My microarray journal watch - year 2004 Apr-Jun  [ this week | 2004 Oct-Dec | 2004 Jul-Sep | 2004 Apr-Jun | 2004 Jan-Mar | 2003 Oct-Dec | 2003 Jul-Sep | 2003 Apr-Jun | 2003 Jan-Mar | 2002 Jul-Dec | 2002 Jan-Jun | 2001 Jul-Dec | 2001 Jan-Jun | 2000 | 1999 | 1998 | 1997 | 1996 & before ]

General
Human disease studies
   Disease screening, profiling and classification
   Diagnosis, 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. Jarvinen AK, Hautaniemi S, Edgren H, Auvinen P, Saarela J, Kallioniemi OP, Monni O. Are data from different gene expression microarray platforms comparable? Genomics. 2004 Jun;83(6):1164-8. [PubMed]
  2. Kawasaki ES. Microarrays and the gene expression profile of a single cell. Ann N Y Acad Sci. 2004 May;1020:92-100. Review. [PubMed]
  3. Rockett JC, Hellmann GM. Confirming microarray data-is it really necessary? Genomics. 2004 Apr;83(4):541-9. [PubMed]

Human disease studies

  1. Glanzer JG, Haydon PG, Eberwine JH. Expression profile analysis of neurodegenerative disease: advances in specificity and resolution. Neurochem Res. 2004 Jun;29(6):1161-8. [PubMed]
  2. Ginsberg SD, Elarova I, Ruben M, Tan F, Counts SE, Eberwine JH, Trojanowski JQ, Hemby SE, Mufson EJ, Che S. Single-cell gene expression analysis: implications for neurodegenerative and neuropsychiatric disorders. Neurochem Res. 2004 Jun;29(6):1053-64. [PubMed]
  3. Grose R. Common ground in the transcriptional profiles of wounds and tumors. Genome Biol. 2004;5(6):228. [PubMed]
  4. D'Agata V, Cavallaro S. Genomic portraits of the nervous system in health and disease. Neurochem Res. 2004 Jun;29(6):1201-12. [PubMed]
  5. Pierce A, Small SA. Combining brain imaging with microarray: isolating molecules underlying the physiologic disorders of the brain. Neurochem Res. 2004 Jun;29(6):1145-52. [PubMed]
  6. Ruse CI, Tan FL, Kinter M, Bond M. Intregrated analysis of the human cardiac transcriptome, proteome and phosphoproteome. Proteomics. 2004 May;4(5):1505-16. [PubMed]
  7. Miklos GL, Maleszka R. Microarray reality checks in the context of a complex disease. Nat Biotechnol. 2004 May;22(5):615-21. [PubMed]
  8. Mirnics K, Pevsner J. Progress in the use of microarray technology to study the neurobiology of disease. Nat Neurosci. 2004 May;7(5):434-9.[PubMed]
  9. Yang HH, Lee MP. Application of bioinformatics in cancer epigenetics. Ann N Y Acad Sci. 2004 May;1020:67-76. [PubMed]
  10. Rhodes DR, Chinnaiyan AM. Bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers. Ann N Y Acad Sci. 2004 May;1020:32-40. [PubMed]

Disease screening, profiling and classification

  1. DeLeeuw 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 Jun 30 [Epub ahead of print] [PubMed]
  2. Ross ME, Mahfouz R, Onciu M, Liu HC, Zhou X, Song G, Shurtleff SA, Pounds S, Cheng C, Ma J, Ribeiro RC, Rubnitz JE, Girtman K, Williams WK, Raimondi SC, Liang DC, Shih LY, Pui CH, Downing JR. Gene Expression Profiling of Pediatric Acute Myelogenous Leukemia. Blood. 2004 Jun 29;. [Epub ahead of print] [PubMed]
  3. Reis EM, Nakaya HI, Louro R, Canavez FC, Flatschart Á &, Almeida GT, Egidio CM, Paquola AC, Machado AA, Festa F, Yamamoto D, Alvarenga R, Da Silva CC, Brito GC, Simon SD, Moreira-Filho CA, Leite KR, Camara-Lopes LH, Campos FS, Gimba E, Vignal GM, El-Dorry H, Sogayar MC, Barcinski MA, Da Silva AM, Verjovski-Almeida S. Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer. Oncogene. 2004 Jun 28 [Epub ahead of print] [PubMed]
  4. Jiang H, Deng Y, Chen HS, Tao L, Sha Q, Chen J, Tsai CJ, Zhang S. Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics. 2004 Jun 24 [Epub ahead of print] [PubMed]
  5. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A. 2004 Jun 22;101(25):9309-14. [PubMed]
  6. Aguirre AJ, Brennan C, Bailey G, Sinha R, Feng B, Leo C, Zhang Y, Zhang J, Gans JD, Bardeesy N, Cauwels C, Cordon-Cardo C, Redston MS, DePinho RA, Chin L. High-resolution characterization of the pancreatic adenocarcinoma genome. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9067-72. [PubMed]
  7. Pellagatti A, Esoof N, Watkins F, Langford CF, Vetrie D, Campbell LJ, Fidler C, Cavenagh JD, Eagleton H, Gordon P, Woodcock B, Pushkaran B, Kwan M, Wainscoat JS, Boultwood J. Gene expression profiling in the myelodysplastic syndromes using cDNA microarray technology. Br J Haematol. 2004 Jun;125(5):576-83. [PubMed]
  8. Peterson KS, Huang JF, Zhu J, D'Agati V, Liu X, Miller N, Erlander MG, Jackson MR, Winchester RJ. Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis from transcriptional profiles of laser-captured glomeruli. J Clin Invest. 2004 Jun;113(12):1722-33. [PubMed]
  9. Zhao H. et al., Different Gene Expression Patterns in Invasive Lobular and Ductal Carcinomas of the Breast. Mol. Biol. Cell 2004 Jun; 15: 2523-2536. [PubMed]
  10. Xu T, Shu CT, Purdom E, Dang D, Ilsley D, Guo Y, Weber J, Holmes SP, Lee PP. Microarray Analysis Reveals Differences in Gene Expression of Circulating CD8+ T Cells in Melanoma Patients and Healthy Donors. Cancer Res. 2004 May 15;64(10):3661-7. [PubMed]
  11. Modlich O, Prisack HB, Pitschke G, Ramp U, Ackermann R, Bojar H, Vogeli TA, Grimm MO. Identifying superficial, muscle-invasive, and metastasizing transitional cell carcinoma of the bladder: use of cDNA array analysis of gene expression profiles. Clin Cancer Res. 2004 May 15;10(10):3410-21. [PubMed]
  12. Tsukasaki K, Tanosaki S, DeVos S, Hofmann WK, Wachsman W, Gombart AF, Krebs J, Jauch A, Bartram CR, Nagai K, Tomonaga M, Said JW, Koeffler HP. Identifying progression-associated genes in adult T-cell leukemia/lymphoma by using oligonucleotide microarrays. Int J Cancer. 2004 May 10;109(6):875-81. [PubMed]
  13. Santin AD, Zhan F, Bellone S, Palmieri M, Cane S, Gokden M, Roman JJ, O'Brien TJ, Tian E, Cannon MJ, Shaughnessy J Jr, Pecorelli S. Discrimination between uterine serous papillary carcinomas and ovarian serous papillary tumours by gene expression profiling. Br J Cancer. 2004 May 4;90(9):1814-24. [PubMed]
  14. Neben K, Korshunov A, Benner A, Wrobel G, Hahn M, Kokocinski F, Golanov A, Joos S, Lichter P. Microarray-Based Screening for Molecular Markers in Medulloblastoma Revealed STK15 as Independent Predictor for Survival. Cancer Res. 2004 May 1;64(9):3103-11. [PubMed]
  15. Jones C, Mackay A, Grigoriadis A, Cossu A, Reis-Filho JS, Fulford L, Dexter T, Davies S, Bulmer K, Ford E, Parry S, Budroni M, Palmieri G, Neville AM, O'Hare MJ, Lakhani SR. Expression profiling of purified normal human luminal and myoepithelial breast cells: identification of novel prognostic markers for breast cancer. Cancer Res. 2004 May 1;64(9):3037-45.[PubMed]
  16. Rihl M, Baeten D, Seta N, Gu J, De Keyser F, Veys EM, Kuipers JG, Zeidler H, Yu DT. Technical validation of cDNA based microarray as screening technique to identify candidate genes in synovial tissue biopsy specimens from patients with spondyloarthropathy. Ann Rheum Dis. 2004 May;63(5):498-507. [PubMed]
  17. Thelen P, Burfeind P, Grzmil M, Voigt S, Ringert RH, Hemmerlein B. cDNA microarray analysis with amplified RNA after isolation of intact cellular RNA from neoplastic and non-neoplastic prostate tissue separated by laser microdissections. Int J Oncol. 2004 May;24(5):1085-92. [PubMed]
  18. Iglesias AH, Camelo S, Hwang D, Villanueva R, Stephanopoulos G, Dangond F. Microarray detection of E2F pathway activation and other targets in multiple sclerosis peripheral blood mononuclear cells. J Neuroimmunol. 2004 May;150(1-2):163-77.  [PubMed]
  19. Segev F, Mor O, Segev A, Belkin M, Assia EI. Downregulation of gene expression in the ageing lens: a possible contributory factor in senile cataract. Eye. 2004 Apr 23 [Epub ahead of print]   [PubMed]
  20. Nagai H, Terada Y, Tajiri T, Yabe A, Onda M, Nagahata T, Ezura Y, Minegishi M, Horiguchi M, Baba M, Konishi N, Emi M. Characterization of liver-cirrhosis nodules by analysis of gene-expression profiles and patterns of allelic loss. J Hum Genet. 2004 Apr 21 [Epub ahead of print]  [PubMed]
  21. Sarrio D, Perez-Mies B, Hardisson D, Moreno-Bueno G, Suarez A, Cano A, Martin-Perez J, Gamallo C, Palacios J. Cytoplasmic localization of p120ctn and E-cadherin loss characterize lobular breast carcinoma from preinvasive to metastatic lesions. Oncogene. 2004 Apr 12 [Epub ahead of print] [PubMed]
  22. Mori Y, Yin J, Sato F, Sterian A, Simms LA, Selaru FM, Schulmann K, Xu Y, Olaru A, Wang S, Deacu E, Abraham JM, Young J, Leggett BA, Meltzer SJ. Identification of genes uniquely involved in frequent microsatellite instability colon carcinogenesis by expression profiling combined with epigenetic scanning. Cancer Res. 2004 Apr 1;64(7):2434-8. [PubMed]
  23. Baelde HJ, Eikmans M, Doran PP, Lappin DW, de Heer E, Bruijn JA. Gene expression profiling in glomeruli from human kidneys with diabetic nephropathy. Am J Kidney Dis. 2004 Apr;43(4):636-50.[PubMed]

Diagnosis, prognosis and clinical applications

  1. Hampton T. Breast cancer gene chip study under way: can new technology help predict treatment success? JAMA. 2004 Jun 23;291(24):2927-30. [PubMed]
  2. Pawitan Y, Bjohle J, Wedren S, Humphreys K, Skoog L, Huang F, Amler L, Shaw P, Hall P, Bergh J. Gene expression profiling for prognosis using Cox regression. Stat Med. 2004 Jun 15;23(11):1767-80. [PubMed]
  3. Pittman J, Huang E, Dressman H, Horng CF, Cheng SH, Tsou MH, Chen CM, Bild A, Iversen ES, Huang AT, Nevins JR, West M. Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8431-6.[PubMed]
  4. Takita J, Ishii M, Tsutsumi S, Tanaka Y, Kato K, Toyoda Y, Hanada R, Yamamoto K, Hayashi Y, Aburatani H. Gene expression profiling and identification of novel prognostic marker genes in neuroblastoma. Genes Chromosomes Cancer. 2004 Jun;40(2):120-32.[PubMed]
  5. Dash PK, Kobori N, Moore AN. A molecular description of brain trauma pathophysiology using microarray technology: an overview. Neurochem Res. 2004 Jun;29(6):1275-86.  [PubMed]
  6. Bodrossy L, Sessitsch A. Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol. 2004 Jun;7(3):245-54. [PubMed]
  7. Hall JL, Grindle S, Han X, Fermin D, Park S, Chen Y, Bache RJ, Mariash A, Guan Z, Ormaza S, Thompson J, Graziano J, De Sam Lazaro SE, Pan S, Simari RD, Miller LW. Genomic Profiling of the Human Heart Before and After Mechanical Support with a Ventricular Assist Device Reveals Alterations in Vascular Signaling Networks. Physiol Genomics. 2004 May 19;17(3):283-91.[PubMed]
  8. Goley EM, Anderson SJ, Menard C, Chuang E, Lu X, Tofilon PJ, Camphausen K. Microarray analysis in clinical oncology: pre-clinical optimization using needle core biopsies from xenograft tumors. BMC Cancer. 2004 May 19 [Epub ahead of print] [PubMed]
  9. Ikehara M, Oshita F, Sekiyama A, Hamanaka N, Saito H, Yamada K, Noda K, Kameda Y, Miyagi Y. Genome-wide cDNA microarray screening to correlate gene expression profile with survival in patients with advanced lung cancer. Oncol Rep. 2004 May;11(5):1041-4. [PubMed]
  10. Greer BT, Khan J. Diagnostic classification of cancer using DNA microarrays and artificial intelligence. Ann N Y Acad Sci. 2004 May;1020:49-66. [PubMed]
  11. Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, Levy R. Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med. 2004 Apr 29;350(18):1828-37. [PubMed]
  12. Ramaswamy S. Translating cancer genomics into clinical oncology. N Engl J Med. 2004 Apr 29;350(18):1814-6. [PubMed]
  13. Kaab S, Barth AS, Margerie D, Dugas M, Gebauer M, Zwermann L, Merk S, Pfeufer A, Steinmeyer K, Bleich M, Kreuzer E, Steinbeck G, Nabauer M. Global gene expression in human myocardium-oligonucleotide microarray analysis of regional diversity and transcriptional regulation in heart failure. J Mol Med. 2004 Apr 23 [Epub ahead of print] [PubMed]
  14. Grimwade D, Haferlach T. Gene-expression profiling in acute myeloid leukemia. N Engl J Med. 2004 Apr 15;350(16):1676-8. [PubMed]
  15. Liu ET, Karuturi KR. Microarrays and clinical investigations. N Engl J Med. 2004 Apr 15;350(16):1595-7. [PubMed]
  16. Bullinger L, Dohner K, Bair E, Frohling S, Schlenk RF, Tibshirani R, Dohner H, Pollack JR. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med. 2004 Apr 15;350(16):1605-16. [PubMed]
  17. Valk PJ, Verhaak RG, Beijen MA, Erpelinck CA, Barjesteh van Waalwijk van Doorn-Khosrovani S, Boer JM, Beverloo HB, Moorhouse MJ, van der Spek PJ, Lowenberg B, Delwel R. Prognostically useful gene-expression profiles in acute myeloid leukemia. N Engl J Med. 2004 Apr 15;350(16):1617-28. [PubMed]
  18. Miller DV, Leontovich AA, Lingle WL, Suman VJ, Mertens ML, Lillie J, Ingalls KA, Perez EA, Ingle JN, Couch FJ, Visscher DW. Utilizing Nottingham Prognostic Index in microarray gene expression profiling of breast carcinomas. Mod Pathol. 2004 Apr 9 [Epub ahead of print][PubMed]
  19. Jeffrey SS, Fero MJ, Borresen-Dale AL, Botstein D. Expression array technology in the diagnosis and treatment of breast cancer. Mol Intervent. 2002 Apr;2(2):101-9. [PubMed]

Animal model studies

  1. Tasheva ES, Ke A, Deng Y, Jun C, Takemoto LJ, Koester A, Conrad GW. Differentially expressed genes in the lens of mimecan-null mice. Mol Vis. 2004 Jun 17;10:403-16. [PubMed]
  2. Reddy PH, McWeeney S, Park BS, Manczak M, Gutala RV, Partovi D, Jung J, Yau V, Searles R, Mori M, Quinn J. Gene expression profiles of transcripts in amyloid precursor protein transgenic mice: up-regulation of mitochondrial metabolism and apoptotic genes is an early cellular change in alzheimer's disease. Hum Mol Genet. 2004 Jun 15;13(12):1225-40. [PubMed]
  3. Theilgaard-Monch K, Knudsen S, Follin P, Borregaard N. The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing. J Immunol. 2004 Jun 15;172(12):7684-93. [PubMed]
  4. Mix E, Ibrahim S, Pahnke J, Koczan D, Sina C, Bottcher T, Thiesen HJ, Rolfs A. Gene-expression profiling of the early stages of MOG-induced EAE proves EAE-resistance as an active process. J Neuroimmunol. 2004 Jun;151(1-2):158-70. [PubMed]
  5. Kim JB, Piao CS, Lee KW, Han PL, Ahn JI, Lee YS, Lee JK. Delayed genomic responses to transient middle cerebral artery occlusion in the rat. J Neurochem. 2004 Jun;89(5):1271-82. [PubMed]
  6. Mansfield ES, Sarwal MM. Arraying the orchestration of allograft pathology. Am J Transplant. 2004 Jun;4(6):853-62. [PubMed]
  7. Sethi N, Palefsky J. Transcriptional profiling of dysplastic lesions in K14-HPV16 transgenic mice using laser microdissection. FASEB J. 2004 Jun 4;. [Epub ahead of print] [PubMed]
  8. Lee KW, Lee SH, Kim H, Song JS, Yang SD, Paik SG, Han PL. Progressive cognitive impairment and anxiety induction in the absence of plaque deposition in C57BL/6 inbred mice expressing transgenic amyloid precursor protein. J Neurosci Res. 2004 May 15;76(4):572-80.[PubMed]
  9. Larkin JE, Frank BC, Gaspard RM, Duka I, Gavras H, Quackenbush J. Cardiac transcriptional response to acute and chronic angiotensin II treatments. Physiol Genomics. 2004 May 4; [Epub ahead of print][PubMed]
  10. Miller LD, McPhie P, Suzuki H, Kato Y, Liu ET, Cheng SY. Multi-tissue gene-expression analysis in a mouse model of thyroid hormone resistance. Genome Biol. 2004;5(5):R31.  [PubMed]
  11. Resnick DK, Schmitt C, Miranpuri GS, Dhodda VK, Isaacson J, Vemuganti R. Molecular evidence of repair and plasticity following spinal cord injury. Neuroreport. 2004 Apr 9;15(5):837-839. [PubMed]
  12. Ahmed F, Brown KM, Stephan DA, Morrison JC, Johnson EC, Tomarev SI. Microarray Analysis of Changes in mRNA Levels in the Rat Retina after Experimental Elevation of Intraocular Pressure. Invest Ophthalmol Vis Sci. 2004 Apr;45(4):1247-1258. [PubMed]
  13. Tang Z, McGowan BS, Huber SA, McTiernan CF, Addya S, Surrey S, Kubota T, Fortina P, Higuchi Y, Diamond MA, Wyre DS, Feldman AM. Gene expression profiling during the transition to failure in TNF-alpha over-expressing mice demonstrates the development of autoimmune myocarditis. J Mol Cell Cardiol. 2004 Apr;36(4):515-30. [PubMed]
  14. Loop T, Leemans R, Stiefel U, Hermida L, Egger B, Xie F, Primig M, Certa U, Fischbach KF, Reichert H, Hirth F. Transcriptional signature of an adult brain tumor in Drosophila. BMC Genomics. 2004 Apr 16;5(1):24.  [PubMed]

In vitro studies

  1. Bachoo RM, Kim RS, Ligon KL, Maher EA, Brennan C, Billings N, Chan S, Li C, Rowitch DH, Wong WH, DePinho RA. Molecular diversity of astrocytes with implications for neurological disorders. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8384-9. [PubMed]
  2. Tanaka T, Tomaru Y, Nomura Y, Miura H, Suzuki M, Hayashizaki Y. Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi. Nucleic Acids Res. 2004;32(9):2740-50. [PubMed]
  3. Koike T, Kimura N, Miyazaki K, Yabuta T, Kumamoto K, Takenoshita S, Chen J, Kobayashi M, Hosokawa M, Taniguchi A, Kojima T, Ishida N, Kawakita M, Yamamoto H, Takematsu H, Suzuki A, Kozutsumi Y, Kanangi R. Hypoxia induces adhesion molecules on cancer cells: A missing link between Warburg effect and induction of selectin-ligand carbohydrates. Proc Natl Acad Sci U S A. 2004 May 25;101(21):8132-7. [PubMed]
  4. Schaefer KL, Brachwitz K, Wai DH, Braun Y, Diallo R, Korsching E, Eisenacher M, Voss R, Van Valen F, Baer C, Selle B, Spahn L, Liao SK, Lee KA, Hogendoorn PC, Reifenberger G, Gabbert HE, Poremba C. Expression Profiling of t(12;22) Positive Clear Cell Sarcoma of Soft Tissue Cell Lines Reveals Characteristic Up-Regulation of Potential New Marker Genes Including ERBB3. Cancer Res. 2004 May 15;64(10):3395-405. [PubMed]
  5. Pompeia C, Hodge DR, Plass C, Wu YZ, Marquez VE, Kelley JA, Farrar WL. Microarray Analysis of Epigenetic Silencing of Gene Expression in the KAS-6/1 Multiple Myeloma Cell Line. Cancer Res. 2004 May 15;64(10):3465-3473. [PubMed]
  6. Schaefer KL, Brachwitz K, Wai DH, Braun Y, Diallo R, Korsching E, Eisenacher M, Voss R, Van Valen F, Baer C, Selle B, Spahn L, Liao SK, Lee KA, Hogendoorn PC, Reifenberger G, Gabbert HE, Poremba C. Expression Profiling of t(12;22) Positive Clear Cell Sarcoma of Soft Tissue Cell Lines Reveals Characteristic Up-Regulation of Potential New Marker Genes Including ERBB3. Cancer Res. 2004 May 15;64(10):3395-405. [PubMed]
  7. Turney MK, Nicholson WE, Kovacs WJ. Gene expression phenotyping of an ACTH-producing small cell lung cancer line. Mol Cell Endocrinol. 2004 Apr 30;219(1-2):105-13. [PubMed]

Basic science studies

  1. Lercher MJ, Chamary JV, Hurst LD. Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res. 2004 Jun;14(6):1002-13. [PubMed]
  2. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res. 2004 Jun;14(6):1085-94. [PubMed]
  3. Costoya JA, Hobbs RM, Barna M, Cattoretti G, Manova K, Sukhwani M, Orwig KE, Wolgemuth DJ, Pandolfi PP. Essential role of Plzf in maintenance of spermatogonial stem cells. Nat Genet. 2004 Jun;36(6):653-9. [PubMed]
  4. Nagano Y, Nagahori K, Yoshiro F, Hamaguchi Y, Ishikawa T, Ichikawa Y, Togo S, Okazaki Y, Hayashizaki Y, Shimada H. Gene expression profile analysis of regenerating liver after portal vein ligation in rats by a cDNA microarray system. Liver Int. 2004 Jun;24(3):253-8. [PubMed]
  5. Kimura S, Tahira Y, Ishibashi T, Mori Y, Mori T, Hashimoto J, Sakaguchi K. DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells. Nucleic Acids Res. 2004;32(9):2760-7. [PubMed]
  6. Silva JM, Mizuno H, Brady A, Lucito R, Hannon GJ. RNA interference microarrays: High-throughput loss-of-function genetics in mammalian cells. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6548-52. [PubMed]
  7. Wang Z, Dooley TP, Curto EV, Davis RL, VandeBerg JL. Cross-species application of cDNA microarrays to profile gene expression using UV-induced melanoma in Monodelphis domestica as the model system. Genomics. 2004 Apr;83(4):588-99. [PubMed]

Gene product function

  1. Ng YS, Ramsauer M, Loureiro RM, D'Amore PA. Identification of genes involved in VEGF-mediated vascular morphogenesis using embryonic stem cell-derived cystic embryoid bodies. Lab Invest. 2004 Jun 28 [Epub ahead of print] [PubMed]
  2. Yin Y, Zhu A, Jin YJ, Liu YX, Zhang X, Hopkins KM, Lieberman HB. Human RAD9 checkpoint control/proapoptotic protein can activate transcription of p21. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):8864-9. [PubMed]
  3. Tanaka T, Tomaru Y, Nomura Y, Miura H, Suzuki M, Hayashizaki Y. Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi. Nucleic Acids Res. 2004 May 17;32(9):2740-50. [PubMed]
  4. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB Binds to Multiple Loci on Human Chromosome 22. Mol Cell Biol. 2004 May;24(9):3804-14. [PubMed]
  5. Redmond TM, Ren X, Kubish G, Atkins S, Low S, Uhler MD. Microarray transfection analysis of transcriptional regulation by cAMP-dependent protein kinase. Mol Cell Proteomics. 2004 Apr 26 [Epub ahead of print][PubMed]
  6. Wang G, Chuang L, Zhang X, Colton S, Dombkowski A, Reiners J, Diakiw A, Xu XS. The initiative role of XPC protein in cisplatin DNA damaging treatment-mediated cell cycle regulation. Nucleic Acids Res. 2004 Apr 23;32(7):2231-40. [PubMed]
  7. Mansson R, Tsapogas P, Akerlund M, Lagergren A, Gisler R, Sigvardsson M. Pearson Correlation Analysis of Microarray Data Allows for the Identification of Genetic Targets for Early B-cell Factor. J Biol Chem. 2004 Apr 23;279(17):17905-13. [PubMed]

General physiology

  1. Ning W, Chu TJ, Li CJ, Choi AM, Peters DG. Genome-wide analysis of the endothelial transcriptome under short-term chronic hypoxia. Physiol Genomics. 2004 Jun 17;18(1):70-8. [PubMed]
  2. Connolly PH, Caiozzo VJ, Zaldivar F, Nemet D, Larson J, Hung SP, Heck JD, Hatfield GW, Cooper DM. EFFECTS OF EXERCISE ON GENE EXPRESSION IN HUMAN PERIPHERAL BLOOD MONONUCLEAR CELLS. J Appl Physiol. 2004 Jun 11;. [Epub ahead of print] [PubMed]
  3. Mao M, Biery MC, Kobayashi SV, Ward T, Schimmack G, Burchard J, Schelter JM, Dai H, He YD, Linsley PS. T lymphocyte activation gene identification by coregulated expression on DNA microarrays. Genomics. 2004 Jun;83(6):989-99. [PubMed]
  4. Mobbs CV, Yen K, Mastaitis J, Nguyen H, Watson E, Wurmbach E, Sealfon SC, Brooks A, Salton SR. Mining microarrays for metabolic meaning: nutritional regulation of hypothalamic gene expression. Neurochem Res. 2004 Jun;29(6):1093-103. [PubMed]
  5. Radich JP, Mao M, Stepaniants S, Biery M, Castle J, Ward T, Schimmack G, Kobayashi S, Carleton M, Lampe J, Linsley PS. Individual-specific variation of gene expression in peripheral blood leukocytes. Genomics. 2004 Jun;83(6):980-8. [PubMed]
  6. Pavlidis P, Qin J, Arango V, Mann JJ, Sibille E. Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex. Neurochem Res. 2004 Jun;29(6):1213-22. [PubMed]
  7. DuPree MG, Mustanski BS, Bocklandt S, Nievergelt C, Hamer DH. A Candidate Gene Study of CYP19 (Aromatase) and Male Sexual Orientation. Behav Genet. 2004 May;34(3):243-250. [PubMed]
  8. Arai M, Yokosuka O, Fukai K, Imazeki F, Chiba T, Sumi H, Kato M, Takiguchi M, Saisho H, Muramatsu M, Seki N. Gene expression profiles in liver regeneration with oval cell induction. Biochem Biophys Res Commun. 2004 Apr 30;317(2):370-6. [PubMed]
  9. McKay BC, Stubbert LJ, Fowler CC, Smith JM, Cardamore RA, Spronck JC. Regulation of ultraviolet light-induced gene expression by gene size. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6582-6. [PubMed]
  10. Nguyen DH, Toshida H, Schurr J, Beuerman RW. Microarray analysis of the rat lacrimal gland following the loss of parasympathetic control of secretion. Physiol Genomics. 2004 Apr 13 [Epub ahead of print]  [PubMed]
  11. Dhahbi JM, Kim HJ, Mote PL, Beaver RJ, Spindler SR. Temporal linkage between the phenotypic and genomic responses to caloric restriction. Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5524-9. [PubMed]
  12. Mirnics ZK, Caudell E, Gao Y, Kuwahara K, Sakaguchi N, Kurosaki T, Burnside J, Mirnics K, Corey SJ.  Microarray analysis of Lyn-deficient B cells reveals germinal center-associated nuclear protein and other genes associated with the lymphoid germinal center. J Immunol. 2004 Apr 1;172(7):4133-41. [PubMed]
  13. Kwon JY, Hong M, Choi MS, Kang S, Duke K, Kim S, Lee S, Lee J. Ethanol-response genes and their regulation analyzed by a microarray and comparative genomic approach in the nematode Caenorhabditis elegans. Genomics. 2004 Apr;83(4):600-14. [PubMed]
  14. Urs S, Smith C, Campbell B, Saxton AM, Taylor J, Zhang B, Snoddy J, Jones Voy B, Moustaid-Moussa N. Gene Expression Profiling in Human Preadipocytes and Adipocytes by Microarray Analysis. J Nutr. 2004 Apr;134(4):762-770. [PubMed]

Development & differentiation

  1. Brandenberger R, Wei H, Zhang S, Lei S, Murage J, Fisk GJ, Li Y, Xu C, Fang R, Guegler K, Rao MS, Mandalam R, Lebkowski J, Stanton LW. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat Biotechnol. 2004 Jun;22(6):707-16.  [PubMed]
  2. Okubo T, Hogan BL. Hyperactive Wnt signaling changes the developmental potential of embryonic lung endoderm. J Biol. 2004 Jun 8;3(3):11. [Epub ahead of print] [PubMed]
  3. Wang D, Jensen R, Gendeh G, Williams K, Pallavicini MG. Proteome and transcriptome analysis of retinoic acid-induced differentiation of human acute promyelocytic leukemia cells, NB4. J Proteome Res. 2004 May-Jun;3(3):627-35. [PubMed]
  4. Lim CR, Fukakusa A, Matsubara K. Gene expression profiling of mouse postnatal cerebellar development using cDNA microarrays. Gene. 2004 May 26;333:3-13. [PubMed]
  5. Kowanetz M, Valcourt U, Bergstrom R, Heldin CH, Moustakas A. Id2 and Id3 define the potency of cell proliferation and differentiation responses to transforming growth factor beta and bone morphogenetic protein. Mol Cell Biol. 2004 May;24(10):4241-54.  [PubMed]
  6. Kluger Y, Tuck DP, Chang JT, Nakayama Y, Poddar R, Kohya N, Lian Z, Nasr AB, Halaban HR, Krause DS, Zhang X, Newburger PE, Weissman SM. Lineage specificity of gene expression patterns. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6508-13.  [PubMed]  
  7. Araki H, Katayama N, Yamashita Y, Mano H, Fujieda A, Usui E, Mitani H, Ohishi K, Nishii K, Masuya M, Minami N, Nobori T, Shiku H. Reprogramming of human postmitotic neutrophils into macrophages by growth factors. Blood. 2004 Apr 15;103(8):2973-80. [PubMed]
  8. Powles N, Babbs C, Ficker M, Schimmang T, Maconochie M. Identification and analysis of genes from the mouse otic vesicle and their association with developmental subprocesses through in situ hybridization. Dev Biol. 2004 Apr 1;268(1):24-38. [PubMed]
  9. Liu T, Dhanasekaran SM, Jin H, Hu B, Tomlins SA, Chinnaiyan AM, Phan SH. FIZZ1 stimulation of myofibroblast differentiation. Am J Pathol. 2004 Apr;164(4):1315-26. [PubMed]
  10. Flentke GR, Baker MW, Docterman KE, Power S, Lough J, Smith SM. Microarray analysis of retinoid-dependent gene activity during rat embryogenesis: increased collagen fibril production in a model of retinoid insufficiency. Dev Dyn. 2004 Apr;229(4):886-98. [PubMed]

Neurobiology

  1. Lim CR, Fukakusa A, Matsubara K.  Gene expression profiling of mouse postnatal cerebellar development using cDNA microarrays. Gene. 2004 May 26;333:3-13. [PubMed]
  2. Funatsu N, Inoue T, Nakamura S. Gene Expression Analysis of the Late Embryonic Mouse Cerebral Cortex Using DNA Microarray: Identification of Several Region- and Layer-specific Genes. Cereb Cortex. 2004 May 13 [Epub ahead of print] [PubMed]
  3. Wang P, Saraswati S, Guan Z, Watkins CJ, Wurtman RJ, Littleton JT. A Drosophila temperature-sensitive seizure mutant in phosphoglycerate kinase disrupts ATP generation and alters synaptic function. J Neurosci. 2004 May 12;24(19):4518-29. [PubMed]
  4. Boeshore KL, Schreiber RC, Vaccariello SA, Sachs HH, Salazar R, Lee J, Ratan RR, Leahy P, Zigmond RE. Novel changes in gene expression following axotomy of a sympathetic ganglion: A microarray analysis. J Neurobiol. 2004 May;59(2):216-35.[PubMed]
  5. Mirnics K, Pevsner J. Progress in the use of microarray technology to study the neurobiology of disease. Nat Neurosci. 2004 May;7(5):434-9.[PubMed]
  6. Lein ES, Zhao X, Gage FH. Defining a molecular atlas of the hippocampus using DNA microarrays and high-throughput in situ hybridization. J Neurosci. 2004 Apr 14;24(15):3879-89. [PubMed]
  7. Gustincich S, Contini M, Gariboldi M, Puopolo M, Kadota K, Bono H, LeMieux J, Walsh P, Carninci P, Hayashizaki Y, Okazaki Y, Raviola E. Gene discovery in genetically labeled single dopaminergic neurons of the retina. Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):5069-74. [PubMed]
  8. Walker SJ, Worst TJ, Freeman WM, Vrana KE. Functional genomic analysis in pain research using hybridization arrays. Methods Mol Med. 2004;99:239-54. [PubMed]

Signal transduction

  1. Huang YH, Li D, Winoto A, Robey EA. Distinct transcriptional programs in thymocytes responding to T cell receptor, Notch, and positive selection signals. Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):4936-41.[PubMed]

Apoptosis

  1. Nair VD, Yuen T, Olanow CW, Sealfon SC. Early single cell bifurcation of pro-and anti-apoptotic states during oxidative stress. J Biol Chem. 2004 Apr 12 [Epub ahead of print] [PubMed]

Human

  1. Dobson AT, Raja R, Abeyta MJ, Taylor T, Shen S, Haqq C, Pera RA. The unique transcriptome through day 3 of human preimplantation development. Hum Mol Genet. 2004 May 18;. [Epub ahead of print][PubMed]

Animal

  1. Parisi M, Nuttall R, Edwards P, Minor J, Naiman D, Lu J, Doctolero M, Vainer M, Chan C, Malley J, Eastman S, Oliver B. A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. Genome Biol. 2004;5(6):R40. [PubMed]
  2. Cui XL, Soteropoulos P, Tolias P, Ferraris RP. Fructose-responsive genes in the small intestine of neonatal rats. Physiol Genomics. 2004 May 18;. [Epub ahead of print][PubMed]
  3. Landis GN, Abdueva D, Skvortsov D, Yang J, Rabin BE, Carrick J, Tavare S, Tower J. Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2004 May 18;101(20):7663-8. [PubMed]
  4. Pedra JH, McIntyre LM, Scharf ME, Pittendrigh BR. Genome-wide transcription profile of field- and laboratory-selected dichlorodiphenyltrichloroethane (DDT)-resistant Drosophila. Proc Natl Acad Sci U S A. 2004 May 4;101(18):7034-9.[PubMed]
  5. Wang Z, Dooley TP, Curto EV, Davis RL, VandeBerg JL. Cross-species application of cDNA microarrays to profile gene expression using UV-induced melanoma in Monodelphis domestica as the model system. Genomics. 2004 Apr;83(4):588-99. [PubMed]

Plant

  1. Tepperman JM, Hudson ME, Khanna R, Zhu T, Chang SH, Wang X, Quail PH. Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J. 2004 Jun;38(5):725-39. [PubMed]
  2. Wang G, Kong H, Sun Y, Zhang X, Zhang W, Altman N, DePamphilis CW, Ma H. Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. Plant Physiol. 2004 Jun;135(2):1084-99. [PubMed]
  3. Williams EJ, Bowles DJ. Coexpression of Neighboring Genes in the Genome of Arabidopsis thaliana. Genome Res. 2004 Jun;14(6):1060-7. [PubMed]
  4. Kimura S, Tahira Y, Ishibashi T, Mori Y, Mori T, Hashimoto J, Sakaguchi K. DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells. Nucleic Acids Res. 2004;32(9):2760-7. [PubMed]
  5. Wellmer F, Riechmann JL, Alves-Ferreira M, Meyerowitz EM. Genome-Wide Analysis of Spatial Gene Expression in Arabidopsis Flowers. Plant Cell. 2004 Apr 20 [Epub ahead of print]  [PubMed]
  6. Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A. Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev. 2004 Apr 12 [Epub ahead of print]  [PubMed]
  7. Kushiro T, Okamoto M, Nakabayashi K, Yamagishi K, Kitamura S, Asami T, Hirai N, Koshiba T, Kamiya Y, Nambara E. The Arabidopsis cytochrome P450 CYP707A encodes ABA 8'-hydroxylases: key enzymes in ABA catabolism. EMBO J. 2004 Apr 7;23(7):1647-56.[PubMed]
  8. Himanen K, Vuylsteke M, Vanneste S, Vercruysse S, Boucheron E, Alard P, Chriqui D, Van Montagu M, Inze D, Beeckman T. Transcript profiling of early lateral root initiation. Proc Natl Acad Sci U S A. 2004 Apr 6;101(14):5146-51. [PubMed]
  9. Yang J, Kamdem DP, Keathley DE, Han KH. Seasonal changes in gene expression at the sapwood-heartwood transition zone of black locust (Robinia pseudoacacia) revealed by cDNA microarray analysis. Tree Physiol. 2004 Apr;24(4):461-74. [PubMed]
  10. Andersson A, Keskitalo J, Sjodin A, Bhalerao R, Sterky F, Wissel K, Tandre K, Aspeborg H, Moyle R, Ohmiya Y, Bhalerao R, Brunner A, Gustafsson P, Karlsson J, Lundeberg J, Nilsson O, Sandberg G, Strauss S, Sundberg B, Uhlen M, Jansson S, Nilsson P. A transcriptional timetable of autumn senescence. Genome Biol. 2004;5(4):R24. [PubMed]

Microbiology

  1. Manna D, Breier AM, Higgins NP. Microarray analysis of transposition targets in Escherichia coli: The impact of transcription. Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9780-5. [PubMed]
  2. Martell M, Briones C, de Vicente A, Piron M, Esteban JI, Esteban R, Guardia J, Gomez J. Structural analysis of hepatitis C RNA genome using DNA microarrays. Nucleic Acids Res. 2004 Jun 24;32(11):e90. [PubMed]
  3. Peplies J, Lau SC, Pernthaler J, Amann R, Glockner FO. Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environ Microbiol. 2004 Jun;6(6):638-45. [PubMed]
  4. Edwards-Ingram LC, Gent ME, Hoyle DC, Hayes A, Stateva LI, Oliver SG. Comparative genomic hybridization provides new insights into the molecular taxonomy of the Saccharomyces sensu stricto complex. Genome Res. 2004 Jun;14(6):1043-51. [PubMed]
  5. Bodrossy L, Sessitsch A. Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol. 2004 Jun;7(3):245-54. [PubMed]
  6. Fujita K, Matsuyama A, Kobayashi Y, Iwahashi H. Comprehensive gene expression analysis of the response to straight-chain alcohols in Saccharomyces cerevisiae using cDNA microarray. J Appl Microbiol. 2004;97(1):57-67. [PubMed]
  7. Onda M, Ota K, Chiba T, Sakaki Y, Ito T. Analysis of gene network regulating yeast multidrug resistance by artificial activation of transcription factors: involvement of Pdr3 in salt tolerance. Gene. 2004 May 12;332:51-9. [PubMed]
  8. Ren D, Bedzyk LA, Setlow P, Thomas SM, Ye RW, Wood TK. Gene expression in Bacillus subtilis surface biofilms with and without sporulation and the importance of yver for biofilm maintenance. Biotechnol Bioeng. 2004 May 5;86(3):344-64.[PubMed]
  9. Moqtaderi Z, Struhl K. Genome-Wide Occupancy Profile of the RNA Polymerase III Machinery in Saccharomyces cerevisiae Reveals Loci with Incomplete Transcription Complexes. Mol Cell Biol. 2004 May;24(10):4118-27.  [PubMed] [Supplemental material]
  10. Duncan R. DNA microarray analysis of protozoan parasite gene expression: outcomes correlate with mechanisms of regulation. Trends Parasitol. 2004 May;20(5):211-5. [PubMed]
  11. Moqtaderi Z, Struhl K. Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol. 2004 May;24(10):4118-27.   [PubMed]
  12. Bond U, Neal C, Donnelly D, James TC. Aneuploidy and copy number breakpoints in the genome of lager yeasts mapped by microarray hybridisation. Curr Genet. 2004 Apr 21 [Epub ahead of print][PubMed]
  13. Lyons TJ, Villa NY, Regalla LM, Kupchak BR, Vagstad A, Eide DJ. Metalloregulation of yeast membrane steroid receptor homologs. Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5506-11. [PubMed]
  14. Prouty AM, Brodsky IE, Falkow S, Gunn JS. Bile-salt-mediated induction of antimicrobial and bile resistance in Salmonella typhimurium. Microbiology. 2004 Apr;150(Pt 4):775-783.  [PubMed]
  15. Fay JC, McCullough HL, Sniegowski PD, Eisen MB. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol. 2004;5(4):R26. [PubMed]

Genome scale studies

  1. Kurdistani SK, Tavazoie S, Grunstein M. Mapping global histone acetylation patterns to gene expression. Cell. 2004 Jun 11;117(6):721-33. [PubMed]
  2. Kondo Y, Shen L, Yan PS, Huang TH, Issa JP. Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc Natl Acad Sci U S A. 2004 May 11;101(19):7398-403. [PubMed]
  3. Silva JM, Mizuno H, Brady A, Lucito R, Hannon GJ. RNA interference microarrays: High-throughput loss-of-function genetics in mammalian cells. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6548-52. [PubMed]

Comparative Genomics

  1. Gu Z, Rifkin SA, White KP, Li WH. Duplicate genes increase gene expression diversity within and between species. Nat Genet. 2004 Jun;36(6):577-9.[PubMed]
  2. Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, Muetzel B, Wirkner U, Ansorge W, Paabo S. A neutral model of transcriptome evolution. PLoS Biol. 2004 May;2(5):E132.[PubMed]
  3. Grigoryev DN, Ma SF, Irizarry RA, Ye SQ, Quackenbush J, Garcia JG. Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biol. 2004;5(5):R34. [PubMed]

Network/pathway reconstruction and analysis

  1. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 6;429(6987):92-6.  [PubMed]
  2. Cakir T, Kirdar B, Ulgen KO. Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks. Biotechnol Bioeng. 2004 May 5;86(3):251-60. [PubMed]
  3. Chen G, Hata N, Zhang MQ. Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res. 2004 Apr 28;32(8):2362-71.[PubMed]
  4. Tringe SG, Wagner A, Ruby SW. Enriching for direct regulatory targets in perturbed gene-expression profiles. Genome Biol. 2004;5(4):R29.[PubMed]

Genetic analysis

  1. Moutereau S, Narwa R, Matheron C, Vongmany N, Simon E, Goossens M. An improved electronic microarray-based diagnostic assay for identification of MEFV mutations. Hum Mutat. 2004 Jun;23(6):621-8. [PubMed]
  2. Brunelle BW, Nicholson TL, Stephens RS. Microarray-based genomic surveying of gene polymorphisms in Chlamydia trachomatis. Genome Biol. 2004;5(6):R42. [PubMed]
  3. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C. dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics. 2004 May 22;20(8):1233-40.[PubMed]
  4. Wong KK, Tsang YT, Shen J, Cheng RS, Chang YM, Man TK, Lau CC. Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA. Nucleic Acids Res. 2004 May 17;32(9):e69. [PubMed]
  5. Yamamoto F, Yamamoto M. A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses. Mol Genet Genomics. 2004 May 14 [Epub ahead of print] [PubMed]
  6. Maitra A, Cohen Y, Gillespie SE, Mambo E, Fukushima N, Hoque MO, Shah N, Goggins M, Califano J, Sidransky D, Chakravarti A. The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res. 2004 May;14(5):812-9. [PubMed]
  7. Seo TS, Bai X, Ruparel H, Li Z, Turro NJ, Ju J. Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry. Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5488-93. [PubMed]
  8. Vainrub A, Pettitt BM. Theoretical aspects of genomic variation screening using DNA microarrays. Biopolymers. 2004 Apr 5;73(5):614-20. [PubMed]
  9. Tsang S, Sun Z, Stewart C, Lum N, Frankenberger C, Subleski M, Rasmussen L, Munroe DJ. Development of multiplex DNA electronic microarrays using a universal adaptor system for detection of single nucleotide polymorphisms. Biotechniques. 2004 Apr;36(4):682-8.[PubMed]
  10. Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques. 2004 Apr;36(4):664-70, 672, 674-5.  [PubMed]

ArrayCGH

  1. DeLeeuw 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 Jun 30 [Epub ahead of print] [PubMed]
  2. Jong K, Marchiori E, Meijer G, Van Der Vaart A, Ylstra B. Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics. 2004 Jun 16 [Epub ahead of print] [PubMed]
  3. Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J Clin Pathol. 2004 Jun;57(6):644-6. [PubMed]
  4. Edwards-Ingram LC, Gent ME, Hoyle DC, Hayes A, Stateva LI, Oliver SG. Comparative genomic hybridization provides new insights into the molecular taxonomy of the Saccharomyces sensu stricto complex. Genome Res. 2004 Jun;14(6):1043-51. [PubMed]
  5. Yano S, Matsuyama H, Matsuda K, Matsumoto H, Yoshihiro S, Naito K. Accuracy of an array comparative genomic hybridization (CGH) technique in detecting DNA copy number aberrations: comparison with conventional CGH and loss of heterozygosity analysis in prostate cancer. Cancer Genet Cytogenet. 2004 Apr 15;150(2):122-7. [PubMed]
  6. Shaw-Smith C, Redon R, Rickman L, Rio M, Willatt L, Fiegler H, Firth H, Sanlaville D, Winter R, Colleaux L, Bobrow M, Carter NP. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet. 2004 Apr;41(4):241-248. [PubMed]
  7. Kwon JY, Hong M, Choi MS, Kang S, Duke K, Kim S, Lee S, Lee J. Ethanol-response genes and their regulation analyzed by a microarray and comparative genomic approach in the nematode Caenorhabditis elegans. Genomics. 2004 Apr;83(4):600-14. [PubMed]

Pharmacogenomics and pharmacogenetics

  1. Krishnan AV, Shinghal R, Raghavachari N, Brooks JD, Peehl DM, Feldman D. Analysis of vitamin D-regulated gene expression in LNCaP human prostate cancer cells using cDNA microarrays. Prostate. 2004 May 15;59(3):243-51.[PubMed]
  2. Ohara N, Hayashi Y, Yamada S, Kim SK, Matsunaga T, Yanagiguchi K, Ikeda T. Early gene expression analyzed by cDNA microarray and RT-PCR in osteoblasts cultured with water-soluble and low molecular chitooligosaccharide. Biomaterials. 2004 May;25(10):1749-54. [PubMed]
  3. Newman SP, Leese MP, Purohit A, James DR, Rennie CE, Potter BV, Reed MJ. Inhibition of in vitro angiogenesis by 2-methoxy- and 2-ethyl-estrogen sulfamates. Int J Cancer. 2004 Apr 20;109(4):533-40. [PubMed]
  4. 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 Apr 13;17(2):201-14. [PubMed]
  5. Tanaka Y, Kobayashi H, Suzuki M, Hirashima Y, Kanayama N, Terao T. Genetic downregulation of pregnancy-associated plasma protein-A (PAPP-A) by bikunin reduces IGF-I-dependent Akt and ERK1/2 activation and subsequently reduces ovarian cancer cell growth, invasion and metastasis. Int J Cancer. 2004 Apr 10;109(3):336-47. [PubMed]
  6. Kim S, Kang BY, Cho SY, Sung DS, Chang HK, Yeom MH, Kim DH, Sim YC, Lee YS. Compound K induces expression of hyaluronan synthase 2 gene in transformed human keratinocytes and increases hyaluronan in hairless mouse skin. Biochem Biophys Res Commun. 2004 Apr 2;316(2):348-55. [PubMed]
  7. Levitt RJ, Buckley J, Blouin MJ, Schaub B, Triche TJ, Pollak M. Growth inhibition of breast epithelial cells by celecoxib is associated with upregulation of insulin-like growth factor binding protein-3 expression. Biochem Biophys Res Commun. 2004 Apr 2;316(2):421-8. [PubMed]
  8. Meloni R, Khalfallah O, Biguet NF. DNA microarrays and pharmacogenomics. Pharmacol Res. 2004 Apr;49(4):303-8. [PubMed]

Toxicogenomics

  1. Ammon-Treiber S, Tischmeyer H, Riechert U, Hollt V. Gene expression of transcription factors in the rat brain after morphine withdrawal. Neurochem Res. 2004 Jun;29(6):1267-73. [PubMed]
  2. Faiola B, Fuller ES, Wong VA, Recio L. Gene expression profile in bone marrow and hematopoietic stem cells in mice exposed to inhaled benzene. Mutat Res. 2004 May 18;549(1-2):195-212.[PubMed]
  3. Huang Q, Jin X, Gaillard ET, Knight BL, Pack FD, Stoltz JH, Jayadev S, Blanchard KT. Gene expression profiling reveals multiple toxicity endpoints induced by hepatotoxicants. Mutat Res. 2004 May 18;549(1-2):147-67. [PubMed]
  4. Kier LD, Neft R, Tang L, Suizu R, Cook T, Onsurez K, Tiegler K, Sakai Y, Ortiz M, Nolan T, Sankar U, Li AP. Applications of microarrays with toxicologically relevant genes (tox genes) for the evaluation of chemical toxicants in Sprague Dawley rats in vivo and human hepatocytes in vitro. Mutat Res. 2004 May 18;549(1-2):101-13. [PubMed]
  5. Harris AJ, Dial SL, Casciano DA. Comparison of basal gene expression profiles and effects of hepatocarcinogens on gene expression in cultured primary human hepatocytes and HepG2 cells. Mutat Res. 2004 May 18;549(1-2):79-99.  [PubMed]
  6. Koch-Paiz CA, Amundson SA, Bittner ML, Meltzer PS, Fornace AJ Jr. Functional genomics of UV radiation responses in human cells. Mutat Res. 2004 May 18;549(1-2):65-78. [PubMed]
  7. Hu T, Gibson DP, Carr GJ, Torontali SM, Tiesman JP, Chaney JG, Aardema MJ. Identification of a gene expression profile that discriminates indirect-acting genotoxins from direct-acting genotoxins. Mutat Res. 2004 May 18;549(1-2):5-27. [PubMed]
  8. Tong W, Harris S, Cao X, Fang H, Shi L, Sun H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, Casciano D. Development of public toxicogenomics software for microarray data management and analysis. Mutat Res. 2004 May 18;549(1-2):241-53.[PubMed]
  9. De Longueville F, Bertholet V, Remacle J. DNA microarrays as a tool in toxicogenomics. Comb Chem High Throughput Screen. 2004 May;7(3):207-11. [PubMed]

Technical development

  1. Ghadessy FJ, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, Vaisman A, Woodgate R, Holliger P. Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol. 2004 Jun;22(6):755-9. [PubMed]
  2. Korn EL, Habermann JK, Upender MB, Ried T, McShane LM. Objective method of comparing DNA microarray image analysis systems. Biotechniques. 2004 Jun;36(6):960-7. [PubMed]
  3. Gutmann O, Kuehlewein R, Reinbold S, Niekrawietz R, Steinert CP, de Heij B, Zengerle R, Daub M. A highly parallel nanoliter dispenser for microarray fabrication. Biomed Microdevices. 2004 Jun;6(2):131-7. [PubMed]
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  4. Mecham BH, Wetmore DZ, Szallasi Z, Sadovsky Y, Kohane I, Mariani TJ. Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics. 2004 May 25;. [Epub ahead of print][PubMed]
  5. Yu F, Yao D, Knoll W. Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS). Nucleic Acids Res. 2004 May 20;32(9):e75. [PubMed]
  6. Mary-Huard T, Daudin JJ, Robin S, Bitton F, Cabannes E, Hilson P. Spotting effect in microarray experiments. BMC Bioinformatics. 2004 May 19 [Epub ahead of print] [PubMed]
  7. Fixe F, Chu V, Prazeres DM, Conde JP. An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays. Nucleic Acids Res. 2004 May 17;32(9):e70.[PubMed]
  8. Smirnov DA, Burdick JT, Morley M, Cheung VG. Method for manufacturing whole-genome microarrays by rolling circle amplification. Genes Chromosomes Cancer. 2004 May;40(1):72-7. [PubMed]
  9. Sartor M, Schwanekamp J, Halbleib D, Mohamed I, Karyala S, Medvedovic M, Tomlinson CR. Microarray results improve significantly as hybridization approaches equilibrium. Biotechniques. 2004 May;36(5):790-6. [PubMed]
  10. Gunderson KL, Kruglyak S, Graige MS, Garcia F, Kermani BG, Zhao C, Che D, Dickinson T, Wickham E, Bierle J, Doucet D, Milewski M, Yang R, Siegmund C, Haas J, Zhou L, Oliphant A, Fan JB, Barnard S, Chee MS. Decoding Randomly Ordered DNA Arrays. Genome Res. 2004 May;14(5):870-7. [PubMed]
  11. Fan JB, Yeakley JM, Bibikova M, Chudin E, Wickham E, Chen J, Doucet D, Rigault P, Zhang B, Shen R, McBride C, Li HR, Fu XD, Oliphant A, Barker DL, Chee MS. A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 2004 May;14(5):878-85.  [PubMed]
  12. Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res. 2004 May;32(9):e74. [PubMed]
  13. Kimura N, Oda R, Inaki Y, Suzuki O. Attachment of oligonucleotide probes to poly carbodiimide-coated glass for microarray applications. Nucleic Acids Res. 2004 Apr 23;32(7):e68. [PubMed]
  14. Liu RH, Yang J, Lenigk R, Bonanno J, Grodzinski P. Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection. Anal Chem. 2004 Apr 1;76(7):1824-31. [PubMed]
  15. Wang Z, Dooley TP, Curto EV, Davis RL, VandeBerg JL. Cross-species application of cDNA microarrays to profile gene expression using UV-induced melanoma in Monodelphis domestica as the model system. Genomics. 2004 Apr;83(4):588-99. [PubMed]
  16. Chandler DP. Unshackling expression profiling arrays. Nat Biotechnol. 2004 Apr;22(4):396-7. [PubMed]
  17. Rockett JC, Hellmann GM. Confirming microarray data-is it really necessary? Genomics. 2004 Apr;83(4):541-9. [PubMed]
  18. Roth ME, Feng L, McConnell KJ, Schaffer PJ, Guerra CE, Affourtit JP, Piper KR, Guccione L, Hariharan J, Ford MJ, Powell SW, Krishnaswamy H, Lane J,Guccione L, Intrieri G, Merkel JS, Perbost C, Valerio A, Zolla B, Graham CD, Hnath J, Michaelson C, Wang R, Ying B, Halling C, Parman CE, Raha D, Orr B, Jedrzkiewicz B, Liao J, Tevelev A, Mattessich MJ, Kranz DM, Lacey M, Kaufman JC, Kim J, Latimer DR, Lizardi PM. Expression profiling using a hexamer-based universal microarray. Nat Biotechnol. 2004 Apr;22(4):418-26. [PubMed]
  19. Hoffmann KF, Fitzpatrick JM. Gene expression studies using self-fabricated parasite cDNA microarrays. Methods Mol Biol. 2004;270:219-36. [PubMed]
  20. Beier V, Bauer A, Baum M, Hoheisel JD. Fluorescent sample labeling for DNA microarray analyses. Methods Mol Biol. 2004;283:127-36. [PubMed]

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

  1. Szaniszlo P, Wang N, Sinha M, Reece LM, Van Hook JW, Luxon BA, Leary JF. Getting the right cells to the array: Gene expression microarray analysis of cell mixtures and sorted cells. Cytometry. 2004 Jun;59A(2):191-202. [PubMed]
  2. Croner RS, Guenther K, Foertsch T, Siebenhaar R, Brueckl WM, Stremmel C, Hlubek F, Hohenberger W, Reingruber B. Tissue preparation for gene expression profiling of colorectal carinoma: Three alternatives to laser microdissection with preamplification. J Lab Clin Med. 2004 Jun;143(6):344-51. [PubMed]
  3. Williams BA, Gwirtz RM, Wold BJ. Genomic DNA as a cohybridization standard for mammalian microarray measurements. Nucleic Acids Res. 2004 Jun;32(10):e81. [PubMed]
  4. Spruessel A, Steimann G, Jung M, Lee SA, Carr T, Fentz AK, Spangenberg J, Zornig C, Juhl HH, David KA. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. Biotechniques. 2004 Jun;36(6):1030-7. [PubMed]
  5. Cronin M, Ghosh K, Sistare F, Quackenbush J, Vilker V, O'Connell C. Universal RNA Reference Materials for Gene Expression. Clin Chem. 2004 May 20 [Epub ahead of print] [PubMed]
  6. Burke PV, Lai LC, Kwast KE. A rapid filtration apparatus for harvesting cells under controlled conditions for use in genome-wide temporal profiling studies. Anal Biochem. 2004 May 1;328(1):29-34. [PubMed]
  7. Egyhazi S, Bjohle J, Skoog L, Huang F, Borg AL, Frostvik Stolt M, Hagerstrom T, Ringborg U, Bergh J. Proteinase k added to the extraction procedure markedly increases RNA yield from primary breast tumors for use in microarray studies. Clin Chem. 2004 May;50(5):975-6. [PubMed]
  8. Schneider J, Buness A, Huber W, Volz J, Kioschis P, Hafner M, Poustka A, Sultmann H. Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments. BMC Genomics. 2004 Apr 30;5(1):29.[PubMed]
  9. Cao W, Epstein C, Liu H, DeLoughery C, Ge N, Lin J, Diao R, Cao H, Long F, Zhang X, Chen Y, Wright PS, Busch S, Wenck M, Wong K, Saltzman AG, Tang Z, Liu L, Zilberstein A. Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study. BMC Genomics. 2004 Apr 27 [Epub ahead of print][PubMed]
  10. Kenzelmann M, Klaren R, Hergenhahn M, Bonrouhi M, Grone HJ, Schmid W, Schutz G. High-accuracy amplification of nanogram total RNA amounts for gene profiling. Genomics. 2004 Apr;83(4):550-8. [PubMed]
  11. Etienne W, Meyer MH, Peppers J, Meyer RA Jr. Comparison of mRNA gene expression by RT-PCR and DNA microarray. Biotechniques. 2004 Apr;36(4):618-20, 622, 624-6. [PubMed]

Experimental design, sample size & power

  1. Zhang SD, Gant TW. A statistical framework for the design of microarray experiments and effective detection of differential gene expression. Bioinformatics. 2004 Jun 4 [Epub ahead of print] [PubMed]
  2. Barrera L, Benner C, Tao YC, Winzeler E, Zhou Y. Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays. BMC Bioinformatics. 2004 Apr 20;5(1):42. [PubMed]

Data analysis

  1. Li Z, Chan C. Integrating gene expression and metabolic profiles. J Biol Chem. 2004 Jun 25;279(26):27124-37. [PubMed]
  2. Thygesen HH, Zwinderman AH. Comparing transformation methods for DNA microarray data. BMC Bioinformatics. 2004 Jun 17;5(1):77. [Epub ahead of print] [PubMed]
  3. Girolami M, Breitling R. Biologically valid linear factor models of gene expression. Bioinformatics. 2004 Jun 16 [Epub ahead of print] [PubMed]
  4. Bhattacharjee M, Pritchard CC, Nelson PS, Arjas E. Bayesian integrated functional analysis of microarray data. Bioinformatics. 2004 Jun 4 [Epub ahead of print] [PubMed]
  5. Jarvinen AK, Hautaniemi S, Edgren H, Auvinen P, Saarela J, Kallioniemi OP, Monni O. Are data from different gene expression microarray platforms comparable? Genomics. 2004 Jun;83(6):1164-8. [PubMed]
  6. Kauermann G, Eilers P. Modeling microarray data using a threshold mixture model. Biometrics. 2004 Jun;60(2):376-87.  [PubMed]
  7. Aimone JB, Gage FH. Unbiased characterization of high-density oligonucleotide microarrays using probe-level statistics. J Neurosci Methods. 2004 May 30;135(1-2):27-33. [PubMed]
  8. Yang ZR. Mining gene expression data based on template theory. Bioinformatics. 2004 May 27 [Epub ahead of print] [PubMed]
  9. Curtis RK, Brand MD. Analysing microarray data using modular regulation analysis. Bioinformatics. 2004 May 22;20(8):1272-84.[PubMed]
  10. Archer KJ, Dumur CI, Ramakrishnan V. Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals. BMC Bioinformatics. 2004 May 17;5(1):60. [PubMed]
  11. Dodd LE, Korn EL, McShane LM, Chandramouli GV, Chuang EY. Correcting log ratios for signal saturation in cDNA microarrays. Bioinformatics. 2004 May 14 [Epub ahead of print] [PubMed]
  12. Gunderson KL, Kruglyak S, Graige MS, Garcia F, Kermani BG, Zhao C, Che D, Dickinson T, Wickham E, Bierle J, Doucet D, Milewski M, Yang R, Siegmund C, Haas J, Zhou L, Oliphant A, Fan JB, Barnard S, Chee MS. Decoding randomly ordered DNA arrays. Genome Res. 2004 May;14(5):870-7. [PubMed]
  13. Gu X. Statistical framework for phylogenomic analysis of gene family expression profiles. Genetics. 2004 May;167(1):531-42. [PubMed]
  14. Ochs MF, Moloshok TD, Bidaut G, Toby G. Bayesian decomposition: analyzing microarray data within a biological context. Ann N Y Acad Sci. 2004 May;1020:212-26. [PubMed]
  15. Rosenfeld S, Wang T, Kim Y, Milner J. Numerical deconvolution of cDNA microarray signal: simulation study. Ann N Y Acad Sci. 2004 May;1020:110-23. [PubMed]
  16. Tadesse MG, Ibrahim JG. A bayesian hierarchical model for the analysis of Affymetrix arrays.Ann N Y Acad Sci. 2004 May;1020:41-8. [PubMed]
  17. Nilsson J, Fioretos T, Hoglund M, Fontes M. Approximate geodesic distances reveal biologically relevant structures in microarray data. Bioinformatics 2004 Apr 12; 20:874-880 [PubMed]
  18. Robinson PN, Wollstein A, Bohme U, Beattie B. Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology. Bioinformatics 2004 Apr 12; 20:979-981 [PubMed]
  19. Ouyang M, Welsh WJ, Georgopoulos P. Gaussian mixture clustering and imputation of microarray data. Bioinformatics 2004 Apr 12; 20:917-923 [PubMed]
  20. Ekstrom CT, Bak S, Kristensen C, Rudemo M. Spot shape modelling and data transformations for microarrays. Bioinformatics. 2004 Apr 1 [Epub ahead of print] [PubMed]
  21. van Eijk R, Oosting J, Sieben N, van Wezel T, Cleton-Jansen AM. Visualization of regional gene expression biases by microarray data sorting. Biotechniques. 2004 Apr;36(4):592-4, 596.[PubMed]
  22. Cui Y, Zhou M, Wong WH. Integrated analysis of microarray data and gene function information. OMICS. 2004 Summer;8(2):106-17. [PubMed]

Oligo design for array manufacturing

  1. Chou HH, Hsia AP, Mooney DL, Schnable PS. PICKY: oligo microarray design for large genomes. Bioinformatics. 2004 Jun 4 [Epub ahead of print] [PubMed]
  2. Wang J, Li KB, Sung WK. G-PRIMER: greedy algorithm for selecting minimal primer set. Bioinformatics. 2004 Apr 8 [Epub ahead of print] [PubMed]
  3. Boutros PC, Okey AB. PUNS: transcriptomic- and genomic- in silico PCR for enhanced primer design. Bioinformatics. 2004 Apr 8 [Epub ahead of print][PubMed]
  4. Zheng J, Close TJ, Jiang T, Lonardi S. Efficient selection of unique and popular oligos for large EST databases* Bioinformatics. 2004 Apr 1 [Epub ahead of print] [PubMed]

Image analysis

  1. Korn EL, Habermann JK, Upender MB, Ried T, McShane LM. Objective method of comparing DNA microarray image analysis systems. Biotechniques. 2004 Jun;36(6):960-7. [PubMed]
  2. Ryu M, Dae Kim J, Goo Min B, Pang MG, Kim J. Nonlinear matching measure for the analysis of on-off type DNA microarray images. J Biomed Opt. 2004 May-Jun;9(3):432-8. [PubMed]
  3. Rahnenfuhrer J, Bozinov D. Hybrid clustering for microarray image analysis combining intensity and shape features. BMC Bioinformatics. 2004 Apr 29 [Epub ahead of print] [PubMed]

Affymetrix probe level analysis

  1. Wu Z, Irizarry RA. Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004 Jun;22(6):656-8. [PubMed]
  2. Zhang L, Wu C, Carta R, Baggerly K, Coombes KR. Response to Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004 Jun;22(6):658. [PubMed]
  3. James AC, Veitch JG, Zareh AR, Triche T. Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarrays. Bioinformatics. 2004 May 1;20(7):1060-5.[PubMed]
  4. Tadesse MG, Ibrahim JG. A bayesian hierarchical model for the analysis of Affymetrix arrays. Ann N Y Acad Sci. 2004 May;1020:41-8. Review. [PubMed]
  5. Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP. Optimizing signal/noise ratios in expression profiling: project-specific algorithm selection and detection p value weighting in affymetrix microarrays. Bioinformatics. 2004 Apr 29 [Epub ahead of print][PubMed]
  6. Barash Y, Dehan E, Krupsky M, Franklin W, Geraci M, Friedman N, Kaminski N. Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics 2004 Apr 12; 20: 839-846 [PubMed]
  7. Chen DT, Lin SH, Soong SJ. Gene selection for oligonucleotide array: an approach using PM probe level data. Bioinformatics 2004 Apr 12; 20:854-862 [PubMed]

Normalization

Pattern recognition, classification & data mining by unsupervised methods

  1. Duan F, Zhang H. Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights. Bioinformatics. 2004 May 27 [Epub ahead of print] [PubMed]
  2. Medvedovic M, Yeung KY, Bumgarner RE. Bayesian mixture model based clustering of replicated microarray data. Bioinformatics. 2004 May 22;20(8):1222-32.[PubMed]
  3. Lepre J, Rice JJ, Tu Y, Stolovitzky G. Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data. Bioinformatics. 2004 May 1;20(7):1033-44. [PubMed]
  4. Tang C, Zhang A, Ramanathan M.  ESPD: a pattern detection model underlying gene expression profiles. Bioinformatics 2004 Apr 12; 20: 829-838 [PubMed]
  5. Dugas M, Merk S, Breit S, Dirschedl P. mdclust—exploratory microarray analysis by multidimensional clustering. Bioinformatics 2004 Apr 12; 20:931-936 [PubMed]
  6. Zhou X, Wang X, Dougherty ER, Russ D, Suh E. Gene clustering based on clusterwide mutual information. J Comput Biol. 2004;11(1):147-61. [PubMed]

Pattern recognition, classification & data mining by supervised methods

  1. Liu Y, Ringner M. Multiclass discovery in array data. BMC Bioinformatics. 2004 Jun 04;5(1):70.  [PubMed]
  2. McCarthy JF, Marx KA, Hoffman PE, Gee AG, O'Neil P, Ujwal ML, Hotchkiss J. Applications of machine learning and high-dimensional visualization in cancer detection, diagnosis, and management. Ann N Y Acad Sci. 2004 May;1020:239-62. [PubMed]
  3. Broet P, Lewin A, Richardson S, Dalmasso C, Magdelenat H. A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments. Bioinformatics. 2004 Apr 29 [Epub ahead of print][PubMed]
  4. Alexandridis R, Lin S, Irwin M. Class discovery and classification of tumor samples using mixture modeling of gene expression data. Bioinformatics. 2004 Apr 29 [Epub ahead of print][PubMed]
  5. Li T, Zhang C, Ogihara M. A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression. Bioinformatics. 2004 Apr 15 [Epub ahead of print] [PubMed]
  6. Glinsky GV, Higashiyama T, Glinskii AB. Classification of human breast cancer using gene expression profiling as a component of the survival predictor algorithm. Clin Cancer Res. 2004 Apr 1;10(7):2272-83.  [PubMed]
  7. Bair E, Tibshirani R. Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol. 2004 Apr;2(4):E108 [PubMed]

Network/pathway reconstruction and analysis

  1. Pournara I, Wernisch L. Reconstruction of gene networks using Bayesian learning and manipulation experiments. Bioinformatics. 2004 Jun 4 [Epub ahead of print] [PubMed]
  2. Chen G, Hata N, Zhang MQ. Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res. 2004;32(8):2362-71. [PubMed]
  3. Hashimoto RF, Kim S, Shmulevich I, Zhang W, Bittner ML, Dougherty ER. Growing genetic regulatory networ