My microarray journal watch - year 2004 Jul-Sep [ 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
   Affymetrix probe level 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
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General

  1. Kuo WP, Kim EY, Trimarchi J, Jenssen TK, Vinterbo SA, Ohno-Machado L. A primer on gene expression and microarrays for machine learning researchers. J Biomed Inform. 2004 Aug;37(4):293-303. [PubMed]

Human disease studies

  1. van 't Veer L. Laura van 't Veer, PhD: bringing tumor gene profiles into the clinic. Interview. JAMA. 2004 Aug 11;292(6):675. [PubMed]
  2. Hanash S. Integrated global profiling of cancer. Nat Rev Cancer. 2004 Aug;4(8):638-44. [PubMed]
  3. Skubitz KM, Skubitz AP. Role of gene expression arrays in sarcomas. Curr Oncol Rep. 2004 Jul;6(4):309-14. [PubMed]

Disease screening, profiling and classification

  1. Jurata LW, Bukhman YV, Charles V, Capriglione F, Bullard J, Lemire AL, Mohammed A, Pham Q, Laeng P, Brockman JA, Altar CA. Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures. J Neurosci Methods. 2004 Sep 30;138(1-2):173-88. [PubMed]
  2. Aston C, Jiang L, Sokolov BP. Microarray analysis of postmortem temporal cortex from patients with schizophrenia. J Neurosci Res. 2004 Sep 15;77(6):858-66.  [PubMed]
  3. Aldred MA, Huang Y, Liyanarachchi S, Pellegata NS, Gimm O, Jhiang S, Davuluri RV, De La Chapelle A, Eng C. Papillary and follicular thyroid carcinomas show distinctly different microarray expression profiles and can be distinguished by a minimum of five genes. J Clin Oncol. 2004 Sep 1;22(17):3531-9. [PubMed]
  4. Husson H, Manavalan P, Akmaev VR, Russo RJ, Cook B, Richards B, Barberio D, Liu D, Cao X, Landes GM, Wang CJ, Roberts BL, Klinger KW, Grubman SA, Jefferson DM, Ibraghimov-Beskrovnaya O. New insights into ADPKD molecular pathways using combination of SAGE and microarray technologies. Genomics. 2004 Sep;84(3):497-510. [PubMed]
  5. Pereira E, Tamia-Ferreira MC, Cardoso RS, Mello SS, Sakamoto-Hojo ET, Passos GA, Donadi EA. Immunosuppressive therapy modulates T lymphocyte gene expression in patients with systemic lupus erythematosus. Immunology. 2004 Sep;113(1):99-105. [PubMed]
    6. <>Baumgarth N, Szubin R, Dolganov GM, Watnik MR, Greenspan D, Da Costa M, Palefsky JM, Jordan R, Roederer M, Greenspan JS. Highly Tissue Substructure-Specific Effects of Human Papilloma Virus in Mucosa of HIV-Infected Patients Revealed by Laser-Dissection Microscopy-Assisted Gene Expression Profiling. Am J Pathol. 2004 Sep;165(3):707-18. [PubMed]
  6. Chen G, Zeng W, Miyazato A, Billings E, Maciejewski JP, Kajigaya S, Sloand EM, Young NS. Distinctive gene expression profiles of CD34 cells from patients with myelodysplastic syndrome characterized by specific chromosomal abnormalities. Blood. 2004 Aug 17;. [Epub ahead of print][PubMed]
  7. Hoefnagel JJ, Dijkman R, Basso K, Jansen PM, Hallermann C, Willemze R, Tensen CP, Vermeer MH. Distinct types of primary cutaneous large B-cell lymphoma identified by gene expression profiling. Blood. 2004 Aug 12 [Epub ahead of print] [PubMed]
  8. Calin GA, Liu CG, Sevignani C, Ferracin M, Felli N, Dumitru CD, Shimizu M, Cimmino A, Zupo S, Dono M, Dell'Aquila ML, Alder H, Rassenti L, Kipps TJ, Bullrich F, Negrini M, Croce CM. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11755-60. [PubMed]
  9. Ueda HR, Chen W, Minami Y, Honma S, Honma K, Iino M, Hashimoto S. Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles. Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11227-32. [PubMed]
  10. Aigner T, Saas J, Zien A, Zimmer R, Gebhard PM, Knorr T. Analysis of differential gene expression in healthy and osteoarthritic cartilage and isolated chondrocytes by microarray analysis. Methods Mol Med. 2004;100:109-28. [PubMed]
  11. Morrison C, Farrar W, Kneile J, Williams N, Liu-Stratton Y, Bakaletz A, Aldred MA, Eng C. Molecular classification of parathyroid neoplasia by gene expression profiling. Am J Pathol. 2004 Aug;165(2):565-76. [PubMed]
  12. Jinawath N, Furukawa Y, Hasegawa S, Li M, Tsunoda T, Satoh S, Yamaguchi T, Imamura H, Inoue M, Shiozaki H, Nakamura Y. Comparison of gene-expression profiles between diffuse- and intestinal-type gastric cancers using a genome-wide cDNA microarray. Oncogene. 2004 Jul 26 [Epub ahead of print]  [PubMed]
  13. Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics. 2004 Jul 1;. [Epub ahead of print][PubMed]
  14. Lindberg RL, De Groot CJ, Certa U, Ravid R, Hoffmann F, Kappos L, Leppert D. Multiple sclerosis as a generalized CNS disease-comparative microarray analysis of normal appearing white matter and lesions in secondary progressive MS. J Neuroimmunol. 2004 Jul;152(1-2):154-67. [PubMed]
  15. Court EL, Ann Smith M, Avent ND, Hancock JT, Morgan LM, Gray AG, Graham Smith J. DNA microarray screening of differential gene expression in bone marrow samples from AML, non-AML patients and AML cell lines. Leuk Res. 2004 Jul;28(7):743-53. [PubMed]

Diagnosis, prognosis and clinical applications

  1. Diederichs S, Bulk E, Steffen B, Ji P, Tickenbrock L, Lang K, Zanker KS, Metzger R, Schneider PM, Gerke V, Thomas M, Berdel WE, Serve H, Muller-Tidow C. S100 family members and trypsinogens are predictors of distant metastasis and survival in early-stage non-small cell lung cancer. Cancer Res. 2004 Aug 15;64(16):5564-9. [PubMed]
  2. Ein-Dor L, Kela I, Getz G, Givol D, Domany E. Outcome signature genes in breast cancer: is there a unique set? Bioinformatics. 2004 Aug 12 [Epub ahead of print][PubMed]
  3. Lyons-Weiler J, Patel S, Becich MJ, Godfrey TE. Tests for finding complex patterns of differential expression in cancers: towards individualized medicine. BMC Bioinformatics. 2004 Aug 12;5(1):110. [PubMed]
  4. Larrabee PB, Johnson KL, Pestova E, Lucas M, Wilber K, LeShane ES, Tantravahi U, Cowan JM, Bianchi DW. Microarray Analysis of Cell-Free Fetal DNA in Amniotic Fluid: a Prenatal Molecular Karyotype. Am J Hum Genet. 2004 Jul 13;75(3). [Epub ahead of print] [PubMed]
  5. Robison JE, Perreard L, Bernard PS. State of the science: molecular classifications of breast cancer for clinical diagnostics. Clin Biochem. 2004 Jul;37(7):572-578. [PubMed]

Animal model studies

  1. De Fourmestraux V, Neubauer H, Poussin C, Farmer P, Falquet L, Burcelin R, Delorenzi M, Thorens B. Transcript profiling suggests that differential metabolic adaptation of mice to high fat diet is associated with changes in liver to muscle lipid fluxes. J Biol Chem. 2004 Sep 17 [Epub ahead of print] [PubMed]
  2. Zhao M, Chow A, Powers J, Fajardo G, Bernstein D. Microarray analysis of gene expression after transverse aortic constriction in mice. Physiol Genomics. 2004 Sep 16;19(1):93-105. [PubMed]
  3. Lu XC, Williams AJ, Yao C, Berti R, Hartings JA, Whipple R, Vahey MT, Polavarapu RG, Woller KL, Tortella FC, Dave JR. Microarray analysis of acute and delayed gene expression profile in rats after focal ischemic brain injury and reperfusion. J Neurosci Res. 2004 Sep 15;77(6):843-57. [PubMed]
  4. Hackam AS, Strom R, Liu D, Qian J, Wang C, Otteson D, Gunatilaka T, Farkas RH, Chowers I, Kageyama M, Leveillard T, Sahel JA, Campochiaro PA, Parmigiani G, Zack DJ. Identification of Gene Expression Changes Associated with the Progression of Retinal Degeneration in the rd1 Mouse. Invest Ophthalmol Vis Sci. 2004 Sep;45(9):2929-42.[PubMed]
  5. Zhang KH, Xiao HS, Lu PH, Shi J, Li GD, Wang YT, Han S, Zhang FX, Lu YJ, Zhang X, Xu XM. Differential gene expression after complete spinal cord transection in adult rats: An analysis focused on a subchronic post-injury stage. Neuroscience. 2004;128(2):375-88. [PubMed]
  6. Fraga MF, Herranz M, Espada J, Ballestar E, Paz MF, Ropero S, Erkek E, Bozdogan O, Peinado H, Niveleau A, Mao JH, Balmain A, Cano A, Esteller M. A mouse skin multistage carcinogenesis model reflects the aberrant DNA methylation patterns of human tumors. Cancer Res. 2004 Aug 15;64(16):5527-34. [PubMed]
  7. Chen H, Huang XN, Stewart AF, Sepulveda JL. Gene expression changes associated with fibronectin-induced cardiac myocyte hypertrophy. Physiol Genomics. 2004 Aug 11;18(3):273-83. [PubMed]
  8. Zhao M, Chow A, Powers J, Fajardo G, Bernstein D. MICROARRAY ANALYSIS OF GENE EXPRESSION AFTER TRANSVERSE AORTIC CONSTRICTION IN MICE. Physiol Genomics. 2004 Aug 3;. [Epub ahead of print][PubMed]
  9. Vazquez-Chona F, Song BK, Geisert EE Jr. Temporal changes in gene expression after injury in the rat retina. Invest Ophthalmol Vis Sci. 2004 Aug;45(8):2737-46. [PubMed]
  10. Chen L, Wu W, Dentchev T, Zeng Y, Wang J, Tsui I, Tobias JW, Bennett J, Baldwin D, Dunaief JL. Light damage induced changes in mouse retinal gene expression. Exp Eye Res. 2004 Aug;79(2):239-47.[PubMed]
  11. Hertzano R, Montcouquiol M, Rashi-Elkeles S, Elkon R, Yucel R, Frankel WN, Rechavi G, Moroy T, Friedman TB, Kelley MW, Avraham KB. Transcription profiling of inner ears from Pou4f3ddl/ddl identifies Gfi1 as a target of the Pou4f3 deafness gene. Hum Mol Genet. 2004 Jul 14 [Epub ahead of print] [PubMed]
  12. Del Monte F, Dalal R, Tabchy A, Couget J, Bloch KD, Peterson R, Hajjar RJ. Transcriptional changes following restoration of SERCA2a levels in failing rat hearts. FASEB J. 2004 Jul 9 [Epub ahead of print] [PubMed]

In vitro studies

  1. Weisz A, Basile W, Scafoglio C, Altucci L, Bresciani F, Facchiano A, Sismondi P, Cicatiello L, De Bortoli M. Molecular identification of ERalpha-positive breast cancer cells by the expression profile of an intrinsic set of estrogen regulated genes. J Cell Physiol. 2004 Sep;200(3):440-50.  [PubMed]
  2. Schlicht MJ, Matysiak B, Brodzeller T, Wen X, Liu H, Zhou G, Dhir R, Hessner MJ, Tonellato PJ, Suckow M, Pollard M, Datta MW. Cross-Species Global and Subset Gene Expression Profiling Identifies Genes Involved in Prostate Cancer Response to Selenium. BMC Genomics. 2004 Aug 20;5(1):58. [PubMed]
  3. Wang HW, Trotter MW, Lagos D, Bourboulia D, Henderson S, Makinen T, Elliman S, Flanagan AM, Alitalo K, Boshoff C. Kaposi sarcoma herpesvirus-induced cellular reprogramming contributes to the lymphatic endothelial gene expression in Kaposi sarcoma. Nat Genet. 2004 Jul;36(7):687-93. [PubMed]

Basic science studies

  1. Ao W, Gaudet J, Kent WJ, Muttumu S, Mango SE. Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Science. 2004 Sep 17;305(5691):1743-6. [PubMed]
  2. Khanna S, Cheng G, Gong B, Mustari MJ, Porter JD. Genome-wide transcriptional profiles are consistent with functional specialization of the extraocular muscle layers. Invest Ophthalmol Vis Sci. 2004 Sep;45(9):3055-66. [PubMed]
  3. Blais JD, Filipenko V, Bi M, Harding HP, Ron D, Koumenis C, Wouters BG, Bell JC. Activating transcription factor 4 is translationally regulated by hypoxic stress. Mol Cell Biol. 2004 Sep;24(17):7469-82. [PubMed]
  4. Raghavan A, Bohjanen PR. Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression. Brief Funct Genomic Proteomic. 2004 Aug;3(2):112-24. [PubMed]
  5. Shah G, Azizian M, Bruch D, Mehta R, Kittur D. Cross-species comparison of gene expression between human and porcine tissue, using single microarray platform - preliminary results. Clin Transplant. 2004 Aug;18 Suppl 12:76-80. [PubMed]
  6. Wang XF, Cui JZ, Nie W, Prasad SS, Matsubara JA. Differential gene expression of early and late passage retinal pigment epithelial cells. Exp Eye Res. 2004 Aug;79(2):209-21. [PubMed]
  7. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R. Role of transposable elements in heterochromatin and epigenetic control. Nature. 2004 Jul 22;430(6998):471-6.  [PubMed]
  8. Castillo-Davis CI, Hartl DL, Achaz G. cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes. Genome Res. 2004 Jul 15 [Epub ahead of print]  [PubMed]
  9. Badis G, Saveanu C, Fromont-Racine M, Jacquier A. Targeted mRNA degradation by deadenylation-independent decapping. Mol Cell. 2004 Jul 2;15(1):5-15. [PubMed]
  10. Georgantas RW 3rd, Tanadve V, Malehorn M, Heimfeld S, Chen C, Carr L, Martinez-Murillo F, Riggins G, Kowalski J, Civin CI. Microarray and serial analysis of gene expression analyses identify known and novel transcripts overexpressed in hematopoietic stem cells. Cancer Res. 2004 Jul 1;64(13):4434-41. [PubMed]
  11. Hamatani T, Daikoku T, Wang H, Matsumoto H, Carter MG, Ko MS, Dey SK. Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Proc Natl Acad Sci U S A. 2004 Jul 1;. [Epub ahead of print][PubMed]
  12. Abdollahi A, Domhan S, Jenne JW, Hallaj M, Dell' Aqua G, Mueckenthaler M, Richter A, Martin H, Debus J, Ansorge W, Hynynen K, Huber PE. Apoptosis signals in lymphoblasts induced by focused ultrasound. FASEB J. 2004 Jul 1;. [Epub ahead of print] [PubMed]

Gene product function

  1. Janes SM, Ofstad TA, Campbell DH, Watt FM, Prowse DM. Transient activation of FOXN1 in keratinocytes induces a transcriptional programme that promotes terminal differentiation: contrasting roles of FOXN1 and Akt. J Cell Sci. 2004 Aug 15;117(Pt 18):4157-68. [PubMed]
  2. Schick N, Oakeley EJ, Hynes NE, Badache A. TEL/ETV6 is a Stat3-induced repressor of Stat3 activity. J Biol Chem. 2004 Jul 7 [Epub ahead of print] [PubMed]
  3. Liu S, Mirza A, Wang L. Generation of p53 Target Database Via Integration of Microarray and Global p53 DNA-Binding Site Analysis. Methods Mol Biol. 2004;281:33-54. [PubMed]

General physiology

  1. Rinaudo P, Schultz RM. Effects of embryo culture on global pattern of gene expression in preimplantation mouse embryos. Reproduction. 2004 Sep;128(3):301-11. [PubMed]
  2. Pruett SB, Schwab C, Zheng Q, Fan R. Suppression of Innate Immunity by Acute Ethanol Administration: A Global Perspective and a New Mechanism Beginning with Inhibition of Signaling through TLR3. J Immunol. 2004 Aug 15;173(4):2715-24.  [PubMed]

Development & differentiation

  1. Gasa R, Mrejen C, Leachman N, Otten M, Barnes M, Wang J, Chakrabarti S, Mirmira R, German M. Proendocrine genes coordinate the pancreatic islet differentiation program in vitro. Proc Natl Acad Sci U S A. 2004 Sep 7;101(36):13245-50. [PubMed]
  2. Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, Constantine-Paton M, Horvitz HR. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 2004;5(9):R68. [PubMed]
  3. Spin JM, Nallamshetty S, Tabibiazar R, Ashley EA, King JY, Chen M, Tsao PS, Quertermous T. Transcriptional profiling of in vitro smooth muscle cell differentiation identifies specific patterns of gene and pathway activation. Physiol Genomics. 2004 Aug 31;. [Epub ahead of print] [PubMed]
  4. Kniazeva M, Crawford QT, Seiber M, Wang CY, Han M. Monomethyl Branched-Chain Fatty Acids Play an Essential Role in Caenorhabditis elegans Development. PLoS Biol. 2004 Aug 31;2(9):E257. [Epub ahead of print] [PubMed]
  5. Steer DL, Shah MM, Bush KT, Stuart RO, Sampogna RV, Meyer TN, Schwesinger C, Bai X, Esko JD, Nigam SK. Regulation of ureteric bud branching morphogenesis by sulfated proteoglycans in the developing kidney. Dev Biol. 2004 Aug 15;272(2):310-27. [PubMed]
  6. Aoki S, Toda S, Ando T, Sugihara H. Bone Marrow Stromal Cells, Preadipocytes, and Dermal Fibroblasts Promote Epidermal Regeneration in Their Distinctive Fashions. Mol Biol Cell. 2004 Aug 3;. [Epub ahead of print][PubMed]
  7. Kang SK, Putnam LA, Ylostalo J, Popescu IR, Dufour J, Belousov A, Bunnell BA. Neurogenesis of Rhesus adipose stromal cells. J Cell Sci. 2004 Aug 3;Pt. [Epub ahead of print][PubMed]
  8. Chen HW, Yu SL, Chen WJ, Yang PC, Chien CT, Chou HY, Li HN, Peck K, Huang CH, Lin FY, Chen JJ, Lee YT. Dynamic changes of gene expression profiles during postnatal development of the heart in mice. Heart. 2004 Aug;90(8):927-34. [PubMed]
  9. Imai KS, Hino K, Yagi K, Satoh N, Satou Y. Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks. Development. 2004 Aug;131(16):4047-58. [PubMed]
  10. Eng SR, Lanier J, Fedtsova N, Turner EE.  Coordinated regulation of gene expression by Brn3a in developing sensory ganglia. Development. 2004 Jul 14 [Epub ahead of print] [PubMed]
  11. Addya S, Keller MA, Delgrosso K, Ponte CM, Vadigepalli R, Gonye GE, Surrey S. Erythroid-induced Commitment of K562 Cells Results in Clusters of Differentially-expressed Genes Enriched for Specific Transcription Regulatory Elements. Physiol Genomics. 2004 Jul 13;. [Epub ahead of print][PubMed]

Neurobiology

  1. Cavallaro S, D'Agata V, Alessi E, Coffa S, Alkon DL, Manickam P, Ciotti MT, Possenti R, Bonini P, Marlier L, Calissano P. Gene expression profiles of apoptotic neurons. Genomics. 2004 Sep;84(3):485-96. [PubMed]
  2. Ossipow V, Pellissier F, Schaad O, Ballivet M. Gene expression analysis of the critical period in the visual cortex. Mol Cell Neurosci. 2004 Sep;27(1):70-83. [PubMed]
  3. Zhou D, Xue J, Gavrialov O, Haddad GG. Na+/H+ exchanger 1 deficiency alters gene expression in mouse brain. Physiol Genomics. 2004 Aug 11;18(3):331-9. [PubMed]
  4. Kang SK, Putnam LA, Ylostalo J, Popescu IR, Dufour J, Belousov A, Bunnell BA. Neurogenesis of Rhesus adipose stromal cells. J Cell Sci. 2004 Aug 3;Pt. [Epub ahead of print][PubMed]
  5. Nakagawa T, Schwartz JP. Gene expression patterns in in vivo normal adult astrocytes compared with cultured neonatal and normal adult astrocytes. Neurochem Int. 2004 Aug-Sep;45(2-3):203-42. [PubMed]
  6. Haas MJ, Mreyoud A, Fishman M, Mooradian AD. Microarray analysis of thyroid hormone-induced changes in mRNA expression in the adult rat brain. Neurosci Lett. 2004 Jul 15;365(1):14-18. [PubMed]
  7. Chowers I, Kim Y, Farkas RH, Gunatilaka TL, Hackam AS, Campochiaro PA, Finnemann SC, Zack DJ. Changes in retinal pigment epithelial gene expression induced by rod outer segment uptake. Invest Ophthalmol Vis Sci. 2004 Jul;45(7):2098-106. [PubMed]

Signal transduction

  1. Husson H, Manavalan P, Akmaev VR, Russo RJ, Cook B, Richards B, Barberio D, Liu D, Cao X, Landes GM, Wang CJ, Roberts BL, Klinger KW, Grubman SA, Jefferson DM, Ibraghimov-Beskrovnaya O. New insights into ADPKD molecular pathways using combination of SAGE and microarray technologies. Genomics. 2004 Sep;84(3):497-510. [PubMed]

Apoptosis

  1. Cavallaro S, D'Agata V, Alessi E, Coffa S, Alkon DL, Manickam P, Ciotti MT, Possenti R, Bonini P, Marlier L, Calissano P. Gene expression profiles of apoptotic neurons. Genomics. 2004 Sep;84(3):485-96. [PubMed]

   Human

Animal

  1. Girardot F, Monnier V, Tricoire H. Genome wide analysis of common and specific stress responses in adult Drosophila melanogaster. BMC Genomics. 2004 Sep 30;5(1):74 [Epub ahead of print] [PubMed]
  2. Zhang X, Rogers M, Tian H, Zhang X, Zou DJ, Liu J, Ma M, Shepherd GM, Firestein SJ. High-throughput microarray detection of olfactory receptor gene expression in the mouse. Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14168-73. [PubMed]
  3. Rinaudo P, Schultz RM. Effects of embryo culture on global pattern of gene expression in preimplantation mouse embryos. Reproduction. 2004 Sep;128(3):301-11. [PubMed]
  4. Wang J, Kean L, Yang J, Allan AK, Davies SA, Herzyk P, Dow JA. Function-informed transcriptome analysis of Drosophila renal tubule. Genome Biol. 2004;5(9):R69. [PubMed]
  5. Kniazeva M, Crawford QT, Seiber M, Wang CY, Han M. Monomethyl Branched-Chain Fatty Acids Play an Essential Role in Caenorhabditis elegans Development. PLoS Biol. 2004 Aug 31;2(9):E257. [Epub ahead of print] [PubMed]
  6. Hackam AS, Qian J, Liu D, Gunatilaka T, Farkas RH, Chowers I, Kageyama M, Parmigiani G, Zack DJ. Comparative gene expression analysis of murine retina and brain. Mol Vis. 2004 Aug 31;10:637-49. [PubMed]
  7. Hamatani T, Falco G, Carter MG, Akutsu H, Stagg CA, Sharov AA, Dudekula DB, VanBuren V, Ko MS. Age-associated alteration of gene expression patterns in mouse oocytes. Hum Mol Genet. 2004 Aug 18 [Epub ahead of print] [PubMed]
  8. McElwee JJ, Schuster E, Blanc E, Thomas JH, Gems D. Shared transcriptional signature in C. elegans dauer larvae and long-lived daf-2 mutants implicates detoxification system in longevity assurance. J Biol Chem. 2004 Aug 11 [Epub ahead of print] [PubMed]

Plant

  1. Vodkin LO, Khanna A, Shealy R, Clough SJ, Gonzalez DO, Philip R, Zabala G, Thibaud-Nissen F, Sidarous M, Stromvik MV, Shoop E, Schmidt C, Retzel E, Erpelding J, Shoemaker RC, Rodriguez-Huete AM, Polacco JC, Coryell V, Keim P, Gong G, Liu L, Pardinas J, Schweitzer P. Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics. 2004 Sep 29;5(1):73. [Epub ahead of print] [PubMed]
  2. Held M, Gase K, Baldwin IT. Microarrays in ecological research: A case study of a cDNA microarray for plant-herbivore interactions. BMC Ecol. 2004 Sep 7 [Epub ahead of print] [PubMed]
  3. Alba R, Fei Z, Payton P, Liu Y, Moore SL, Debbie P, Cohn J, D'Ascenzo M, Gordon JS, Rose JK, Martin G, Tanksley SD, Bouzayen M, Jahn MM, Giovannoni J. ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant J. 2004 Sep;39(5):697-714. [PubMed]
  4. Wang R, Tischner R, Gutierrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM. Genomic Analysis of the Nitrate Response Using a Nitrate Reductase-Null Mutant of Arabidopsis. Plant Physiol. 2004 Aug 27 [Epub ahead of print] [PubMed]
  5. Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 2004 Aug;16(8):2089-103.  [PubMed]
  6. Mercke P, Kappers IF, Verstappen FW, Vorst O, Dicke M, Bouwmeester HJ. Combined transcript and metabolite analysis reveals genes involved in spider mite induced volatile formation in cucumber plants. Plant Physiol. 2004 Aug;135(4):2012-24. [PubMed]
  7. Taji T, Seki M, Satou M, Sakurai T, Kobayashi M, Ishiyama K, Narusaka Y, Narusaka M, Zhu JK, Shinozaki K. Comparative Genomics in Salt Tolerance between Arabidopsis and Arabidopsis-Related Halophyte Salt Cress Using Arabidopsis Microarray. Plant Physiol. 2004 Jul 9;. [Epub ahead of print][PubMed]
  8. Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K. From The Cover: Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10205-10. [PubMed]
  9. Mitra RM, Shaw SL, Long SR. Six nonnodulating plant mutants defective for Nod factor-induced transcriptional changes associated with the legume-rhizobia symbiosis. Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10217-22. [PubMed]
  10. Brinker M, Van Zyl L, Liu W, Craig D, Sederoff RR, Clapham DH, Von Arnold S. Microarray Analyses of Gene Expression during Adventitious Root Development in Pinus contorta. Plant Physiol. 2004 Jul;135(3):1526-39. Epub 2004 Jul 09. [PubMed]
  11. Hennig L, Gruissem W, Grossniklaus U, Kohler C. Transcriptional programs of early reproductive stages in Arabidopsis. Plant Physiol. 2004 Jul;135(3):1765-75. Epub 2004 Jul 09. [PubMed]
  12. Lopez-Valenzuela JA, Gibbon BC, Holding DR, Larkins BA. Cytoskeletal Proteins Are Coordinately Increased in Maize Genotypes with High Levels of eEF1A. Plant Physiol. 2004 Jul;135(3):1784-97. [PubMed]

Microbiology

  1. Ishii A, Oshima T, Sato T, Nakasone K, Mori H, Kato C. Analysis of hydrostatic pressure effects on transcription in Escherichia coli by DNA microarray procedure. Extremophiles. 2004 Aug 31;. [Epub ahead of print] [PubMed]
  2. Tong X, Campbell JW, Balazsi G, Kay KA, Wanner BL, Gerdes SY, Oltvai ZN.  Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays. Biochem Biophys Res Commun. 2004 Sep 10;322(1):347-54. [PubMed]
  3. Beyer A, Hollunder J, Nasheuer HP, Wilhelm T. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics. 2004 Aug 23;. [Epub ahead of print][PubMed]
  4. Yoshida M, Kashiwagi K, Shigemasa A, Taniguchi S, Yamamoto K, Makinoshima H, Ishihama A, Igarashi K. A Unifying Model for the Role of Polyamines in Bacterial Cell Growth: the Polyamine Modulon. J Biol Chem. 2004 Aug 23;. [Epub ahead of print][PubMed]
  5. Sherlock G. STARTing to recycle. Nat Genet. 2004 Aug;36(8):795-6. [PubMed]
  6. Rustici G, Mata J, Kivinen K, Lio P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, Bahler J. Periodic gene expression program of the fission yeast cell cycle. Nat Genet. 2004 Aug;36(8):809-17. [PubMed]
  7. Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL. Genome-Wide Mapping of the Cohesin Complex in the Yeast Saccharomyces cerevisiae. PLoS Biol. 2004 Jul 27;2(9):E259. [PubMed]

Genome scale studies

  1. Kim J, Iyer VR. Global Role of TATA Box-Binding Protein Recruitment to Promoters in Mediating Gene Expression Profiles. Mol Cell Biol. 2004 Sep;24(18):8104-12. [PubMed]
  2. Beilharz TH, Preiss T. Translational profiling: The genome-wide measure of the nascent proteome. Brief Funct Genomic Proteomic. 2004 Aug;3(2):103-11. [PubMed]
  3. Nagaraj VH, O'Flanagan RA, Bruning AR, Mathias JR, Vershon AK, Sengupta AM. Combined analysis of expression data and transcription factor binding sites in the yeast genome. BMC Genomics. 2004 Aug 26;5(1):59. [PubMed]
  4. Beyer A, Hollunder J, Nasheuer HP, Wilhelm T. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics. 2004 Aug 23;. [Epub ahead of print][PubMed]
  5. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, Cheung VG.  Genetic analysis of genome-wide variation in human gene expression. Nature. 2004 Aug 12;430(7001):743-7. [PubMed]
  6. Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL. Genome-Wide Mapping of the Cohesin Complex in the Yeast Saccharomyces cerevisiae. PLoS Biol. 2004 Jul 27;2(9):E259. [PubMed]
  7. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. Large-scale copy number polymorphism in the human genome. Science. 2004 Jul 23;305(5683):525-8. [PubMed]
  8. Semizarov D, Kroeger P, Fesik S. siRNA-mediated gene silencing: a global genome view. Nucleic Acids Res. 2004 Jul 22;32(13):3836-45. [PubMed]
  9. Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ, Hughes TR. Exploration of essential gene functions via titratable promoter alleles. Cell. 2004 Jul 9;118(1):31-44. [PubMed]
  10. Weil MR, Widlak P, Minna JD, Garner HR. Global survey of chromatin accessibility using DNA microarrays. Genome Res. 2004 Jul;14(7):1374-81. [PubMed]
  11. Lee C, Roy M. Analysis of alternative splicing with microarrays: successes and challenges. Genome Biol. 2004;5(7):231. [PubMed]

Comparative Genomics

  1. Zhang Z, Gu J, Gu X. How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends Genet. 2004 Sep;20(9):403-7. [PubMed]
  2. Renn SC, Aubin-Horth N, Hofmann HA. Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics. 2004 Jul 06;5(1):42. [PubMed]
  3. Zhou XJ, Gibson G. Cross-species comparison of genome-wide expression patterns. Genome Biol. 2004;5(7):232. [PubMed]

Network/pathway reconstruction and analysis

  1. Schmitt WA Jr, Raab RM, Stephanopoulos G. Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data. Genome Res. 2004 Aug;14(8):1654-63. [PubMed]

Genetic analysis

  1. Lu Y, Liu P, Liu Y, Xu F, Deng HW. Quantifying the relationship between gene expressions and trait values in general pedigrees. Genetics. 2004 Sep 15;. [Epub ahead of print][PubMed]
  2. Butcher LM, Meaburn E, Liu L, Fernandes C, Hill L, Al-Chalabi A, Plomin R, Schalkwyk L, Craig IW. Genotyping Pooled DNA on Microarrays: A Systematic Genome Screen of Thousands of SNPs in Large Samples to Detect QTLs for Complex Traits. Behav Genet. 2004 Sep;34(5):549-55. [PubMed]
  3. Tebbutt SJ, Opushnyev IV, Tripp BW, Kassamali AM, Alexander WL, Andersen MI. SNP chart: an integrated platform for visualization and interpretation of microarray genotyping data. Bioinformatics. 2004 Aug 12 [Epub ahead of print][PubMed]
  4. Beres SB, Sylva GL, Sturdevant DE, Granville CN, Liu M, Ricklefs SM, Whitney AR, Parkins LD, Hoe NP, Adams GJ, Low DE, DeLeo FR, McGeer A, Musser JM. Genome-wide molecular dissection of serotype M3 group A Streptococcus strains causing two epidemics of invasive infections. Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11833-8.[PubMed]
  5. Janecke AR, Thompson DA, Utermann G, Becker C, Hubner CA, Schmid E, McHenry CL, Nair AR, Ruschendorf F, Heckenlively J, Wissinger B, Nurnberg P, Gal A. Mutations in RDH12 encoding a photoreceptor cell retinol dehydrogenase cause childhood-onset severe retinal dystrophy. Nat Genet. 2004 Aug;36(8):850-4. [PubMed]
  6. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. Large-Scale Copy Number Polymorphism in the Human Genome. Science. 2004 Jul 23;305(5683):525-528. [PubMed]
  7. Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, Aguirre AJ, Kim M, Protopopov A, Chin L. High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res. 2004 Jul 15;64(14):4744-8.  [PubMed]
  8. Larrabee PB, Johnson KL, Pestova E, Lucas M, Wilber K, LeShane ES, Tantravahi U, Cowan JM, Bianchi DW. Microarray Analysis of Cell-Free Fetal DNA in Amniotic Fluid: a Prenatal Molecular Karyotype. Am J Hum Genet. 2004 Jul 13 [Epub ahead of print] [PubMed]
  9. Stimpson DI, Knepper SM, Shida M, Obata K, Tajima H. Three-dimensional microarray platform applied to single nucleotide polymorphism analysis. Biotechnol Bioeng. 2004 Jul 5;87(1):99-103. [PubMed]
  10. Foldes-Papp Z, Egerer R, Birch-Hirschfeld E, Striebel HM, Demel U, Tilz GP, Wutzler P. Detection of multiple human herpes viruses by DNA microarray technology. Mol Diagn. 2004;8(1):1-9. [PubMed]

ArrayCGH

  1. De Leeuw RJ, Davies JJ, Rosenwald A, Bebb G, Gascoyne RD, Dyer MJ, Staudt LM, Martinez-Climent JA, Lam WL. Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes. Hum Mol Genet. 2004 Sep 1;13(17):1827-37. [PubMed]
  2. Guillaud-Bataille M, Valent A, Soularue P, Perot C, Inda MD, Receveur A, Smaili S, Crollius HR, Benard J, Bernheim A, Gidrol X, Danglot G. Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH. Nucleic Acids Res. 2004 Jul 29;32(13):e112. [PubMed]
  3. Myers CL, Dunham MJ, Kung SY, Troyanskaya OG. Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics. 2004 Jul 29 [Epub ahead of print] [PubMed]

Pharmacogenomics and pharmacogenetics

  1. Lee CH, Macgregor PF. Using microarrays to predict resistance to chemotherapy in cancer patients. Pharmacogenomics. 2004 Sep;5(6):611-25. [PubMed]
  2. Mazzanti CM, Tandle A, Lorang D, Costouros N, Roberts D, Bevilacqua G, Libutti SK. Early genetic mechanisms underlying the inhibitory effects of endostatin and fumagillin on human endothelial cells. Genome Res. 2004 Aug;14(8):1585-93.  [PubMed]
  3. Szakacs G, Annereau JP, Lababidi S, Shankavaram U, Arciello A, Bussey KJ, Reinhold W, Guo Y, Kruh GD, Reimers M, Weinstein JN, Gottesman MM. Predicting drug sensitivity and resistance; Profiling ABC transporter genes in cancer cells. Cancer Cell. 2004 Aug;6(2):129-37. [PubMed]
  4. Lu X, Burgan WE, Cerra MA, Chuang EY, Tsai MH, Tofilon PJ, Camphausen K. Transcriptional signature of flavopiridol-induced tumor cell death. Mol Cancer Ther. 2004 Jul;3(7):861-72.[PubMed]

Toxicogenomics

Technical development

  1. Shippy R, Sendera TJ, Lockner R, Palaniappan C, Kaysser-Kranich T, Watts G, Alsobrook J. Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics. 2004 Sep 02;5(1):61. [PubMed]
  2. Rogler CE, Tchaikovskaya T, Norel R, Massimi A, Plescia C, Rubashevsky E, Siebert P, Rogler LE. RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples. Nucleic Acids Res. 2004 Aug 25;32(15):e120. [PubMed]
  3. Hessner MJ, Meyer L, Tackes J, Muheisen S, Wang X. Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics. 2004 Aug 4;5(1):53. [Epub ahead of print][PubMed]
  4. Lausted C, Dahl T, Warren C, King K, Smith K, Johnson M, Saleem R, Aitchison J, Hood L, Lasky SR. POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol. 2004;5(8):R58. [PubMed]
  5. Dufva M, Petronis S, Jensen LB, Krag C, Christensen CB. Characterization of an inexpensive, nontoxic, and highly sensitive microarray substrate. Biotechniques. 2004 Aug;37(2):286-92, 294, 296. [PubMed]
  6. Weller MG. Optical microarray biosensors. Anal Bioanal Chem. 2004 Jul 23;. [Epub ahead of print] [PubMed]
  7. Shih JH, Michalowska AM, Dobbin K, Ye Y, Qiu TH, Green JE. Effects of pooling mRNA in microarray class comparisons. Bioinformatics. 2004 Jul 9 [Epub ahead of print][PubMed]

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

  1. Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S. Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol. 2004 Sep 9;112(3):225-45. [PubMed]
  2. Yauk CL, Berndt ML, Williams A, Douglas GR. Comprehensive comparison of six microarray technologies. Nucleic Acids Res. 2004 Aug 27;32(15):e124. [PubMed]
  3. Pancoska P, Moravek Z, Moll UM. Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs. Nucleic Acids Res. 2004 Aug 27;32(15):4630-45. [PubMed]
  4. Laayoun A, Bernal-Mendez E, Sothier I, Kotera M, Troesch A. Universal labeling chemistry for nucleic Acid detection on DNA chips. Methods Mol Biol. 2004;288:241-50. [PubMed]
  5. Gregory Cox W, Beaudet MP, Agnew JY, Ruth JL. Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. Anal Biochem. 2004 Aug 15;331(2):243-54. [PubMed]
  6. Dumur CI, Garrett CT, Archer KJ, Nasim S, Wilkinson DS, Ferreira-Gonzalez A. Evaluation of a linear amplification method for small samples used on high-density oligonucleotide microarray analysis. Anal Biochem. 2004 Aug 15;331(2):314-21. [PubMed]
  7. Joseph LJ. RNA reference materials for gene expression studies. RNA metrology: forecast calls for partial clearing. Clin Chem. 2004 Aug;50(8):1290-2. [PubMed]
  8. Gingeras TR. RNA reference materials for gene expression studies. Difficult first steps. Clin Chem. 2004 Aug;50(8):1289-90. [PubMed]
  9. Yao B, Rakhade SN, Li Q, Ahmed S, Krauss R, Draghici S, Loeb JA. Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells. BMC Bioinformatics. 2004 Jul 23;5(1):99. [PubMed]
  10. Hardiman G. Microarray platforms - comparisons and contrasts. Pharmacogenomics. 2004 Jul;5(5):487-502. [PubMed]

Experimental design, sample size & power

  1. Vinciotti V, Khanin R, D'Alimonte D, Liu X, Cattini N, Hotchkiss G, Bucca G, De Jesus O, Rasaiyaah J, Smith CP, Kellam P, Wit E. An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics. 2004 Sep 16 [Epub ahead of print] [PubMed]
  2. Landgrebe J, Bretz F, Brunner E. Efficient two-sample designs for microarray experiments with biological replications. In Silico Biol. 2004 Aug 17;4(3):0038. [Epub ahead of print][PubMed]
  3. Shih JH, Michalowska AM, Dobbin K, Ye Y, Qiu TH, Green JE. Effects of pooling mRNA in microarray class comparisons. Bioinformatics. 2004 Jul 9 [Epub ahead of print][PubMed]

Data analysis

  1. Ghosh D, Chinnaiyan AM. Covariate adjustment in the analysis of microarray data from clinical studies. Funct Integr Genomics. 2004 Sep 17 [Epub ahead of print] [PubMed]
  2. Dumur CI, Nasim S, Best AM, Archer KJ, Ladd AC, Mas VR, Wilkinson DS, Garrett CT, Ferreira-Gonzalez A. Evaluation of Quality-Control Criteria for Microarray Gene Expression Analysis. Clin Chem. 2004 Sep 13 [Epub ahead of print] [PubMed]
  3. Tu IP, Schaner M, Diehn M, Sikic BI, Brown PO, Botstein D, Fero MJ. A method for detecting and correcting feature misidentification on expression microarrays. BMC Genomics. 2004 Sep 9 [Epub ahead of print] [PubMed]
  4. Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N. Submission of Microarray Data to Public Repositories. PLoS Biol. 2004 Aug 31;2(9):E317. [Epub ahead of print] [PubMed]
  5. Kim H, Golub GH, Park H. Missing Value Estimation for DNA Microarray Gene Expression Data: Local Least Squares Imputation. Bioinformatics. 2004 Aug 27 [Epub ahead of print] [PubMed]
  6. De Brevern AG, Hazout S, Malpertuy A. Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering. BMC Bioinformatics. 2004 Aug 23;5(1):114. [Epub ahead of print] [PubMed]
  7. Reverter A, McWilliam SM, Barris W, Dalrymple BP. A rapid method for computationally inferring transcriptome coverage and microarray sensitivity. Bioinformatics. 2004 Aug 12 [Epub ahead of print][PubMed]
  8. Curk T, Demsar J, Xu Q, Leban G, Petrovic U, Bratko I, Shaulsky G, Zupan B. Microarray data mining with visual programming. Bioinformatics. 2004 Aug 12 [Epub ahead of print] [PubMed]
  9. Ueda HR, Chen W, Minami Y, Honma S, Honma K, Iino M, Hashimoto S. Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles. Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11227-32. [PubMed]
  10. Cui Y, Zhou M, Wong WH. Integrated analysis of microarray data and gene function information. OMICS. 2004 Summer;8(2):106-17. [PubMed]
  11. Kostka D, Spang R. Finding disease specific alterations in the co-expression of genes. Bioinformatics. 2004 Aug 4;20 Suppl 1:I194-I199. [PubMed]
  12. Li H, Gui J. Partial Cox regression analysis for high-dimensional microarray gene expression data. Bioinformatics. 2004 Aug 4;20 Suppl 1:I208-I215. [PubMed]
  13. Li Z, Chan C. Extracting novel information from gene expression data. Trends Biotechnol. 2004 Aug;22(8):381-3. [PubMed]
  14. Eckel JE, Gennings C, Chinchilli VM, Burgoon LD, Zacharewski TR. Empirical bayes gene screening tool for time-course or dose-response microarray data. J Biopharm Stat. 2004 Aug;14(3):647-70. [PubMed]
  15. Breitling R, Amtmann A, Herzyk P. Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics. 2004 Jul 23;5(1):100. [PubMed]
  16. Li L, Li H. Dimension reduction methods for microarrays with application to censored survival data. Bioinformatics. 2004 Jul 15 [Epub ahead of print]  [PubMed]
  17. Famili AF, Liu G, Liu Z. Evaluation and optimization of clustering in gene expression data analysis. Bioinformatics. 2004 Jul 1;20(10):1535-45. [PubMed]
  18. Balagurunathan Y, Wang N, Dougherty ER, Nguyen D, Chen Y, Bittner ML, Trent J, Carroll R. Noise factor analysis for cDNA microarrays. J Biomed Opt. 2004 Jul;9(4):663-678. [PubMed]
  19. Li W, Sun F, Grosse I. Extreme value distribution based gene selection criteria for discriminant microarray data analysis using logistic regression. J Comput Biol. 2004;11(2-3):215-26. [PubMed]

Oligo design for array manufacturing

  1. Gordon PM, Sensen CW. Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. Nucleic Acids Res. 2004 Sep 29;32(17):e133. [PubMed]
  2. Pancoska P, Moravek Z, Moll UM. Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs. Nucleic Acids Res. 2004 Aug 27;32(15):4630-45. [PubMed]
  3. Andersson A, Bernander R, Nilsson P. Dual-genome primer design for construction of DNA microarrays. Bioinformatics. 2004 Aug 27 [Epub ahead of print] [PubMed]
  4. Mecham BH, Wetmore DZ, Szallasi Z, Sadovsky Y, Kohane I, Mariani TJ. Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics. 2004 Aug 11;18(3):308-15. [PubMed]
  5. Chou CC, Chen CH, Lee TT, Peck K. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res. 2004 Jul 08;32(12):e99.  [PubMed]

Image analysis

  1. Ekstrom CT, Bak S, Kristensen C, Rudemo M. Spot shape modelling and data transformations for microarrays. Bioinformatics. 2004 Sep 22;20(14):2270-8. [PubMed]

Affymetrix probe level analysis

  1. Huber W, Gentleman R. matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements. Bioinformatics. 2004 Jul 10;20(10):1651-2. [PubMed]

Normalization

  1. Wang H, Huang H. SED, a normalization free method for DNA microarray data analysis. BMC Bioinformatics. 2004 Sep 02;5(1):121. [PubMed]
  2. Futschik M, Crompton T. Model selection and efficiency testing for normalization of cDNA microarray data. Genome Biol. 2004;5(8):R60. [PubMed]
  3. Lu C. Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays. BMC Bioinformatics. 2004 Jul 29;5(1):103. [PubMed]
  4. Stoyanova R, Querec TD, Brown TR, Patriotis C. Normalization of single-channel DNA array data by principal component analysis. Bioinformatics 2004 Jul 22; 20: 1772-1784. [PubMed]
  5. Yoon D, Yi SG, Kim JH, Park T. Two-stage Normalization Using Background Intensities in cDNA Microarray Data. BMC Bioinformatics. 2004 Jul 21 [Epub ahead of print]  [PubMed]
  6. Vaquerizas JM, Dopazo J, Diaz-Uriarte R. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics. 2004 Jul 9 [Epub ahead of print] [PubMed]
  7. Baird D, Johnstone P, Wilson T.  "Normalization of microarray data using a spatial mixed model analysis which includes splines" Bioinformatics. 2004 Jul 1 [Epub ahead of print] [PubMed]

Pattern recognition, classification & data mining by unsupervised methods

  1. Varma S, Simon R. Iterative class discovery and feature selection using Minimal Spanning Trees. BMC Bioinformatics. 2004 Sep 8;5(1):126. [PubMed]
  2. Belacel N, Cuperlovic-Culf M, Laflamme M, Ouellette R. Fuzzy J-Means and VNS methods for clustering genes from microarray data. Bioinformatics 2004 Jul 22; 20: 1690-1701. [PubMed]
  3. Hubert M, Engelen S. Robust PCA and classification in biosciences. Bioinformatics 2004 Jul 22; 20: 1728-1736. [PubMed]
  4. Duan F, Zhang H. Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights. Bioinformatics 2004 Jul 22; 20: 1766-1771. [PubMed]

Pattern recognition, classification & data mining by supervised methods

  1. Attoor S, Dougherty ER, Chen Y, Bittner ML, Trent JM. Which is better for cDNA-microarray-based classification: ratios or direct intensities. Bioinformatics. 2004 Sep 28;. [Epub ahead of print] [PubMed]
  2. Liu B, Cui Q, Jiang T, Ma S. A combinational feature selection and ensemble neural network method for classification of gene expression data. BMC Bioinformatics. 2004 Sep 27;5(1):136. [PubMed]
  3. Statnikov A, Aliferis CF, Tsamardinos I, Hardin D, Levy S. A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis. Bioinformatics. 2004 Sep 16;. [Epub ahead of print] [PubMed]
  4. Takahashi H, Kobayashi T, Honda H. Construction of robust prognostic predictors by using projective adaptive resonance theory as a gene filtering method. Bioinformatics. 2004 Aug 12 [Epub ahead of print] [PubMed]
  5. Pan F, Wang B, Hu X, Perrizo W. Comprehensive vertical sample-based KNN/LSVM classification for gene expression analysis. J Biomed Inform. 2004 Aug;37(4):240-8. [PubMed]
  6. Zhou X, Liu KY, Wong ST. Cancer classification and prediction using logistic regression with Bayesian gene selection. J Biomed Inform. 2004 Aug;37(4):249-259. [PubMed]
  7. Cho JH, Lee D, Park JH, Lee IB. Gene selection and classification from microarray data using kernel machine. FEBS Lett. 2004 Jul 30;571(1-3):93-8. [PubMed]
  8. Linder R, Dew D, Sudhoff H, Theegarten D, Remberger K, Poppl SJ, Wagner M. The "subsequent artificial neural network" (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses. Bioinformatics. 2004 Jul 29 [Epub ahead of print] [PubMed]
  9. Zhu J, Hastie T. Classification of gene microarrays by penalized logistic regression. Biostatistics. 2004 Jul;5(3):427-43. [PubMed]
  10. Tan Y, Shi L, Tong W, Gene Hwang GT, Wang C. Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Comput Biol Chem. 2004 Jul;28(3):235-43.  [PubMed]

Network/pathway reconstruction and analysis

  1. Carter SL, Brechbuhler CM, Griffin M, Bond AT. Gene expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics. 2004 Sep 22;20(14):2242-50. [PubMed]
  2. Ott S, Hansen A, Kim SY, Miyano S. Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution. Bioinformatics. 2004 Sep 17 [Epub ahead of print] [PubMed]
  3. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004 Sep 16;431(7006):308-12.[PubMed]
  4. Beal MJ, Falciani F, Ghahramani Z, Rangel C, Wild DL. A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics. 2004 Sep 7;. [Epub ahead of print][PubMed]
  5. Ihmels J, Bergmann S, Barkai N. Defining transcription modules using large-scale gene expression data. Bioinformatics. 2004 Sep 1; [PubMed]
  6. Xiong M, Zhao J, Xiong H. Network-based regulatory pathways analysis. Bioinformatics. 2004 Sep 1; [PubMed]
  7. Pandey R, Guru RK, Mount DW. Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics. 2004 Sep 1; [PubMed]
  8. Zou M, Conzen SD. A new Dynamic Bayesian Network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics. 2004 Aug 12 [Epub ahead of print] [PubMed]
  9. Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C. Predicting genetic regulatory response using classification. Bioinformatics. 2004 Aug 4;20 Suppl 1:I232-I240. [PubMed]
  10. Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ. Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol. 2004;5(8):R56.  [PubMed]
  11. Wu CC, Huang HC, Juan HF, Chen ST. GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. Bioinformatics. 2004 Jul 22 [Epub ahead of print] [PubMed]
  12. Thomas R, Mehrotra S, Papoutsakis ET, Hatzimanikatis V. A model-based optimization framework for the inference of gene regulatory networks from DNA array data. Bioinformatics. 2004 Jul 9 [Epub ahead of print][PubMed]
  13. Shaw OJ, Harwood C, Steggles LJ, Wipat A. SARGE: A tool for creation of putative genetic networks. Bioinformatics. 2004 Jul 9 [Epub ahead of print][PubMed]
  14. Sohler F, Hanisch D, Zimmer R. New methods for joint analysis of biological networks and expression data. Bioinformatics. 2004 Jul 1;20(10):1517-21. [PubMed]
  15. Konig R, Eils R. Gene expression analysis on biochemical networks using the Potts spin model. Bioinformatics. 2004 Jul 1;20(10):1500-5. [PubMed]
  16. Yang HH, Hu Y, Buetow KH, Lee MP. A computational approach to measuring coherence of gene expression in pathways. Genomics. 2004 Jul;84(1):211-217. [PubMed]

Statistical significance of analysis

  1. Bakewell DJ, Wit E. Weighted analysis of microarray gene expression using maximum likelihood. Bioinformatics. 2004 Sep 28;. [Epub ahead of print] [PubMed]
  2. Kim BS, Kim I, Lee S, Kim S, Rha SY, Chung HC. Statistical methods of translating microarray data into clinically relevant diagnostic information in colorectal cancer. Bioinformatics. 2004 Sep 16;. [Epub ahead of print] [PubMed]
  3. Asyali MH, Alci M. Reliability analysis of microarray data using fuzzy C-means and normal mixture modeling based classification methods. Bioinformatics. 2004 Sep 16 [Epub ahead of print] [PubMed]
  4. Osier MV, Zhao H, Cheung KH. Handling multiple testing while interpreting microarrays with the Gene Ontology Database. BMC Bioinformatics. 2004 Sep 06;5(1):124. [PubMed]
  5. Aubert J, Bar-Hen A, Daudin JJ, Robin S. Determination of the differentially expressed genes in microarray experiments using local FDR. BMC Bioinformatics. 2004 Sep 6 [Epub ahead of print] [PubMed]
  6. Cho H, Lee JK. Bayesian hierarchical error model for analysis of gene expression data. Bioinformatics. 2004 Sep 1; [PubMed]
  7. Delongchamp RR, Bowyer JF, Chen JJ, Kodell RL. Multiple-testing strategy for analyzing cDNA array data on gene expression. Biometrics. 2004 Sep;60(3):774-82. [PubMed]
  8. Kim RD, Park PJ. Improving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biol. 2004;5(9):R70. [PubMed]
  9. Breitling R, Armengaud P, Amtmann A, Herzyk P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 2004 Aug 27;573(1-3):83-92. [PubMed]
  10. Szabo A, Perou CM, Karaca M, Perreard L, Quackenbush JF, Bernard PS.  Statistical modeling for selecting housekeeper genes. Genome Biol. 2004;5(8):R59. [PubMed]
  11. Kim BS, Rha SY, Cho GB, Chung HC. Spearman's footrule as a measure of cDNA microarray reproducibility. Genomics. 2004 Aug;84(2):441-448. [PubMed]
  12. Kim JH, Jeoung D, Lee S, Kim H. Discovering significant and interpretable patterns from multifactorial DNA microarray data with poor replication. J Biomed Inform. 2004 Aug;37(4):260-8. [PubMed]
  13. Tsai CA, Hsueh HM, Chen JJ. A generalized additive model for microarray gene expression data analysis. J Biopharm Stat. 2004 Aug;14(3):553-73. [PubMed]
  14. Joo J, Ahn H, Lombardo F, Hadjiargyrou M, Zhu W. Statistical approaches in the analysis of gene expression data derived from bone regeneration specific cDNA microarrays. J Biopharm Stat. 2004 Aug;14(3):607-28. [PubMed]
  15. Zhao HY, Yue PY, Fang KT. Identification of differentially expressed genes with multivariate outlier analysis. J Biopharm Stat. 2004 Aug;14(3):629-46. [PubMed]
  16. Churchill GA. Using ANOVA to analyze microarray data. Biotechniques. 2004 Aug;37(2):173-5, 177. [PubMed]
  17. Neuhauser M, Senske R. The Baumgartner-Wei{beta}-Schindler test for the detection of differentially expressed genes in replicated microarray experiments. Bioinformatics. 2004 Jul 29 [Epub ahead of print] [PubMed]
  18. Ghosh D. Mixture models for assessing differential expression in complex tissues using microarray data. Bioinformatics 2004 Jul 22; 20: 1663-1669. [PubMed]
  19. Pounds S, Cheng C. Improving false discovery rate estimation. Bioinformatics 2004 Jul 22; 20: 1737-1745. [PubMed]
  20. Anderssen RS, Wu Y, Dolferus R, Saunders I. An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments. Bioinformatics 2004 Jul 22; 20: 1721-1727. [PubMed]
  21. Fathallah-Shaykh HM, He B, Zhao LJ, Badruddin A. Mathematical algorithm for discovering states of expression from direct genetic comparison by microarrays. Nucleic Acids Res. 2004 Jul 20;32(13):3807-14. [PubMed]
  22. Pochet N, De Smet F, Suykens JA, De Moor BL. Systematic benchmarking of microarray data classification: assessing the role of nonlinearity and dimensionality reduction. Bioinformatics. 2004 Jul 1 [Epub ahead of print] [PubMed]
  23. Lai Y, Wu B, Chen L, Zhao H. Statistical method for identifying differential gene-gene coexpression patterns. Bioinformatics. 2004 Jul 1 [Epub ahead of print] [PubMed]
  24. Yeung KY, Medvedovic M, Bumgarner RE. From co-expression to co-regulation: how many microarray experiments do we need? Genome Biol. 2004;5(7):R48. [PubMed]

Software

  1. Buness A, Huber W, Steiner K, Sultmann H, Poustka A. arrayMagic: two-colour cDNA microarray quality control and preprocessing. Bioinformatics. 2004 Sep 28;. [Epub ahead of print] [PubMed]
  2. Lin DY. An efficient Monte Carlo approach to assessing statistical significance in genomic studies. Bioinformatics. 2004 Sep 28;. [Epub ahead of print] [PubMed]
  3. Delmar P, Robin S, Daudin JJ. VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data. Bioinformatics. 2004 Sep 16 [Epub ahead of print] [PubMed]
  4. Tang X, Shen L, Dickerson JA. BarleyExpress: a web-based submission tool for enriched microarray database annotations. Bioinformatics. 2004 Sep 3 [Epub ahead of print] [PubMed]
  5. Pandey R, Guru RK, Mount DW. Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics. 2004 Sep 1; [PubMed]
  6. Flikka K, Yadetie F, Laegreid A, Jonassen I. XHM: A system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 2004 Aug 27 [Epub ahead of print] [PubMed]
  7. Tebbutt SJ, Opushnyev IV, Tripp BW, Kassamali AM, Alexander WL, Andersen MI. SNP chart: an integrated platform for visualization and interpretation of microarray genotyping data. Bioinformatics. 2004 Aug 12 [Epub ahead of print][PubMed]
  8. Zimmer DP, Paliy O, Thomas B, Gyaneshwar P, Kustu S. Genome Image Programs: Visualization and Interpretation of Escherichia coli Microarray Experiments. Genetics. 2004 Aug;167(4):2111-9. [PubMed]
  9. Reich M, Ohm K, Angelo M, Tamayo P, Mesirov JP. GeneCluster 2.0: an advanced toolset for bioarray analysis. Bioinformatics 2004 Jul 22; 20: 1797-1798. [PubMed]
  10. Knowlton N, Dozmorov IM, Centola M. Microarray data analysis toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics. 2004 Jul 22 [Epub ahead of print] [PubMed]
  11. Masseroli M, Stella A, Meani N, Alcalay M, Pinciroli F. MyWEST: My web extraction software tool for effective mining of annotations from web-based databanks. Bioinformatics. 2004 Jul 9 [Epub ahead of print][PubMed]
  12. Shaw OJ, Harwood C, Steggles LJ, Wipat A. SARGE: A tool for creation of putative genetic networks. Bioinformatics. 2004 Jul 9 [Epub ahead of print][PubMed]
  13. Vaquerizas JM, Dopazo J, Diaz-Uriarte R. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics. 2004 Jul 9 [Epub ahead of print] [PubMed]
  14. Durincky S, Allemeerschy J, Carey VJ, Moreau Y, De Moor B. Importing MAGE-ML format microarray data into BioConductor. Bioinformatics. 2004 Jul 15 [Epub ahead of print] [PubMed]
  15. Nucleic Acids Research Web Server Issue. 2004 Jul 1
  16. Golfier G, Dang MT, Dauphinot L, Graison E, Rossier J, Potier MC. VARAN: a web server for Variability Analysis of DNA microarray experiments. Bioinformatics. 2004 Jul 1;20(10):1641-3. [PubMed]

Database

  1. Ringner M, Veerla S, Andersson S, Staaf J, Hakkinen J.  ACID: a database for microarray clone information. Bioinformatics. 2004 Sep 22;20(14):2305-6. [PubMed]
  2. Cole SW, Yan W, Galic Z, Arevalo J, Zack JA. Expression-based monitoring of transcription factor activity: The TELiS database. Bioinformatics. 2004 Sep 16 [Epub ahead of print] [PubMed]
  3. Webb SC, Attwood A, Brooks T, Freeman T, Gardner P, Pritchard C, Williams D, Underhill P, Strivens MA, Greenfield A, Pilicheva E. LIMaS: the JAVA-based application and database for microarray experiment tracking. Mamm Genome. 2004 Sep;15(9):740-7. [PubMed]
  4. Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N. Submission of Microarray Data to Public Repositories. PLoS Biol. 2004 Aug 31;2(9):E317. [Epub ahead of print] [PubMed]
  5. Zielinski SL. Project creates repository for microarray datasets. J Natl Cancer Inst. 2004 Aug 4;96(15):1126. [PubMed]

Tissue microarray

  1. Miyata H, Chiang AC, Vinters HV. Insulin signaling pathways in cortical dysplasia and TSC-tubers: Tissue microarray analysis. Ann Neurol. 2004 Sep 28;56(4):510-519. [Epub ahead of print] [PubMed]
  2. Makretsov NA, Huntsman DG, Nielsen TO, Yorida E, Peacock M, Cheang MC, Dunn SE, Hayes M, Van De Rijn M, Bajdik C, Gilks CB. Hierarchical clustering analysis of tissue microarray immunostaining data identifies prognostically significant groups of breast carcinoma. Clin Cancer Res. 2004 Sep 15;10(18):6143-51. [PubMed]
  3. Braunschweig T, Chung JY, Hewitt SM. Perspectives in tissue microarrays. Comb Chem High Throughput Screen. 2004 Sep;7(6):575-85. [PubMed]
  4. Iwafuchi H, Mori N, Takahashi T, Yatabe Y. Phenotypic composition of salivary gland tumors: an application of principal component analysis to tissue microarray data. Mod Pathol. 2004 Sep;17(9):1166. [PubMed]
  5. Leitao MM, Soslow RA, Nonaka D, Olshen AB, Aghajanian C, Sabbatini P, Dupont J, Hensley M, Sonoda Y, Barakat RR, Anderson S. Tissue microarray immunohistochemical expression of estrogen, progesterone, and androgen receptors in uterine leiomyomata and leiomyosarcoma. Cancer. 2004 Aug 11;:NA. [Epub ahead of print] [PubMed]
  6. West RB, Harvell J, Linn SC, Lui CL, Prapong W, Hernandez-Boussard T, Montgomery K, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Brown PO, Van De Rijn M. Apo D in Soft Tissue Tumors: A Novel Marker for Dermatofibrosarcoma Protuberans. Am J Surg Pathol. 2004 Aug;28(8):1063-1069. [PubMed]
  7. Spizzo G, Went P, Dirnhofer S, Obrist P, Simon R, Spichtin H, Maurer R, Metzger U, Von Castelberg B, Bart R, Stopatschinskaya S, Kochli OR, Haas P, Mross F, Zuber M, Dietrich H, Bischoff S, Mirlacher M, Sauter G, Gastl G. High Ep-CAM Expression is Associated with Poor Prognosis in Node-positive Breast Cancer. Breast Cancer Res Treat. 2004 Aug;86(3):207-13. [PubMed]
  8. Liu X, Minin V, Huang Y, Seligson DB, Horvath S. Statistical methods for analyzing tissue microarray data. J Biopharm Stat. 2004 Aug;14(3):671-85. [PubMed]
  9. Chitale DA, Jungbluth AA, Marshall DS, Leitao MM, Hedvat CV, Kolb D, Spagnoli GC, Iversen K, Soslow RA. Expression of cancer-testis antigens in endometrial carcinomas using a tissue microarray. Mod Pathol. 2004 Jul 23;. [Epub ahead of print][PubMed]

Protein array

  1. Barzaghi D, Isbister JD, Lauer KP, Born TL. Use of surface-enhanced laser desorption/ionization -time of flight to explore bacterial proteomes. Proteomics. 2004 Sep;4(9):2624-8. [PubMed]
  2. Panicker RC, Huang X, Yao SQ. Recent advances in peptide-based microarray technologies. Comb Chem High Throughput Screen. 2004 Sep;7(6):547-56. [PubMed]
  3. Kersten B, Possling A, Blaesing F, Mirgorodskaya E, Gobom J, Seitz H. Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of protein-DNA interactions. Anal Biochem. 2004 Aug 15;331(2):303-13. [PubMed]
  4. Saviranta P, Okon R, Brinker A, Warashina M, Eppinger J, Geierstanger BH. Evaluating Sandwich Immunoassays in Microarray Format in Terms of the Ambient Analyte Regime. Clin Chem. 2004 Aug 12 [Epub ahead of print] [PubMed]
  5. Wong YF, Cheung TH, Lo KW, Wang VW, Chan CS, Ng TB, Chung TK, Mok SC. Protein profiling of cervical cancer by protein-biochips: proteomic scoring to discriminate cervical cancer from normal cervix. Cancer Lett. 2004 Aug 10;211(2):227-34. [PubMed]
  6. Hsu HY, Huang YY. RCA combined nanoparticle-based optical detection technique for protein microarray: a novel approach. Biosens Bioelectron. 2004 Jul 30;20(1):123-6. [PubMed]
  7. Wacker R, Schroder H, Niemeyer CM. Performance of antibody microarrays fabricated by either DNA-directed immobilization, direct spotting, or streptavidin-biotin attachment: a comparative study. Anal Biochem. 2004 Jul 15;330(2):281-7. [PubMed]
  8. Lee SJ, Lee SY. Microarrays of peptides elevated on the protein layer for efficient protein kinase assay. Anal Biochem. 2004 Jul 15;330(2):311-316. [PubMed]
  9. Warren EN, Elms PJ, Parker CE, Borchers CH. Development of a Protein Chip: A MS-Based Method for Quantitation of Protein Expression and Modification Levels Using an Immunoaffinity Approach. Anal Chem. 2004 Jul 15;76(14):4082-92.  [PubMed]
  10. Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, Walter JC, LaBaer J. Self-assembling protein microarrays. Science. 2004 Jul 2;305(5680):86-90. [PubMed]
  11. Boutell JM, Hart DJ, Godber BL, Kozlowski RZ, Blackburn JM. Functional protein microarrays for parallel characterisation of p53 mutants. Proteomics. 2004 Jul;4(7):1950-8. [PubMed]

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

  1. Maroc N, Morel A, Beillard E, De La Chapelle AL, Fund X, Mozziconacci MJ, Dupont M, Cayuela JM, Gabert J, Koki A, Fert V, Hermitte F. A diagnostic biochip for the comprehensive analysis of MLL translocations in acute leukemia. Leukemia. 2004 Sep;18(9):1522-30. [PubMed]
  2. Koehne JE, Chen H, Cassell AM, Ye Q, Han J, Meyyappan M, Li J. Miniaturized Multiplex Label-Free Electronic Chip for Rapid Nucleic Acid Analysis Based on Carbon Nanotube Nanoelectrode Arrays. Clin Chem. 2004 Aug 19 [Epub ahead of print] [PubMed]

Cell microarray

Other array platforms

  1. Walsh DP, Chang YT. Recent advances in small molecule microarrays: applications and technology. Comb Chem High Throughput Screen. 2004 Sep;7(6):557-64. [PubMed]
  2. Kato K, Umezawa K, Miyake M, Miyake J, Nagamune T. Transfection microarray of nonadherent cells on an oleyl poly(ethylene glycol) ether-modified glass slide. Biotechniques. 2004 Sep;37(3):444-8, 450, 452. [PubMed]
  3. Wu Y, de Kievit P, Vahlkamp L, Pijnenburg D, Smit M, Dankers M, Melchers D, Stax M, Boender PJ, Ingham C, Bastiaensen N, de Wijn R, van Alewijk D, van Damme H, Raap AK, Chan AB, van Beuningen R. Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles. Nucleic Acids Res. 2004 Aug 27;32(15):e123. [PubMed]
  4. Rogler CE, Tchaikovskaya T, Norel R, Massimi A, Plescia C, Rubashevsky E, Siebert P, Rogler