quo and perspectives. Int J Colorectal Dis. 2004 Jan 24 [Epub ahead of print] [PubMed]
  12. Permana PA, Del Parigi A, Tataranni PA. Microarray gene expression profiling in obesity and insulin resistance. Nutrition. 2004 Jan;20(1):134-138. [PubMed]
  13. Claudio JO, Masih-Khan E, Stewart AK. Insights from the Gene Expression Profiling of Multiple Myeloma. Curr Hematol Rep. 2004 Jan;3(1):67-73. [PubMed]

Disease screening, profiling and classification

  1. Tsuchiya T, Dhahbi JM, Cui X, Mote PL, Bartke A, Spindler SR. Additive Regulation of Hepatic Gene Expression by Dwarfism and Caloric Restriction. Physiol Genomics. 2004 Mar 23 [Epub ahead of print] [PubMed]
  2. Laprise C, Sladek R, Ponton A, Bernier MC, Hudson TJ, Laviolette M. Functional classes of bronchial mucosa genes that are differentially expressed in asthma. BMC Genomics. 2004 Mar 23;5(1):21. [PubMed]
  3. Daiba A, Inaba N, Ando S, Kajiyama N, Yatsuhashi H, Terasaki H, Ito A, Ogasawara M, Abe A, Yoshioka J, Hayashida K, Kaneko S, Kohara M, Ito S. A low-density cDNA microarray with a unique reference RNA: pattern recognition analysis for IFN efficacy prediction to HCV as a model. Biochem Biophys Res Commun. 2004 Mar 19;315(4):1088-96. [PubMed]
  4. Hao X, Sun B, Hu L, Lahdesmaki H, Dunmire V, Feng Y, Zhang SW, Wang H, Wu C, Wang H, Fuller GN, Symmans WF, Shmulevich I, Zhang W. Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis. Cancer. 2004 Mar 15;100(6):1110-22. [PubMed]
  5. Samaco RC, Nagarajan RP, Braunschweig D, LaSalle JM. Multiple pathways regulate MeCP2 expression in normal brain development and exhibit defects in autism-spectrum disorders. Hum Mol Genet. 2004 Mar 15;13(6):629-39. [PubMed]
  6. Vawter MP, Ferran E, Galke B, Cooper K, Bunney WE, Byerley W. Microarray screening of lymphocyte gene expression differences in a multiplex schizophrenia pedigree. Schizophr Res. 2004 Mar 1;67(1):41-52. [PubMed]
  7. Iizuka N, Oka M, Yamada-Okabe H, Hamada K, Nakayama H, Mori N, Tamesa T, Okada T, Takemoto N, Matoba K, Takashima M, Sakamoto K, Tangoku A, Miyamoto T, Uchimura S, Hamamoto Y. Molecular signature in three types of hepatocellular carcinoma with different viral origin by oligonucleotide microarray. Int J Oncol. 2004 Mar;24(3):565-74. [PubMed]
  8. Mircean C, Tabus I, Kobayashi T, Yamaguchi M, Shiku H, Shmulevich I, Zhang W. Pathway analysis of informative genes from microarray data reveals that metabolism and signal transduction genes distinguish different subtypes of lymphomas. Int J Oncol. 2004 Mar;24(3):497-504. [PubMed]
  9. Albertson DN, Pruetz B, Schmidt CJ, Kuhn DM, Kapatos G, Bannon MJ. Gene expression profile of the nucleus accumbens of human cocaine abusers: evidence for dysregulation of myelin. J Neurochem. 2004 Mar;88(5):1211-9. [PubMed]
  10. Xu L, Zhang L, Yi Y, Kang HK, Datta SK. Human lupus T cells resist inactivation and escape death by upregulating COX-2. Nat Med. 2004 Feb 29 [Epub ahead of print] [PubMed]
  11. Bourdeau I, Antonini SR, Lacroix A, Kirschner LS, Matyakhina L, Lorang D, Libutti SK, Stratakis CA. Gene array analysis of macronodular adrenal hyperplasia confirms clinical heterogeneity and identifies several candidate genes as molecular mediators. Oncogene. 2004 Feb 26;23(8):1575-1585. [PubMed]
  12. Sakamoto S, Yokoyama M, Zhang X, Prakash K, Nagao K, Hatanaka T, Getzenberg RH, Kakehi Y. Increased Expression of CYR61, an Extracellular Matrix Signaling Protein, in Human Benign Prostatic Hyperplasia and Its Regulation by Lysophosphatidic Acid. Endocrinology. 2004 Feb 26 [Epub ahead of print] [PubMed]
  13. Shimoji T, Kanda H, Kitagawa T, Kadota K, Asai R, Takahashi K, Kawaguchi N, Matsumoto S, Hayashizaki Y, Okazaki Y, Shinomiya K. Clinico-molecular study of dedifferentiation in well-differentiated liposarcoma. Biochem Biophys Res Commun. 2004 Feb 20;314(4):1133-40. [PubMed]
  14. Bertucci F, Salas S, Eysteries S, Nasser V, Finetti P, Ginestier C, Charafe-Jauffret E, Loriod B, Bachelart L, Montfort J, Victorero G, Viret F, Ollendorff V, Fert V, Giovaninni M, Delpero JR, Nguyen C, Viens P, Monges G, Birnbaum D, Houlgatte R. Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters. Oncogene. 2004 Feb 19;23(7):1377-91. [PubMed]
  15. Blalock EM, Geddes JW, Chen KC, Porter NM, Markesbery WR, Landfield PW. Incipient Alzheimer's disease: Microarray correlation analyses reveal major transcriptional and tumor suppressor responses. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):2173-8. [PubMed]
  16. Adib TR, Henderson S, Perrett C, Hewitt D, Bourmpoulia D, Ledermann J, Boshoff C. Predicting biomarkers for ovarian cancer using gene-expression microarrays. Br J Cancer. 2004 Feb 9;90(3):686-92. [PubMed]
  17. Nakamura T, Furukawa Y, Nakagawa H, Tsunoda T, Ohigashi H, Murata K, Ishikawa O, Ohgaki K, Kashimura N, Miyamoto M, Hirano S, Kondo S, Katoh H, Nakamura Y, Katagiri T. Genome-wide cDNA microarray analysis of gene expression profiles in pancreatic cancers using populations of tumor cells and normal ductal epithelial cells selected for purity by laser microdissection. Oncogene. 2004 Feb 9 [Epub ahead of print] [PubMed]
  18. Kobayashi K, Nishioka M, Kohno T, Nakamoto M, Maeshima A, Aoyagi K, Sasaki H, Takenoshita S, Sugimura H, Yokota J. Identification of genes whose expression is upregulated in lung adenocarcinoma cells in comparison with type II alveolar cells and bronchiolar epithelial cells in vivo. Oncogene. 2004 Feb 2 [Epub ahead of print] [PubMed]
  19. Gronert K, Kantarci A, Levy BD, Clish CB, Odparlik S, Hasturk H, Badwey JA, Colgan SP, Van Dyke TE, Serhan CN. A Molecular Defect in Intracellular Lipid Signaling in Human Neutrophils in Localized Aggressive Periodontal Tissue Damage. J Immunol. 2004 Feb 1; 172(3): 1856-1861. [PubMed]
  20. Kote-Jarai Z, Williams RD, Cattini N, Copeland M, Giddings I, Wooster R, TePoele RH, Workman P, Gusterson B, Peacock J, Gui G, Campbell C, Eeles R. Gene Expression Profiling after Radiation-Induced DNA Damage Is Strongly Predictive of BRCA1 Mutation Carrier Status. Clin Cancer Res. 2004 Feb 1;10(3):958-63.[PubMed]
  21. Amatschek S, Koenig U, Auer H, Steinlein P, Pacher M, Gruenfelder A, Dekan G, Vogl S, Kubista E, Heider KH, Stratowa C, Schreiber M, Sommergruber W. Tissue-wide expression profiling using cDNA subtraction and microarrays to identify tumor-specific genes. Cancer Res. 2004 Feb 1;64(3):844-56. [PubMed]
  22. Li M, Lin YM, Hasegawa S, Shimokawa T, Murata K, Kameyama M, Ishikawa O, Katagiri T, Tsunoda T, Nakamura Y, Furukawa Y. Genes associated with liver metastasis of colon cancer, identified by genome-wide cDNA microarray. Int J Oncol. 2004 Feb; 24(2): 305-12. [PubMed]
  23. Ferguson SE, Olshen AB, Viale A, Awtrey CS, Barakat RR, Boyd J. Gene expression profiling of tamoxifen-associated uterine cancers: evidence for two molecular classes of endometrial carcinoma. Gynecol Oncol. 2004 Feb;92(2):719-25.[PubMed]
  24. Kim JW, Ye Q, Forgues M, Chen Y, Budhu A, Sime J, Hofseth LJ, Kaul R, Wang XW. Cancer-associated molecular signature in the tissue samples of patients with cirrhosis. Hepatology. 2004 Feb;39(2):518-27. [PubMed]
  25. Yung CK, Halperin VL, Tomaselli GF, Winslow RL. Gene expression profiles in end-stage human idiopathic dilated cardiomyopathy: altered expression of apoptotic and cytoskeletal genes. Genomics. 2004 Feb;83(2):281-97. [PubMed]
  26. Hashimoto T, Lawton MT, Wen G, Yang GY, Chaly T JR, T, Stewart CL, Dressman HK, Barbaro NM, Marchuk DA, Young WL. Gene Microarray Analysis of Human Brain Arteriovenous Malformations. Neurosurgery. 2004 Feb;54(2):410-425. [PubMed]
  27. Leonard EE 2nd, Tompkins LS, Falkow S, Nachamkin I. Comparison of Campylobacter jejuni Isolates Implicated in Guillain-Barre Syndrome and Strains That Cause Enteritis by a DNA Microarray. Infect Immun. 2004 Feb;72(2):1199-203. [PubMed]
  28. Staber PB, Linkesch W, Zauner D, Beham-Schmid C, Guelly C, Schauer S, Sill H, Hoefler G. Common alterations in gene expression and increased proliferation in recurrent acute myeloid leukemia. Oncogene. 2004 Jan 29;23(4):894-904. [PubMed]
  29. Iwamoto K, Kakiuchi C, Bundo M, Ikeda K, Kato T. Molecular characterization of bipolar disorder by comparing gene expression profiles of postmortem brains of major mental disorders. Mol Psychiatry. 2004 Jan 26 [Epub ahead of print] [PubMed]
  30. Choi YL, Makishima H, Ohashi J, Yamashita Y, Ohki R, Koinuma K, Ota J, Isobe Y, Ishida F, Oshimi K, Mano H. DNA microarray analysis of natural killer cell-type lymphoproliferative disease of granular lymphocytes with purified CD3(-)CD56(+) fractions. Leukemia. 2004 Jan 22 [Epub ahead of print] [PubMed]
  31. Lapointe J, Li C, Higgins JP, Van De Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A. 2004 Jan 20; 101(3): 811-6. [PubMed]
  32. Mohr S, Keith G, Galateau-Salle F, Icard P, Rihn BH. Cell protection, resistance and invasiveness of two malignant mesotheliomas as assessed by 10K-microarray. Biochim Biophys Acta. 2004 Jan 20; 1688(1): 43-60. [PubMed]
  33. Samaco RC, Nagarajan RP, Braunschweig D, LaSalle JM. Multiple pathways regulate MeCP2 expression in normal brain development and exhibit defects in autism-spectrum disorders. Hum Mol Genet. 2004 Jan 20 [Epub ahead of print] [PubMed]
  34. Dangond F, Hwang D, Camelo S, Pasinelli P, Frosch MP, Stephanopoulos G, Stephanopoulos G, Brown RH Jr, Gullans SR. Molecular signature of late-stage human ALS revealed by expression profiling of postmortem spinal cord gray matter. Physiol Genomics. 2004 Jan 15; 16(2): 229-39. [PubMed]
  35. Stuart RO, Wachsman W, Berry CC, Wang-Rodriguez J, Wasserman L, Klacansky I, Masys D, Arden K, Goodison S, McClelland M, Wang Y, Sawyers A, Kalcheva I, Tarin D, Mercola D. In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2): 615-20. [PubMed][PDF]
  36. Ying SY, Lin SL. Gene expression in precursor cells of prostate cancer associated with activin by combination of subtractive hybridization and microarray technologies. Biochem Biophys Res Commun. 2004 Jan 2;313(1):104-9. [PubMed]
  37. Raza SM, Fuller GN, Rhee CH, Huang S, Hess K, Zhang W, Sawaya R. Identification of necrosis-associated genes in glioblastoma by cDNA microarray analysis. Clin Cancer Res. 2004 Jan 1; 10(1): 212-21. [PubMed]
  38. Ginos MA, Page GP, Michalowicz BS, Patel KJ, Volker SE, Pambuccian SE, Ondrey FG, Adams GL, Gaffney PM. Identification of a gene expression signature associated with recurrent disease in squamous cell carcinoma of the head and neck. Cancer Res. 2004 Jan 1;64(1):55-63. [PubMed]
  39. Bloom G, Yang IV, Boulware D, Kwong KY, Coppola D, Eschrich S, Quackenbush J, Yeatman TJ. Multi-Platform, Multi-Site, Microarray-Based Human Tumor Classification. Am J Pathol. 2004 Jan;164(1):9-16. [PubMed]
  40. Okabe H, Furukawa Y, Kato T, Hasegawa S, Yamaoka Y, Nakamura Y. Isolation of development and differentiation enhancing factor-like 1 (DDEFL1) as a drug target for hepatocellular carcinomas. Int J Oncol. 2004 Jan;24(1):43-8. [PubMed]
  41. Gomez-Ambrosi J, Catalan V, Diez-Caballero A, Martinez-Cruz LA, Gil MJ, Garcia-Foncillas J, Cienfuegos JA, Salvador J, Mato JM, Fruhbeck G. Gene expression profile of omental adipose tissue in human obesity. FASEB J. 2004 Jan; 18(1): 215-7. [PubMed]
  42. Tretiakova MS, Sahoo S, Takahashi M, Turkyilmaz M, Vogelzang NJ, Lin F, Krausz T, Teh BT, Yang XJ. Expression of Alpha-Methylacyl-CoA Racemase in Papillary Renal Cell Carcinoma. Am J Surg Pathol. 2004 Jan;28(1):69-76. [PubMed]
  43. Lancaster JM, Dressman HK, Whitaker RS, Havrilesky L, Gray J, Marks JR, Nevins JR, Berchuck A. Gene expression patterns that characterize advanced stage serous ovarian cancers. J Soc Gynecol Investig. 2004 Jan; 11(1): 51-9. [PubMed]
  44. Gomez-Ambrosi J, Catalan V, Diez-Caballero A, Martinez-Cruz LA, Gil MJ, Garcia-Foncillas J, Cienfuegos JA, Salvador J, Mato JM, Fruhbeck G. Gene expression profile of omental adipose tissue in human obesity. FASEB J. 2004 Jan;18(1):215-7. [PubMed]
  45. McDonald SL, Edington HD, Kirkwood JM, Becker D. Expression Analysis of Genes Identified by Molecular Profiling of VGP Melanomas and MGP Melanoma-Positive Lymph Nodes. Cancer Biol Ther. 2004 Jan [Epub ahead of print] [PubMed]

Diagnosis, prognosis and clinical applications

  1. Cleator S, Ashworth A. Molecular profiling of breast cancer: clinical implications. Br J Cancer. 2004 Mar 22;90(6):1120-4. [PubMed]
  2. Kalish JA, Willis DJ, Li C, Link JJ, Deutsch ER, Contreras MA, Quist WC, Logerfo FW. Temporal genomics of vein bypass grafting through oligonucleotide microarray analysis. J Vasc Surg. 2004 Mar;39(3):645-54.[PubMed]
  3. Nagahata T, Onda M, Emi M, Nagai H, Tsumagari K, Fujimoto T, Hirano A, Sato T, Nishikawa K, Akiyama F, Sakamoto G, Kasumi F, Miki Y, Tanaka T, Tsunoda T. Expression profiling to predict postoperative prognosis for estrogen receptor-negative breast cancers by analysis of 25,344 genes on a cDNA microarray. Cancer Sci. 2004 Mar;95(3):218-25. [PubMed]
  4. The Tumor Analysis Best Practices Working Group. Guidelines: Expression profiling - best practices for data generation and interpretation in clinical trials. Nat Rev Genet. 2004 Mar;5(3):229-237.  [PubMed]
  5. Fernandez-Teijeiro A, Betensky RA, Sturla LM, Kim JY, Tamayo P, Pomeroy SL. Combining Gene Expression Profiles and Clinical Parameters for Risk Stratification in Medulloblastomas. J Clin Oncol. 2004 Feb 17 [Epub ahead of print] [PubMed]
  6. Bueno R, Loughlin KR, Powell MH, Gordon GJ. A Diagnostic Test for Prostate Cancer From Gene Expression Profiling Data. J Urol. 2004 Feb; 171(2): 903-906. [PubMed]
  7. Gruvberger-Saal SK, Eden P, Ringner M, Baldetorp B, Chebil G, Borg A, Ferno M, Peterson C, Meltzer PS. Predicting continuous values of prognostic markers in breast cancer from microarray gene expression profiles. Mol Cancer Ther. 2004 Feb;3(2):161-8. [PubMed]
  8. Zhang HQ, Lu H, Enosawa S, Suzuki S, Takahara S, Nakajima T, Saito H, Sakamoto K. Comprehensive examination of gene expression associated with long-term stable graft acceptance by renal transplant recipients. Clin Transplant. 2004 Feb;18(1):70-8. [PubMed]
  9. Schwaenen C, Nessling M, Wessendorf S, Salvi T, Wrobel G, Radlwimmer B, Kestler HA, Haslinger C, Stilgenbauer S, Dohner H, Bentz M, Lichter P. Automated array-based genomic profiling in chronic lymphocytic leukemia: Development of a clinical tool and discovery of recurrent genomic alterations. Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):1039-44. [PubMed]
  10. Lotze MT, Rees RC. Identifying biomarkers and surrogates of tumors (cancer biometrics): correlation with immunotherapies and immune cells. Cancer Immunol Immunother. 2004 Jan 21 [Epub ahead of print] [PubMed]
  11. Salvado CS, Trounson AO, Cram DS. Towards preimplantation diagnosis of cystic fibrosis using microarrays. Reprod Biomed Online. 2004 Jan;8(1):107-14. [PubMed]
  12. Campbell CJ, Ghazal P. Molecular signatures for diagnosis of infection: application of microarray technology. J Appl Microbiol. 2004;96(1):18-23. [PubMed]
  13. Shimizu D, Ishikawa T, Ichikawa Y, Togo S, Hayasizaki Y, Okazaki Y, Shimada H. Current progress in the prediction of chemosensitivity for breast cancer. Breast Cancer. 2004; 11(1): 42-8. [PubMed]

Animal model studies

  1. Arlinde C, Sommer W, Bjork K, Reimers M, Hyytia P, Kiianmaa K, Heilig M. A cluster of differentially expressed signal transduction genes identified by microarray analysis in a rat genetic model of alcoholism. Pharmacogenomics J. 2004 Mar 30 [Epub ahead of print] [PubMed]
  2. Talaat AM, Lyons R, Howard ST, Johnston SA. The temporal expression profile of Mycobacterium tuberculosis infection in mice. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4602-7. [PubMed]
  3. Syder AJ, Karam SM, Mills JC, Ippolito JE, Ansari HR, Farook V, Gordon JI. A transgenic mouse model of metastatic carcinoma involving transdifferentiation of a gastric epithelial lineage progenitor to a neuroendocrine phenotype. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4471-6. [PubMed]
  4. Puskas LG, Nagy ZB, Giricz Z, Onody A, Csonka C, Kitajka K, Hackler L Jr, Zvara A, Ferdinandy P. Cholesterol diet-induced hyperlipidemia influences gene expression pattern of rat hearts: a DNA microarray study. FEBS Lett. 2004 Mar 26;562(1-3):99-104. [PubMed]
  5. Kim DJ, Akiyama TE, Harman FS, Burns AM, Shan W, Ward JM, Kennett MJ, Gonzalez FJ, Peters JM.  PPARbeta {(d)}-dependent regulation of ubiquitin C expression contributes to attenuation of skin carcinogenesis. J Biol Chem. 2004 Mar 19 [Epub ahead of print] [PubMed]
  6. Sadlier DM, Connolly SB, Kieran NE, Roxburgh S, Brazil DP, Kairaitis L, Wang Y, Harris DC, Doran P, Brady HR. Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin induced nephropathy. J Biol Chem. 2004 Mar 18 [Epub ahead of print] [PubMed]
  7. Nakatani N, Aburatani H, Nishimura K, Semba J, Yoshikawa T. Comprehensive expression analysis of a rat depression model. Pharmacogenomics J. 2004;4(2):114-26. [PubMed]
  8. Advani AS, Dressman HK, Quiroz M, Taylor GA, Pendergast AM. Elevated expression of a subset of interferon inducible genes in primary bone marrow cells expressing p185 Bcr-Abl versus p210 Bcr-Abl by DNA microarray analysis. Leuk Res. 2004 Mar;28(3):285-94. [PubMed]
  9. Grunblatt E, Hoyer S, Riederer P. Gene expression profile in streptozotocin rat model for sporadic Alzheimer's disease. J Neural Transm. 2004 Mar;111(3):367-86. [PubMed]
  10. Susztak K, Bottinger E, Novetsky A, Liang D, Zhu Y, Ciccone E, Wu D, Dunn S, McCue P, Sharma K. Molecular profiling of diabetic mouse kidney reveals novel genes linked to glomerular disease. Diabetes. 2004 Mar;53(3):784-94. [PubMed]
  11. Ding JH, Xu X, Yang D, Chu PH, Dalton ND, Ye Z, Yeakley JM, Cheng H, Xiao RP, Ross J, Chen J, Fu XD. Dilated cardiomyopathy caused by tissue-specific ablation of SC35 in the heart. EMBO J. 2004 Feb 25;23(4):885-96. [PubMed]
  12. Xu H, Lee SJ, Suzuki E, Dugan KD, Stoddard A, Li HS, Chodosh LA, Montell C. A lysosomal tetraspanin associated with retinal degeneration identified via a genome-wide screen. EMBO J. 2004 Feb 25;23(4):811-22.[PubMed]
  13. Sonna LA, Wenger CB, Flinn S, Sheldon HK, Sawka MN, Lilly CM. Exertional heat injury and gene expression changes: A DNA microarray analysis study. J Appl Physiol. 2004 Feb 20 [Epub ahead of print] [PubMed]
  14. Dasu MR, Cobb JP, Laramie JM, Chung TP, Spies M, Barrow RE. Gene expression profiles of livers from thermally injured rats. Gene. 2004 Feb 18;327:51-60. [PubMed]
  15. Solnick JV, Hansen LM, Salama NR, Boonjakuakul JK, Syvanen M. Modification of Helicobacter pylori outer membrane protein expression during experimental infection of rhesus macaques. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):2106-11. [PubMed]
  16. Pan JZ, Jornsten R, Hart RP. Screening anti-inflammatory compounds in injured spinal cord with microarrays: A comparison of bioinformatics analysis approaches. Physiol Genomics. 2004 Feb 17 [Epub ahead of print] [PubMed]
  17. Porter JD, Merriam AP, Leahy P, Gong B, Feuerman J, Cheng G, Khanna S. Temporal gene expression profiling of dystrophin-deficient (mdx) mouse diaphragm identifies conserved and muscle group-specific mechanisms in the pathogenesis of muscular dystrophy. Hum Mol Genet. 2004 Feb 1; 13(3): 257-69.[PubMed] [Supplementary Material]
  18. Kawahara N, Wang Y, Mukasa A, Furuya K, Shimizu T, Hamakubo T, Aburatani H, Kodama T, Kirino T. Genome-wide Gene Expression Analysis for Induced Ischemic Tolerance and Delayed Neuronal Death Following Transient Global Ischemia in Rats. J Cereb Blood Flow Metab. 2004 Feb;24(2):212-223. [PubMed]
  19. Deaciuc IV, Doherty DE, Burikhanov R, Lee EY, Stromberg AJ, Peng X, de Villiers WJ. Large-scale gene profiling of the liver in a mouse model of chronic, intragastric ethanol infusion. J Hepatol. 2004 Feb;40(2):219-27. [PubMed]
  20. Park JW, Taube C, Swasey C, Kodama T, Joetham A, Balhorn A, Takeda K, Miyahara N, Allen CB, Dakhama A, Kim SH, Dinarello CA, Gelfand EW. IL-1 Receptor Antagonist Attenuates Airway Hyperresponsiveness Following Exposure to Ozone. Am J Respir Cell Mol Biol. 2004 Jan 30 [Epub ahead of print] [PubMed]
  21. Norkina O, Kaur S, Ziemer D, De Lisle RC. Inflammation of the Cystic Fibrosis Mouse Small Intestine. Am J Physiol Gastrointest Liver Physiol. 2004 Jan 22 [Epub ahead of print] [PubMed]
  22. Okuda T, Sumiya T, Iwai N, Miyata T. Pyridoxine 5(')-phosphate oxidase is a candidate gene responsible for hypertension in Dahl-S rats. Biochem Biophys Res Commun. 2004 Jan 16;313(3):647-53. [PubMed]
  23. Prima V, Tennant M, Gorbatyuk OS, Muzyczka N, Scarpace PJ, Zolotukhin S. Differential Modulation of Energy Balance by Leptin, CNTF, and LIF Gene Delivery: Microarray DNA-chip Analysis of Gene Expression. Endocrinology. 2004 Jan 8 [Epub ahead of print] [PubMed]
  24. Clarke LL, Gawenis LR, Bradford EM, Judd LM, Boyle KT, Simpson JE, Shull GE, Tanabe H, Ouellette AJ, Franklin CL, Walker NM. Abnormal Paneth cell granule dissolution and compromised resistance to bacterial colonization in the intestine of CF mice. Am J Physiol Gastrointest Liver Physiol. 2004 Jan 8 [Epub ahead of print] [PubMed]
  25. Kruse JJ, Te Poele JA, Velds A, Kerkhoven RM, Boersma LJ, Russell NS, Stewart FA. Identification of Differentially Expressed Genes in Mouse Kidney after Irradiation using Microarray Analysis. Radiat Res. 2004 Jan;161(1):28-38. [PubMed]
  26. Politi K, Szabolcs M, Fisher P, Kljuic A, Ludwig T, Efstratiadis A. A Mouse Model of Uterine Leiomyosarcoma. Am J Pathol. 2004 Jan;164(1):325-336. [PubMed]
  27. Samuel S, Bernstein LR. Adhesion, migration, transcriptional, interferon-inducible, and other signaling molecules newly implicated in cancer susceptibility and resistance of JB6 cells by cDNA microarray analyses. Mol Carcinog. 2004 Jan;39(1):34-60. [PubMed]
  28. Thomas DM, Francescutti-Verbeem DM, Liu X, Kuhn DM. Identification of differentially regulated transcripts in mouse striatum following methamphetamine treatment - an oligonucleotide microarray approach. J Neurochem. 2004 Jan;88(2):380-93. [PubMed]
  29. Yu J, Mears AJ, Yoshida S, Farjo R, Carter TA, Ghosh D, Hero A, Barlow C, Swaroop A. From disease genes to cellular pathways: a progress report. Novartis Found Symp. 2004;255:147-60; discussion 160-4, 177-8. [PubMed]

In vitro studies

  1. Pavey S, Johansson P, Packer L, Taylor J, Stark M, Pollock PM, Walker GJ, Boyle GM, Harper U, Cozzi SJ, Hansen K, Yudt L, Schmidt C, Hersey P, Ellem KA, O'Rourke MG, Parsons PG, Meltzer P, Ringner M, Hayward NK. Microarray expression profiling in melanoma reveals a BRAF mutation signature. Oncogene. 2004 Mar 29 [Epub ahead of print][PubMed]
  2. Morrison J, Knoll K, Hessner MJ, Liang M. Effect of high glucose on gene expression in mesangial cells: Up-regulation of the thiol pathway is an adaptational response. Physiol Genomics. 2004 Mar 23 [Epub ahead of print] [PubMed]
  3. Daibata M, Matsuo Y, Machida H, Taguchi T, Ohtsuki Y, Taguchi H. Differential gene-expression profiling in the leukemia cell lines derived from indolent and aggressive phases of CD56+ T-cell large granular lymphocyte leukemia. Int J Cancer. 2004 Mar 1;108(6):845-51. [PubMed]
  4. Ordway JM, Williams K, Curran T. Transcription repression in oncogenic transformation: common targets of epigenetic repression in cells transformed by Fos, Ras or Dnmt1. Oncogene. 2004 Mar 1 [Epub ahead of print] [PubMed]
  5. Chatterji U, Riby JE, Taniguchi T, Bjeldanes EL, Bjeldanes LF, Firestone GL. Indole-3-carbinol stimulates transcription of the interferon gamma receptor 1 gene and augments interferon responsiveness in human breast cancer cells. Carcinogenesis. 2004 Feb 26 [Epub ahead of print] [PubMed]
  6. Hur J, Chesnes J, Coser KR, Lee RS, Geck P, Isselbacher KJ, Shioda T. The Bik BH3-only protein is induced in estrogen-starved and antiestrogen-exposed breast cancer cells and provokes apoptosis. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2351-6. [PubMed]
  7. Janket ML, Manickam P, Majumder B, Thotala D, Wagner M, Schafer EA, Collman RG, Srinivasan A, Ayyavoo V. Differential regulation of host cellular genes by HIV-1 viral protein R (Vpr): cDNA microarray analysis using isogenic virus. Biochem Biophys Res Commun. 2004 Feb 20;314(4):1126-32. [PubMed]
  8. Yanagawa T, Watanabe H, Takeuchi T, Fujimoto S, Kurihara H, Takagishi K. Overexpression of autocrine motility factor in metastatic tumor cells: possible association with augmented expression of KIF3A and GDI-beta. Lab Invest. 2004 Feb 16 [Epub ahead of print][PubMed]
  9. Abramovitch R, Tavor E, Jacob-Hirsch J, Zeira E, Amariglio N, Pappo O, Rechavi G, Galun E, Honigman A. A Pivotal Role of Cyclic AMP-Responsive Element Binding Protein in Tumor Progression. Cancer Res. 2004 Feb 15;64(4):1338-1346.[PubMed]
  10. Yu Y, Khan J, Khanna C, Helman L, Meltzer PS, Merlino G. Expression profiling identifies the cytoskeletal organizer ezrin and the developmental homeoprotein Six-1 as key metastatic regulators. Nat Med. 2004 Feb;10(2):175-81. [PubMed]
  11. Cui W, Bryant MR, Sweet PM, McDonnell PJ. Changes in gene expression in response to mechanical strain in human scleral fibroblasts. Exp Eye Res. 2004 Feb;78(2):275-84. [PubMed]
  12. Scott LA, Vass JK, Parkinson EK, Gillespie DA, Winnie JN, Ozanne BW.  Invasion of Normal Human Fibroblasts Induced by v-Fos Is Independent of Proliferation, Immortalization, and the Tumor Suppressors p16(INK4a) and p53. Mol Cell Biol. 2004 Feb;24(4):1540-59. [PubMed]
  13. Yang P, Agapova O, Parker A, Shannon W, Pecen P, Duncan J, Salvador-Silva M, Hernandez MR. DNA microarray analysis of gene expression in human optic nerve head astrocytes in response to hydrostatic pressure. Physiol Genomics. 2004 Jan 27 [Epub ahead of print] [PubMed]
  14. Mori K, Aoyagi K, Ueda T, Danjoh I, Tsubosa Y, Yanagihara K, Matsuno Y, Sasako M, Sakamoto H, Mafune K, Kaminishi M, Yoshida T, Terada M, Sasaki H. Highly specific marker genes for detecting minimal gastric cancer cells in cytology negative peritoneal washings. Biochem Biophys Res Commun. 2004 Jan 23; 313(4): 931-7. [PubMed]
  15. Treff NR, Pouchnik D, Dement GA, Britt RL, Reeves R. High-mobility group A1a protein regulates Ras/ERK signaling in MCF-7 human breast cancer cells. Oncogene. 2004 Jan 22; 23(3): 777-785. [PubMed]
  16. Mohr S, Keith G, Galateau-Salle F, Icard P, Rihn BH. Cell protection, resistance and invasiveness of two malignant mesotheliomas as assessed by 10K-microarray. Biochim Biophys Acta. 2004 Jan 20; 1688(1): 43-60. [PubMed]
  17. Kluger HM, Kluger Y, Gilmore-Hebert M, DiVito K, Chang JT, Rodov S, Mironenko O, Kacinski BM, Perkins AS, Sapi E. cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model. Lab Invest. 2004 Jan 19 [Epub ahead of print] [PubMed]
  18. Wright JM, Zeitlin PL, Cebotaru L, Guggino SE, Guggino WB. Gene expression profile analysis of 4-phenylbutyrate treatment of IB3-1 bronchial epithelial cell line demonstrates a major influence on heat-shock proteins. Physiol Genomics. 2004 Jan 15; 16(2): 204-11. [PubMed]
  19. Pierer M, Rethage J, Seibl R, Lauener R, Brentano F, Wagner U, Hantzschel H, Michel BA, Gay RE, Gay S, Kyburz D. Chemokine secretion of rheumatoid arthritis synovial fibroblasts stimulated by toll-like receptor 2 ligands. J Immunol. 2004 Jan 15;172(2):1256-65. [PubMed]
  20. Kang HC, Kim IJ, Park JH, Shin Y, Ku JL, Jung MS, Yoo BC, Kim HK, Park JG. Identification of genes with differential expression in acquired drug-resistant gastric cancer cells using high-density oligonucleotide microarrays. Clin Cancer Res. 2004 Jan 1; 10(1): 272-84. [PubMed]
  21. van Ginkel PR, Gee RL, Shearer RL, Subramanian L, Walker TM, Albert DM, Meisner LF, Varnum BC, Polans AS. Expression of the receptor tyrosine kinase Axl promotes ocular melanoma cell survival. Cancer Res. 2004 Jan 1;64(1):128-34. [PubMed]
  22. Naranatt PP, Krishnan HH, Svojanovsky SR, Bloomer C, Mathur S, Chandran B. Host gene induction and transcriptional reprogramming in Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8)-infected endothelial, fibroblast, and B cells: insights into modulation events early during infection. Cancer Res. 2004 Jan 1;64(1):72-84. [PubMed]
  23. Ray ME, Yang ZQ, Albertson D, Kleer CG, Washburn JG, Macoska JA, Ethier SP. Genomic and expression analysis of the 8p11-12 amplicon in human breast cancer cell lines. Cancer Res. 2004 Jan 1;64(1):40-7. [PubMed]
  24. Nightingale J, Patel S, Suzuki N, Buxton R, Takagi KI, Suzuki J, Sumi Y, Imaizumi A, Mason RM, Zhang Z. Oncostatin M, a Cytokine Released by Activated Mononuclear Cells, Induces Epithelial Cell-Myofibroblast Transdifferentiation via Jak/Stat Pathway Activation. J Am Soc Nephrol. 2004 Jan;15(1):21-32. [PubMed]
  25. Wang X, Li H, De Leo D, Guo W, Koshkin V, Fantus IG, Giacca A, Chan CB, Der S, Wheeler MB. Gene and Protein Kinase Expression Profiling of Reactive Oxygen Species-Associated Lipotoxicity in the Pancreatic beta-Cell Line MIN6. Diabetes. 2004 Jan;53(1):129-140. [PubMed]
  26. Bektic J, Wrulich OA, Dobler G, Kofler K, Ueberall F, Culig Z, Bartsch G, Klocker H. Identification of genes involved in estrogenic action in the human prostate using microarray analysis. Genomics. 2004 Jan;83(1):34-44.  [PubMed]
  27. Yamasaki R, Yokota K, Okada H, Hayashi S, Mizuno M, Yoshino T, Hirai Y, Saitou D, Akagi T, Oguma K. Immune response in Helicobacter pylori-induced low-grade gastric-mucosa-associated lymphoid tissue (MALT) lymphoma. J Med Microbiol. 2004 Jan;53(1):21-29. [PubMed]
  28. Chen HW, Yu SL, Chen JJ, Li HN, Lin YC, Yao PL, Chou HY, Chien CT, Chen WJ, Lee YT, Yang PC. Anti-invasive gene expression profile of curcumin in lung adenocarcinoma based on a high throughput microarray analysis. Mol Pharmacol. 2004 Jan; 65(1): 99-110. [PubMed]

Basic science studies

  1. Togo S, Makino H, Kobayashi T, Morita T, Shimizu T, Kubota T, Ichikawa Y, Ishikawa T, Okazaki Y, Hayashizaki Y, Shimada H. Mechanism of liver regeneration after partial hepatectomy using mouse cDNA microarray. J Hepatol. 2004 Mar;40(3):464-71. [PubMed]
  2. Anderssen RS, Wu Y, Dolferus R, Saunders I.  An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments. Bioinformatics. 2004 Feb 26 [Epub ahead of print] [PubMed]
  3. Klevecz RR, Bolen J, Forrest G, Murray DB. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1200-5. [PubMed]
  4. Hou P, Ji M, He N, Lu Z. Microarray-based method to evaluate the accuracy of restriction endonucleases HpaII and MspI. Biochem Biophys Res Commun. 2004 Jan 30; 314(1): 110-7. [PubMed]
  5. Qin X, Sarnow P. Preferential translation of IRES-containing mRNAs during the mitotic cycle in mammalian cells. J Biol Chem. 2004 Jan 21 [Epub ahead of print] [PubMed]
  6. Korke R, Gatti Mde L, Lau AL, Lim JW, Seow TK, Chung MC, Hu WS. Large scale gene expression profiling of metabolic shift of mammalian cells in culture. J Biotechnol. 2004 Jan 8;107(1):1-17. [PubMed]
  7. Hurowitz EH, Brown PO. Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol. 2003;5(1):R2. [PubMed]
  8. Amundson SA, Fornace AJ Jr. Microarray approaches for analysis of cell cycle regulatory genes. Methods Mol Biol. 2004;241:125-41. [PubMed]
  9. Gribble SM, Fiegler H, Burford DC, Prigmore E, Yang F, Carr P, Ng BL, Sun T, Kamberov ES, Makarov VL, Langmore JP, Carter NP. Applications of combined DNA microarray and chromosome sorting technologies. Chromosome Res. 2004;12(1):35-43. [PubMed]
  10. Leonard MO, O'Reilly S, Comerford KM, Taylor CT. Identification of cyclic AMP response element-binding protein-dependent transcriptional responses in hypoxia by microarray analysis. Methods Enzymol. 2004;381:511-24. [PubMed]

Gene product function

  1. Keen HL, Ryan MJ, Beyer A, Mathur S, Scheetz TE, Gackle BD, Faraci FM, Casavant TL, Sigmund CD. GENE EXPRESSION PROFILING OF POTENTIAL PPAR{gamma} TARGET GENES IN MOUSE AORTA. Physiol Genomics. 2004 Mar 30 [Epub ahead of print] [PubMed]
  2. Uesaka T, Kageyama N, Watanabe H. Identifying target genes regulated downstream of cdx2 by microarray analysis. J Mol Biol. 2004 Mar 26;337(3):647-60. [PubMed]
  3. Alimardani P, Regnacq M, Moreau-Vauzelle C, Ferreira T, Rossignol T, Blondin B, Berges T. SUT1-promoted sterol uptake involves the ABC transporter Aus1 and the mannoprotein Dan1 whose synergistic action is sufficient for this process. Biochem J. 2004 Mar 22 [Epub ahead of print] [PubMed]
  4. Zhao H, Jhanwar-Uniyal M, Datta PK, Yemul S, Ho L, Khitrov G, Kupershmidt I, Pasinetti GM, Ray T, Athwal RS, Achary MP. Expression profile of genes associated with antimetastatic gene: nm23-Mediated metastasis inhibition in breast carcinoma cells. Int J Cancer. 2004 Mar 10; 109(1): 65-70. [PubMed]
  5. Palliser D, Huang Q, Hacohen N, Lamontagne SP, Guillen E, Young RA, Eisen HN. A role for toll-like receptor 4 in dendritic cell activation and cytolytic CD8(+) T cell differentiation in response to a recombinant heat shock fusion protein. J Immunol. 2004 Mar 1;172(5):2885-93. [PubMed]
  6. Albrecht EA, Chinnaiyan AM, Varambally S, Kumar-Sinha C, Barrette TR, Sarma JV, Ward PA. C5a-induced gene expression in human umbilical vein endothelial cells. Am J Pathol. 2004 Mar;164(3):849-59. [PubMed]
  7. Chen WV, Delrow J, Corrin PD, Frazier JP, Soriano P. Identification and validation of PDGF transcriptional targets by microarray-coupled gene-trap mutagenesis. Nat Genet. 2004 Mar;36(3):304-312. [PubMed]
  8. Kulkarni RN, Kahn CR. Molecular biology. HNFs--linking the liver and pancreatic islets in diabetes. Science. 2004 Feb 27;303(5662):1311-2. [PubMed]
  9. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA. Control of pancreas and liver gene expression by HNF transcription factors. Science. 2004 Feb 27;303(5662):1378-81.[PubMed]
  10. Kravets A, Hu Z, Miralem T, Torno MD, Maines MD. Biliverdin reductase: A novel regulator for Induction of activating transcription factor-2 and heme oxygenase-1. J Biol Chem. 2004 Feb 25 [Epub ahead of print] [PubMed]
    11. <>
  11. Shibayama H, Takai E, Matsumura I, Kouno M, Morii E, Kitamura Y, Takeda J, Kanakura Y. Identification of a Cytokine-induced Antiapoptotic Molecule Anamorsin Essential for Definitive Hematopoiesis. J Exp Med. 2004 Feb 16;199(4):581-92. [PubMed]
  12. Abramovitch R, Tavor E, Jacob-Hirsch J, Zeira E, Amariglio N, Pappo O, Rechavi G, Galun E, Honigman A. A Pivotal Role of Cyclic AMP-Responsive Element Binding Protein in Tumor Progression. Cancer Res. 2004 Feb 15;64(4):1338-1346.[PubMed]
  13. Meyer-Kirchrath J, Debey S, Glandorff C, Kirchrath L, Schror K. Gene expression profile of the Gs-coupled prostacyclin receptor in human vascular smooth muscle cells. Biochem Pharmacol. 2004 Feb 15;67(4):757-65. [PubMed]
  14. Kassed CA, Butler TL, Patton GW, De Mesquita DD, Navidomskis MT, Memet S, Israel A, Pennypacker KR. Injury-induced NF-kappaB activation in the hippocampus: implications for neuronal survival. FASEB J. 2004 Feb 6 [Epub ahead of print][PubMed]
  15. Brodsky MH, Weinert BT, Tsang G, Rong YS, McGinnis NM, Golic KG, Rio DC, Rubin GM. Drosophila melanogaster MNK/Chk2 and p53 regulate multiple DNA repair and apoptotic pathways following DNA damage. Mol Cell Biol. 2004 Feb;24(3):1219-31. [PubMed]
  16. Treff NR, Pouchnik D, Dement GA, Britt RL, Reeves R. High-mobility group A1a protein regulates Ras/ERK signaling in MCF-7 human breast cancer cells. Oncogene. 2004 Jan 22; 23(3): 777-785. [PubMed]
  17. Joo A, Aburatani H, Morii E, Iba H, Yoshimura A. STAT3 and MITF cooperatively induce cellular transformation through upregulation of c-fos expression. Oncogene. 2004 Jan 22; 23(3): 726-734. [PubMed]
  18. De Nadal E, Zapater M, Alepuz PM, Sumoy L, Mas G, Posas F. The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature. 2004 Jan 22;427(6972):370-4. [PubMed]
  19. Cortes-Canteli M, Wagner M, Ansorge W, Perez-Castillo A. Microarray analysis supports a role for CCAAT/enhancer binding protein beta in brain injury. J Biol Chem. 2004 Jan 21 [Epub ahead of print] [PubMed]
  20. Zeisig BB, Milne T, Garcia-Cuellar MP, Schreiner S, Martin ME, Fuchs U, Borkhardt A, Chanda SK, Walker J, Soden R, Hess JL, Slany RK. Hoxa9 and Meis1 Are Key Targets for MLL-ENL-Mediated Cellular Immortalization. Mol Cell Biol. 2004 Jan 15;24(2):617-628. [PubMed]
  21. Ziegelbauer J, Wei J, Tjian R. Myc-interacting protein 1 target gene profile: A link to microtubules, extracellular signal-regulated kinase, and cell growth. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2): 458-63. [PubMed]
  22. Inada M, Guthrie C. Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2): 434-9. [PubMed]
  23. Voz ML, Mathys J, Hensen K, Pendeville H, Van Valckenborgh I, Van Huffel C, Chavez M, Van Damme B, De Moor B, Moreau Y, Van De Ven WJ. Microarray screening for target genes of the proto-oncogene PLAG1. Oncogene. 2004 Jan 8;23(1):179-191. [PubMed]
  24. Fisher RC, Slayton WB, Chien C, Guthrie SM, Bray C, Scott EW. PU.1 supports proliferation of immature erythroid progenitors. Leuk Res. 2004 Jan;28(1):83-9. [PubMed]
  25. Hendricks KB, Shanahan F, Lees E. Role for BRG1 in Cell Cycle Control and Tumor Suppression. Mol Cell Biol. 2004 Jan;24(1):362-76. [PubMed]
  26. Zhukovskaya NV, Fukuzawa M, Tsujioka M, Jermyn KA, Kawata T, Abe T, Zvelebil M, Williams JG. Dd-STATb, a Dictyostelium STAT protein with a highly aberrant SH2 domain, functions as a regulator of gene expression during growth and early development. Development. 2004 Jan;131(2):447-458. [PubMed]
  27. Ermak G, Cheadle C, Becker KG, Harris CD, Davies KJ. DSCR1(Adapt78) modulates expression of SOD1. FASEB J. 2004 Jan; 18(1): 62-9. [PubMed]
  28. Bunai K, Ariga M, Inoue T, Nozaki M, Ogane S, Kakeshita H, Nemoto T, Nakanishi H, Yamane K. Profiling and comprehensive expression analysis of ABC transporter solute-binding proteins of Bacillus subtilis membrane based on a proteomic approach. Electrophoresis. 2004 Jan;25(1):141-55. [PubMed]
  29. Gu K, Zhang L, Jin T, Rutherford RB. Identification of Potential Modifiers of Runx2/Cbfa1 Activity in C2C12 Cells in Response to Bone Morphogenetic Protein-7. Cells Tissues Organs. 2004;176(1-3):28-40. [PubMed]

General physiology

  1. Taylor KR, Trowbridge JM, Rudisill JA, Termeer CC, Simon JC, Gallo RL. Hyaluronan fragments stimulate dermal endothelial recognition of injury through TLR4. J Biol Chem. 2004 Feb 5 [Epub ahead of print] [PubMed]
  2. Unami A, Shinohara Y, Kajimoto K, Baba Y. Comparison of gene expression profiles between white and brown adipose tissues of rat by microarray analysis. Biochem Pharmacol. 2004 Feb 1;67(3):555-64. [PubMed]
  3. Cheng RY, Birely LA, Lum NL, Perella CM, Cherry JM, Bhat NK, Kasprzak KS, Powell DA, Alvord WG, Anderson LM. Expressions of hepatic genes, especially IGF-binding protein-1, correlating with serum corticosterone in microarray analysis. J Mol Endocrinol. 2004 Feb;32(1):257-78. [PubMed]
  4. Bohn E, Muller S, Lauber J, Geffers R, Speer N, Spieth C, Krejci J, Manncke B, Buer J, Zell A, Autenrieth IB. Gene expression patterns of epithelial cells modulated by pathogenicity factors of Yersinia enterocolitica. Cell Microbiol. 2004 Feb; 6(2): 129-141. [PubMed]
  5. Seta KA, Millhorn DE. Functional genomics approach to hypoxia signaling. J Appl Physiol. 2004 Feb; 96(2): 765-73. [PubMed]
  6. Maglova LM, Crowe WE, Russell JM. Perinuclear localization of Na,K,Cl cotransporter protein after human cytomegalovirus infection. Am J Physiol Cell Physiol. 2004 Jan 28 [Epub ahead of print] [PubMed]
  7. Herath CB, Shiojima S, Ishiwata H, Katsuma S, Kadowaki T, Ushizawa K, Imai K, Takahashi T, Hirasawa A, Tsujimoto G, Hashizume K. Pregnancy-associated changes in genome-wide gene expression profiles in the liver of cow throughout pregnancy. Biochem Biophys Res Commun. 2004 Jan 16;313(3):666-80. [PubMed]
  8. Wong MS, Raab RM, Rigoutsos I, Stephanopoulos GN, Kelleher JK. Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks. Physiol Genomics. 2004 Jan 15; 16(2): 247-55. [PubMed]
  9. Tollet-Egnell P, Parini P, Stahlberg N, Lonnstedt I, Lee NH, Rudling M, Flores-Morales A, Norstedt G. Growth hormone-mediated alteration of fuel metabolism in the aged rat as determined from transcript profiles. Physiol Genomics. 2004 Jan 15; 16(2): 261-7. [PubMed]
  10. Szczesna-Skorupa E, Chen CD, Liu H, Kemper B. Gene expression changes associated with the endoplasmic reticulum stress response induced by microsomal cytochrome P450 overproduction. J Biol Chem. 2004 Jan 12 [Epub ahead of print] [PubMed]
  11. Liang M, Cowley AW, Greene AS. High throughput gene expression profiling: a molecular approach to integrative physiology. J Physiol. 2004 Jan 1;554(Pt 1):22-30. [PubMed]
  12. Hummasti S, Laffitte BA, Watson MA, Galardi C, Chao LC, Ramamurthy L, Moore JT, Tontonoz P. Liver X receptors are regulators of adipocyte gene expression but not differentiation. Identification of apoD as a direct target. J Lipid Res. 2004 Jan 1 [Epub ahead of print] [PubMed]
  13. Anderle P, Huang Y, Sadee W. Intestinal membrane transport of drugs and nutrients: genomics of membrane transporters using expression microarrays. Eur J Pharm Sci. 2004 Jan; 21(1): 17-24. [PubMed]
  14. Kindermann B, Doring F, Pfaffl M, Daniel H. Identification of Genes Responsive to Intracellular Zinc Depletion in the Human Colon Adenocarcinoma Cell Line HT-29. J Nutr. 2004 Jan; 134(1): 57-62. [PubMed]
  15. Argyropoulos C, Nikiforidis GC, Theodoropoulou M, Adamopoulos P, Boubali S, Georgakopoulos TN, Paliogianni F, Papavassiliou AG, Mouzaki A. Mining microarray data to identify transcription factors expressed in naive resting but not activated T lymphocytes. Genes Immun. 2004 Jan; 5(1): 16-25. [PubMed]

Development & differentiation

  1. Burton GR, Nagarajan R, Peterson CA, McGehee RE Jr. Microarray analysis of differentiation-specific gene expression during 3T3-L1 adipogenesis. Gene. 2004 Mar 31;329:167-85. [PubMed]
  2. Lin Q, Inselman A, Han X, Xu H, Zhang W, Handel MA, Skoultchi AI. Reductions in linker histone levels are tolerated in developing spermatocytes but cause changes in specific gene expression. J Biol Chem. 2004 Mar 23 [Epub ahead of print] [PubMed]
  3. Cheng YH, Aronow BJ, Hossain S, Trapnell B, Kong S, Handwerger S. Critical role for transcription factor AP-2' in human trophoblast differentiation. Physiol Genomics. 2004 Mar 23 [Epub ahead of print] [PubMed]
  4. Samaco RC, Nagarajan RP, Braunschweig D, LaSalle JM. Multiple pathways regulate MeCP2 expression in normal brain development and exhibit defects in autism-spectrum disorders. Hum Mol Genet. 2004 Mar 15;13(6):629-39. [PubMed]
  5. Musatov S, Roberts J, Brooks AI, Pena J, Betchen S, Pfaff DW, Kaplitt MG. Inhibition of neuronal phenotype by PTEN in PC12 cells. Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3627-31. [PubMed]
  6. Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 2004;5(3):R13.[PubMed]
  7. Dorrell MI, Aguilar E, Weber C, Friedlander M. Global gene expression analysis of the developing postnatal mouse retina. Invest Ophthalmol Vis Sci. 2004 Mar;45(3):1009-19. [PubMed]
  8. Mu X, Beremand PD, Zhao S, Pershad R, Sun H, Scarpa A, Liang S, Thomas TL, Klein WH. Discrete gene sets depend on POU domain transcription factor Brn3b/Brn-3.2/POU4f2 for their expression in the mouse embryonic retina. Development. 2004 Feb 18 [Epub ahead of print][PubMed]
  9. Hedlund E, Karsten SL, Kudo L, Geschwind DH, Carpenter EM. Identification of a Hoxd10-regulated transcriptional network and combinatorial interactions with Hoxa10 during spinal cord development. J Neurosci Res. 2004 Feb 1;75(3):307-19. [PubMed]
  10. Dickmeis T, Plessy C, Rastegar S, Aanstad P, Herwig R, Chalmel F, Fischer N, Strahle U. Expression Profiling and Comparative Genomics Identify a Conserved Regulatory Region Controlling Midline Expression in the Zebrafish Embryo. Genome Res. 2004 Feb;14(2):228-38. [PubMed]
  11. Schnable PS, Hochholdinger F, Nakazono M. Global expression profiling applied to plant development. Curr Opin Plant Biol. 2004 Feb;7(1):50-6. [PubMed]
  12. Dickmeis T, Plessy C, Rastegar S, Aanstad P, Herwig R, Chalmel F, Fischer N, Strahle U. Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo. Genome Res. 2004 Feb;14(2):228-38. [PubMed][Supplemental Research Data] 
  13. Wesolowski SR, Raney NE, Ernst CW. Developmental changes in the fetal pig transcriptome. Physiol Genomics. 2004 Jan 15; 16(2): 268-74. [PubMed]
  14. Maratou K, Forster T, Costa Y, Taggart M, Speed RM, Ireland J, Teague P, Roy D, Cooke HJ. Expression profiling of the developing testis in wild-type and Dazl knockout mice. Mol Reprod Dev. 2004 Jan;67(1):26-54. [PubMed]
  15. Fisher RC, Slayton WB, Chien C, Guthrie SM, Bray C, Scott EW. PU.1 supports proliferation of immature erythroid progenitors. Leuk Res. 2004 Jan;28(1):83-9. [PubMed]
  16. Zhukovskaya NV, Fukuzawa M, Tsujioka M, Jermyn KA, Kawata T, Abe T, Zvelebil M, Williams JG. Dd-STATb, a Dictyostelium STAT protein with a highly aberrant SH2 domain, functions as a regulator of gene expression during growth and early development. Development. 2004 Jan;131(2):447-458. [PubMed]
  17. Burton GR, McGehee RE. Identification of candidate genes involved in the regulation of adipocyte differentiation using microarray-based gene expression profiling. Nutrition. 2004 Jan;20(1):109-114. [PubMed]

Neurobiology

  1. Piedras-Renteria ES, Pyle JL, Diehn M, Glickfeld LL, Harata NC, Cao Y, Kavalali ET, Brown PO, Tsien RW. Presynaptic homeostasis at CNS nerve terminals compensates for lack of a key Ca2+ entry pathway. P Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3609-14.  [PubMed]
  2. Musatov S, Roberts J, Brooks AI, Pena J, Betchen S, Pfaff DW, Kaplitt MG. Inhibition of neuronal phenotype by PTEN in PC12 cells. Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3627-31. [PubMed]
  3. Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 2004;5(3):R13.[PubMed]
  4. Dorrell MI, Aguilar E, Weber C, Friedlander M. Global gene expression analysis of the developing postnatal mouse retina. Invest Ophthalmol Vis Sci. 2004 Mar;45(3):1009-19. [PubMed]
  5. Yao WD, Gainetdinov RR, Arbuckle MI, Sotnikova TD, Cyr M, Beaulieu JM, Torres GE, Grant SG, Caron MG. Identification of PSD-95 as a Regulator of Dopamine-Mediated Synaptic and Behavioral Plasticity. Neuron. 2004 Feb 19;41(4):625-38. [PubMed]
  6. Hong SJ, Li H, Becker KG, Dawson VL, Dawson TM.  Identification and analysis of plasticity-induced late-response genes. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):2145-50. [PubMed]
  7. Bragin A, Karsten SL, Almajano J, Wilson CL, Geschwind DH, Engel J. Large-scale microarray gene expression analysis in discrete electrophysiologically identified neuronal clusters. J Neurosci Methods. 2004 Feb 15;133(1-2):49-55.  [PubMed]
  8. Gan L, Ye S, Chu A, Anton K, Yi S, Vincent VA, Von Schack D, Chin D, Murray J, Lohr S, Patthy L, Gonzalez-Zulueta M, Nikolich K, Urfer R. Identification of Cathepsin B as a Mediator of Neuronal Death Induced by A{beta}-activated Microglial Cells Using a Functional Genomics Approach. J Biol Chem. 2004 Feb 13;279(7):5565-5572. [PubMed]
  9. Wang CC, Kadota M, Nishigaki R, Kazuki Y, Shirayoshi Y, Rogers MS, Gojobori T, Ikeo K, Oshimura M. Molecular hierarchy in neurons differentiated from mouse ES cells containing a single human chromosome 21. Biochem Biophys Res Commun. 2004 Feb 6;314(2):335-50. [PubMed]
  10. Kassed CA, Butler TL, Patton GW, De Mesquita DD, Navidomskis MT, Memet S, Israel A, Pennypacker KR. Injury-induced NF-kappaB activation in the hippocampus: implications for neuronal survival. FASEB J. 2004 Feb 6 [Epub ahead of print][PubMed]
  11. Konu O, Xu X, Ma JZ, Kane J, Wang J, Shi SJ, Li MD. Application of a customized pathway-focused microarray for gene expression profiling of cellular homeostasis upon exposure to nicotine in PC12 cells. Brain Res Mol Brain Res. 2004 Feb 5;121(1-2):102-13. [PubMed]
  12. Kraft AD, Johnson DA, Johnson JA. Nuclear factor E2-related factor 2-dependent antioxidant response element activation by tert-butylhydroquinone and sulforaphane occurring preferentially in astrocytes conditions neurons against oxidative insult. J Neurosci. 2004 Feb 4;24(5):1101-12. [PubMed]
  13. Del Signore A, Mandillo S, Rizzo A, Di Mauro E, Mele A, Negri R, Oliverio A, Paggi P. Hippocampal gene expression is modulated by hypergravity. Eur J Neurosci. 2004 Feb;19(3):667-77. [PubMed]
  14. Parrish ML, Wei N, Duenwald S, Tokiwa GY, Wang Y, Holder D, Dai H, Zhang X, Wright C, Hodor P, Cavet G, Phillips RL, Sun BI, Fare TL. A microarray platform comparison for neuroscience applications. J Neurosci Methods. 2004 Jan 15;132(1):57-68. [PubMed]
  15. Cai J, Cheng A, Luo Y, Lu C, Mattson MP, Rao MS, Furukawa K. Membrane properties of rat embryonic multipotent neural stem cells. J Neurochem. 2004 Jan;88(1):212-26. [PubMed]
  16. Gohil K, Chakraborty AA. Applications of microarray and bioinformatics tools to dissect molecular responses of the central nervous system to antioxidant micronutrients. Nutrition. 2004 Jan;20(1):50-55. [PubMed]
  17. Carmel JB, Kakinohana O, Mestril R, Young W, Marsala M, Hart RP. Mediators of ischemic preconditioning identified by microarray analysis of rat spinal cord. Exp Neurol. 2004 Jan;185(1):81-96. [PubMed]

Signal transduction

  1. Kravets A, Hu Z, Miralem T, Torno MD, Maines MD. Biliverdin reductase: A novel regulator for Induction of activating transcription factor-2 and heme oxygenase-1. J Biol Chem. 2004 Feb 25 [Epub ahead of print] [PubMed]
  2. Ijichi H, Otsuka M, Tateishi K, Ikenoue T, Kawakami T, Kanai F, Arakawa Y, Seki N, Shimizu K, Miyazono K, Kawabe T, Omata M. Smad4-independent regulation of p21/WAF1 by transforming growth factor-beta. Oncogene. 2004 Feb 5;23(5):1043-51. [PubMed]
  3. Pierer M, Rethage J, Seibl R, Lauener R, Brentano F, Wagner U, Hantzschel H, Michel BA, Gay RE, Gay S, Kyburz D. Chemokine secretion of rheumatoid arthritis synovial fibroblasts stimulated by toll-like receptor 2 ligands. J Immunol. 2004 Jan 15;172(2):1256-65. [PubMed]
  4. Kapoun AM, Liang F, O'Young G, Damm DL, Quon D, White RT, Munson K, Lam A, Schreiner GF, Protter AA. B-Type Natriuretic Peptide Exerts Broad Functional Opposition to Transforming Growth Factor-{beta} in Primary Human Cardiac Fibroblasts. Fibrosis, Myofibroblast Conversion, Proliferation, and Inflammation. Circ Res. 2004 Jan 15 [Epub ahead of print] [PubMed]
  5. Lai KO, Chen Y, Po HM, Lok KC, Gong K, Ip NY. Identification of the Jak/Stat proteins as novel downstream targets of EphA4 signaling in muscle: Implications in the regulation of acetylcholinesterase expression. J Biol Chem. 2004 Jan 15 [Epub ahead of print] [PubMed]
  6. White SL, Gharbi S, Bertani MF, Chan HL, Waterfield MD, Timms JF. Cellular responses to ErbB-2 overexpression in human mammary luminal epithelial cells: comparison of mRNA and protein expression. Br J Cancer. 2004 Jan 12;90(1):173-81. [PubMed]

Apoptosis

  1. Csiszar A, Ungvari Z, Koller A, Edwards JG, Kaley G. Proinflammatory phenotype of coronary arteries promotes endothelial apoptosis in aging. Physiol Genomics. 2004 Mar 12;17(1):21-30. [PubMed]
  2. Shibayama H, Takai E, Matsumura I, Kouno M, Morii E, Kitamura Y, Takeda J, Kanakura Y. Identification of a Cytokine-induced Antiapoptotic Molecule Anamorsin Essential for Definitive Hematopoiesis. J Exp Med. 2004 Feb 16;199(4):581-92. [PubMed]
  3. Thompson HJ, Zhu Z, Jiang W. Identification of the apoptosis activation cascade induced in mammary carcinomas by energy restriction. Cancer Res. 2004 Feb 15;64(4):1541-5.[PubMed]
  4. Gan L, Ye S, Chu A, Anton K, Yi S, Vincent VA, Von Schack D, Chin D, Murray J, Lohr S, Patthy L, Gonzalez-Zulueta M, Nikolich K, Urfer R. Identification of Cathepsin B as a Mediator of Neuronal Death Induced by A{beta}-activated Microglial Cells Using a Functional Genomics Approach. J Biol Chem. 2004 Feb 13;279(7):5565-5572. [PubMed]
  5. Bai L, Yoon SO, King PD, Merchant JL. ZBP-89-induced apoptosis is p53-independent and requires JNK. Cell Death Differ. 2004 Feb 13 [Epub ahead of print][PubMed]
  6. Brodsky MH, Weinert BT, Tsang G, Rong YS, McGinnis NM, Golic KG, Rio DC, Rubin GM. Drosophila melanogaster MNK/Chk2 and p53 regulate multiple DNA repair and apoptotic pathways following DNA damage. Mol Cell Biol. 2004 Feb;24(3):1219-31. [PubMed]
  7. Ogawa K, Yasumura S, Atarashi Y, Minemura M, Miyazaki T, Iwamoto M, Higuchi K, Watanabe A. Sodium butyrate enhances Fas-mediated apoptosis of human hepatoma cells. J Hepatol. 2004 Feb;40(2):278-84. [PubMed]
  8. Johnson NA, Sengupta S, Saidi SA, Lessan K, Charnock-Jones SD, Scott L, Stephens R, Freeman TC, Tom BD, Harris M, Denyer G, Sundaram M, Sasisekharan R, Smith SK, Print CG. Endothelial cells preparing to die by apoptosis initiate a program of transcriptome and glycome regulation. FASEB J. 2004 Jan;18(1):188-90. [PubMed]

Human

  1. Young TL, Scavello GS, Paluru PC, Choi JD, Rappaport EF, Rada JA. Microarray analysis of gene expression in human donor sclera. Mol Vis. 2004 Mar 22;10:163-76. [PubMed]
  2. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR. Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22. Genome Res. 2004 Mar;14(3):331-42. [PubMed]
  3. Bermudez MG, Wells D, Malter H, Munne S, Cohen J, Steuerwald NM. Expression profiles of individual human oocytes using microarray technology. Reprod Biomed Online. 2004 Mar;8(3):325-37. [PubMed]
  4. Higgins JP, Wang L, Kambham N, Montgomery K, Mason V, Vogelmann SU, Lemley KV, Brown PO, Brooks JD, Van De Rijn M. Gene expression in the normal adult human kidney assessed by complementary DNA microarray. Mol Biol Cell. 2004 Feb;15(2):649-56. [PubMed]
  5. Carpenter MK, Rosler ES, Fisk GJ, Brandenberger R, Ares X, Miura T, Lucero M, Rao MS. Properties of four human embryonic stem cell lines maintained in a feeder-free culture system. Dev Dyn. 2004 Feb;229(2):243-58. [PubMed]
  6. Emerson JJ, Kaessmann H, Betran E, Long M. Extensive gene traffic on the mammalian X chromosome. Science. 2004 Jan 23;303(5657):537-40. [PubMed]
  7. Sanoudou D, Kang PB, Haslett JN, Han M, Kunkel LM, Beggs AH. Transcriptional profile of postmortem skeletal muscle. Physiol Genomics. 2004 Jan 15; 16(2): 222-8. [PubMed][Supplemental Data for: The transcriptional profile of postmortem skeletal muscle]

Animal

  1. Rawls JF, Samuel BS, Gordon JI. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4596-601. [PubMed]
  2. Rise ML, Von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SR, Smailus DE, Jones SJ, Schein JE, Marra MA, Butterfield YS, Stott JM, Ng SH, Davidson WS, Koop BF. Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics. Genome Res. 2004 Mar;14(3):478-90.  [PubMed]
  3. Kodzius R, Matsumura Y, Kasukawa T, Shimokawa K, Fukuda S, Shiraki T, Nakamura M, Arakawa T, Sasaki D, Kawai J, Harbers M, Carninci P, Hayashizaki Y. Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags. FEBS Lett. 2004 Feb 13;559(1-3):22-6. [PubMed]
  4. Jones KL, King SS, Iqbal MJ. Endophyte-infected tall fescue diet alters gene expression in heifer luteal tissue as revealed by interspecies microarray analysis. Mol Reprod Dev. 2004 Feb;67(2):154-61. [PubMed]
  5. Johnson EC, Bohn LM, Taghert PH. Drosophila CG8422 encodes a functional diuretic hormone receptor. J Exp Biol. 2004 Feb 15;207(Pt 5):743-8. [PubMed]
  6. Madsen SA, Chang LC, Hickey MC, Rosa GJ, Coussens PM, Burton JL. Microarray analysis of gene expression in blood neutrophils of parturient cows. Physiol Genomics. 2004 Jan 15; 16(2): 212-21. [PubMed]
  7. Nikawa T, Ishidoh K, Hirasaka K, Ishihara I, Ikemoto M, Kano M, Kominami E, Nonaka I, Ogawa T, Adams GR, Baldwin KM, Yasui N, Kishi K, Takeda S. Skeletal muscle gene expression in space-flown rats. FASEB J. 2004 Jan 8 [Epub ahead of print] [PubMed]
  8. Gladney CD, Bertani GR, Johnson RK, Pomp D. Evaluation of gene expression in pigs selected for enhanced reproduction using differential display PCR and human microarrays: I. Ovarian follicles. J Anim Sci. 2004 Jan;82(1):17-31. [PubMed]
  9. Hild M, Beckmann B, Haas S, Koch B, Solovyev V, Busold C, Fellenberg K, Boutros M, Vingron M, Sauer F, Hoheisel J, Paro R. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol. 2003;5(1):R3. [PubMed]

Plant

  1. Yokoyama R, Rose JK, Nishitani K. A Surprising Diversity and Abundance of Xyloglucan Endotransglucosylase/Hydrolases in Rice. Classification and Expression Analysis. Plant Physiol. 2004 Feb 26 [Epub ahead of print][PubMed]
  2. Ohgishi M, Saji K, Okada K, Sakai T. Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in Arabidopsis. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2223-8.  [PubMed]
  3. Leonhardt N, Kwak JM, Robert N, Waner D, Leonhardt G, Schroeder JI. Microarray Expression Analyses of Arabidopsis Guard Cells and Isolation of a Recessive Abscisic Acid Hypersensitive Protein Phosphatase 2C Mutant. Plant Cell. 2004 Feb 18 [Epub ahead of print] [PubMed]
  4. Schnable PS, Hochholdinger F, Nakazono M. Global expression profiling applied to plant development. Curr Opin Plant Biol. 2004 Feb;7(1):50-6. [PubMed]
  5. Jia L, Clegg MT, Jiang T. Evolutionary Dynamics of the DNA-Binding Domains in Putative R2R3-MYB Genes Identified from Rice Subspecies indica and japonica Genomes. Plant Physiol. 2004 Feb;134(2):575-85. [PubMed]
  6. Thum KE, Shin MJ, Palenchar PM, Kouranov A, Coruzzi GM. Genome-wide investigation of light and carbon signaling interactions in Arabidopsis. Genome Biol. 2004;5(2):R10. [PubMed]
  7. Yamauchi Y, Ogawa M, Kuwahara A, Hanada A, Kamiya Y, Yamaguchi S. Activation of Gibberellin Biosynthesis and Response Pathways by Low Temperature during Imbibition of Arabidopsis thaliana Seeds. Plant Cell. 2004 Jan 16 [Epub ahead of print] [PubMed]
  8. Lister R, Chew O, Lee MN, Heazlewood JL, Clifton R, Parker KL, Millar AH, Whelan J. A Transcriptomic and Proteomic Characterization of the Arabidopsis Mitochondrial Protein Import Apparatus and Its Response to Mitochondrial Dysfunction. Plant Physiol. 2004 Jan 15 [Epub ahead of print] [PubMed]
  9. Weber M, Harada E, Vess C, Roepenack-Lahaye Ev E, Clemens S. Comparative microarray analysis of Arabidopsis thaliana and Arabidopsis halleri roots identifies nicotianamine synthase, a ZIP transporter and other genes as potential metal hyperaccumulation factors. Plant J. 2004 Jan;37(2):269-81. [PubMed]
  10. Becher M, Talke IN, Krall L, Kramer U. Cross-species microarray transcript profiling reveals high constitutive expression of metal homeostasis genes in shoots of the zinc hyperaccumulator Arabidopsis halleri. Plant J. 2004 Jan;37(2):251-68. [PubMed]
  11. Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y. Antisense transcripts with rice full-length cDNAs. Genome Biol. 2003;5(1):R5. [PubMed]

Microbiology

  1. Serizawa M, Yamamoto H, Yamaguchi H, Fujita Y, Kobayashi K, Ogasawara N, Sekiguchi J. Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analyses. Gene. 2004 Mar 31;329:125-36. [PubMed]
  2. Bernstein JA, Lin PH, Cohen SN, Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2758-63. [PubMed]
  3. Hottes AK, Meewan M, Yang D, Arana N, Romero P, McAdams HH, Stephens C. Transcriptional Profiling of Caulobacter crescentus during Growth on Complex and Minimal Media. J Bacteriol. 2004 Mar 1;186(5):1448-1461. [PubMed]
  4. Cummings CA, Brinig MM, Lepp PW, Van De Pas S, Relman DA. Bordetella species are distinguished by patterns of substantial gene loss and host adaptation. J Bacteriol. 2004 Mar;186(5):1484-92. [PubMed]
  5. Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T. Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res. 2004 Mar;14(3):380-90. [PubMed]
  6. Locke DP, Segraves R, Nicholls RD, Schwartz S, Pinkel D, Albertson DG, Eichler EE. BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications. J Med Genet. 2004 Mar;41(3):175-82. [PubMed]
  7. Watanabe T, Murata Y, Oka S, Iwahashi H. A new approach to species determination for yeast strains: DNA microarray-based comparative genomic hybridization using a yeast DNA microarray with 6000 genes. Yeast. 2004 Mar;21(4):351-365. [PubMed]
  8. Garcia R, Bermejo C, Grau C, Perez R, Manuel Rodriguez-Pena J, ;Francois J, Nombela C, Arroyo J. The global transcriptional response to transient cell wall damage in saccharomyces cerevisiae and its regulation by the cell integrity signaling pathway. J Biol Chem. 2004 Feb 27 [Epub ahead of print] [PubMed]
  9. Meibom KL, Li XB, Nielsen AT, Wu CY, Roseman S, Schoolnik GK. The Vibrio cholerae chitin utilization program. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2524-9.  [PubMed]
  10. Xing F, Hiley SL, Hughes TR, Phizicky EM. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J Biol Chem. 2004 Feb 16 [Epub ahead of print] [PubMed]
  11. Lee S, Kim SY, Chung E, Joung YH, Pai HS, Hur CG, Choi D. EST and microarray analyses of pathogen-responsive genes in hot pepper ( Capsicum annuum L.) non-host resistance against soybean pustule pathogen ( Xanthomonas axonopodis pv. glycines). Funct Integr Genomics. 2004 Feb 4 [Epub ahead of print][PubMed]
  12. Scholle F, Li K, Bodola F, Ikeda M, Luxon BA, Lemon SM. Virus-Host Cell Interactions during Hepatitis C Virus RNA Replication: Impact of Polyprotein Expression on the Cellular Transcriptome and Cell Cycle Association with Viral RNA Synthesis. J Virol. 2004 Feb; 78(3): 1513-24. [PubMed]
  13. Paiva S, Devaux F, Barbosa S, Jacq C, Casal M. Ady2p is essential for the acetate permease activity in the yeast Saccharomyces cerevisiae. Yeast. 2004 Feb;21(3):201-10. [PubMed]
  14. Dagkessamanskaia A, Moscoso M, Henard V, Guiral S, Overweg K, Reuter M, Martin B, Wells J, Claverys JP. Interconnection of competence, stress and CiaR regulons in Streptococcus pneumoniae: competence triggers stationary phase autolysis of ciaR mutant cells. Mol Microbiol. 2004 Feb;51(4):1071-86.[PubMed]
  15. Schuller C, Mamnun YM, Mollapour M, Krapf G, Schuster M, Bauer BE, Piper PW, Kuchler K. Global Phenotypic Analysis and Transcriptional Profiling Defines the Weak Acid Stress Response Regulon in Saccharomyces cerevisiae. Mol Biol Cell. 2004 Feb;15(2):706-20. [PubMed]
  16. Afonso CL, Piccone ME, Zaffuto KM, Neilan J, Kutish GF, Lu Z, Balinsky CA, Gibb TR, Bean TJ, Zsak L, Rock DL. African Swine Fever virus multigene family 360 and 530 genes affect host interferon response. J Virol. 2004 Feb;78(4):1858-64. [PubMed]
  17. Sims AH, Robson GD, Hoyle DC, Oliver SG, Turner G, Prade RA, Russell HH, Dunn-Coleman NS, Gent ME. Use of expressed sequence tag analysis and cDNA microarrays of the filamentous fungus Aspergillus nidulans. Fungal Genet Biol. 2004 Feb;41(2):199-212. [PubMed]
  18. Goodman AL. et al., Analysis of regulatory networks in Pseudomonas aeruginosa by genomewide transcriptional profiling. Curr Opin Microbiol. 2004 Feb [PubMed]
  19. Krogan NJ, Peng WT, Cagney G, Robinson MD, Haw R, Zhong G, Guo X, Zhang X, Canadien V, Richards DP, Beattie BK, Lalev A, Zhang W, Davi