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

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General

1. Iyer VR. Exploring the post-transcriptional RNA world with DNA microarrays. Trends Biotechnol. 2004 Oct;22(10):498-500. [PubMed]
   

Human disease studies

1. Di Bartolo D, Cesarman E. Uncovering the complexities of Kaposi's sarcoma through genome-wide expression analysis. Genome Biol. 2004;5(11):247. [PubMed]
2. Mischel PS, Cloughesy TF, Nelson SF. DNA-microarray analysis of brain cancer: molecular classification for therapy. Nat Rev Neurosci. 2004 Oct;5(10):782-92. [PubMed]
   

Disease screening, profiling and classification

1. Clement K, Viguerie N, Poitou C, Carette C, Pelloux V, Curat CA, Sicard A, Rome S, Benis A, Zucker JD, Vidal H, Laville M, Barsh GS, Basdevant A, Stich V, Cancello R, Langin D. Weight loss regulates inflammation-related genes in white adipose tissue of obese subjects. FASEB J. 2004 Nov;18(14):1657-69. [PubMed]
2. Evans SJ, Choudary PV, Neal CR, Li JZ, Vawter MP, Tomita H, Lopez JF, Thompson RC, Meng F, Stead JD, Walsh DM, Myers RM, Bunney WE, Watson SJ, Jones EG, Akil H. Dysregulation of the fibroblast growth factor system in major depression. Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15506-11. [PubMed]
3. Ning W, Li CJ, Kaminski N, Feghali-Bostwick CA, Alber SM, Di YP, Otterbein SL, Song R, Hayashi S, Zhou Z, Pinsky DJ, Watkins SC, Pilewski JM, Sciurba FC, Peters DG, Hogg JC, Choi AM. Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease. Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14895-900. [PubMed]
4. Segal E, Friedman N, Koller D, Regev A. A module map showing conditional activity of expression modules in cancer. Nat Genet. 2004 Oct;36(10):1090-8. [PubMed]
5. Aloy P, Russell RB. Ten thousand interactions for the molecular biologist. Nat Biotechnol. 2004 Oct;22(10):1317-21. [PubMed]

Diagnosis, prognosis and clinical applications

1. Mischel PS, Cloughesy TF, Nelson SF. DNA-microarray analysis of brain cancer: molecular classification for therapy. Nat Rev Neurosci. 2004 Oct;5(10):782-92. [PubMed]
   

Animal model studies

1. Di Giovanni S, Faden AI, Yakovlev A, Duke-Cohan JS, Finn T, Thouin M, Knoblach S, De Biase A, Bregman BS, Hoffman EP. Neuronal plasticity after spinal cord injury: identification of a gene cluster driving neurite outgrowth. FASEB J. 2004 Nov 2;. [Epub ahead of print] [PubMed]
2. Serra HG, Byam CE, Lande JD, Tousey SK, Zoghbi HY, Orr HT. Gene profiling links SCA1 pathophysiology to glutamate signaling in Purkinje cells of transgenic mice. Hum Mol Genet. 2004 Oct 15;13(20):2535-43.  [PubMed]  

In vitro studies

1. Lotem J, Benjamin H, Netanely D, Domany E, Sachs L. Induction in myeloid leukemic cells of genes that are expressed in different normal tissues. Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):16022-7.[PubMed]
2. Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, Yates JR 3rd, Winzeler EA. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004 Nov;14(11):2308-18. [PubMed]
   

Basic science studies

1. Lin KK, Chudova D, Hatfield GW, Smyth P, Andersen B. Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance. Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15955-60. [PubMed]
2. Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. Regulation of gene expression by a metabolic enzyme. Science. 2004 Oct 15;306(5695):482-4. [PubMed]

Gene product function

1. Wang JC, Derynck MK, Nonaka DF, Khodabakhsh DB, Haqq C, Yamamoto KR. Chromatin immunoprecipitation (ChIP) scanning identifies primary glucocorticoid receptor target genes. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15603-8. [PubMed]
2. Wan H, Xu Y, Ikegami M, Stahlman MT, Kaestner KH, Ang SL, Whitsett JA. Foxa2 is required for transition to air breathing at birth. Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14449-54. [PubMed]
   

General physiology

1. Adam RM, Eaton SH, Estrada C, Nimgaonkar A, Shih SC, Smith LE, Kohane IS, Bagli D, Freeman MR. Mechanical Stretch is a Highly Selective Regulator of Gene Expression in Human Bladder Smooth Muscle Cells. Physiol Genomics. 2004 Oct 5 [Epub ahead of print] [PubMed]
   

Development & differentiation

1. Dhanasekaran SM, Dash A, Yu J, Maine IP, Laxman B, Tomlins SA, Creighton CJ, Menon A, Rubin MA, Chinnaiyan AM. Molecular profiling of human prostate tissues: insights into gene expression patterns of prostate development during puberty. FASEB J. 2004 Nov 17; [Epub ahead of print] [PubMed]
2. Kuninger D, Kuzmickas R, Peng B, Pintar JE, Rotwein P. Gene discovery by microarray: identification of novel genes induced during growth factor-mediated muscle cell survival and differentiation. Genomics. 2004 Nov;84(5):876-89. [PubMed]
3. Ahn JI, Lee KH, Shin DM, Shim JW, Kim CM, Kim H, Lee SH, Lee YS. Temporal expression changes during differentiation of neural stem cells derived from mouse embryonic stem cell. J Cell Biochem. 2004 Oct 15;93(3):563. [PubMed]
4. Williams SS, Mear JP, Liang HC, Potter SS, Aronow BJ, Colbert MC. Large-scale reprogramming of cranial neural crest gene expression by retinoic acid exposure. Physiol Genomics. 2004 Oct 4;19(2):184-97.[PubMed]
5. Eichenberger P, Fujita M, Jensen ST, Conlon EM, Rudner DZ, Wang ST, Ferguson C, Haga K, Sato T, Liu JS, Losick R. The Program of Gene Transcription for a Single Differentiating Cell Type during Sporulation in Bacillus subtilis. PLoS Biol. 2004 Oct;2(10):e328. [PubMed]
6. Rowan S, Chen CM, Young TL, Fisher DE, Cepko CL. Transdifferentiation of the retina into pigmented cells in ocular retardation mice defines a new function of the homeodomain gene Chx10. Development. 2004 Oct;131(20):5139-52. [PubMed]

Neurobiology

1. Preuss TM, Caceres M, Oldham MC, Geschwind DH. Human brain evolution: insights from microarrays. Nat Rev Genet. 2004 Nov;5(11):850-60. [PubMed]
2. Ahn JI, Lee KH, Shin DM, Shim JW, Kim CM, Kim H, Lee SH, Lee YS. Temporal expression changes during differentiation of neural stem cells derived from mouse embryonic stem cell. J Cell Biochem. 2004 Oct 15;93(3):563. [PubMed]
   

Signal transduction

1. Yang M, Nelson D, Funakoshi Y, Padgett RW. Genome-wide microarray analysis of TGFb signaling in the Drosophila brain. BMC Dev Biol. 2004 Oct 8;4(1):14 [Epub ahead of print] [PubMed]
   

   Apoptosis

Human

1. Yamashita T, Honda M, Takatori H, Nishino R, Hoshino N, Kaneko S. Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes. Genomics. 2004 Nov;84(5):867-75. [PubMed]
2. Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart KW, Russell A, Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M, Caceres RM, Johnson JM, Armour CD, Garrett-Engele PW, Tsinoremas NF, Shoemaker DD. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol. 2004;5(10):R73. [PubMed]
3. Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol. 2004;5(10):R74. [PubMed]

Animal

1. Budak MT, Bogdanovich S, Wiesen M, Lozynska O, Khurana TS, Rubinstein NA. Layer-specific differences of gene expression in extraocular muscles identified by laser capture microscopy. Physiol Genomics. 2004 Oct 5 [Epub ahead of print][PubMed]
2. Taneri B, Snyder B, Novoradovsky A, Gaasterland T. Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific. Genome Biol. 2004;5(10):R75. [PubMed]
   

Plant

1. Honys D, Twell D. Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol. 2004;5(11):R85. [PubMed]
2. Gong JM, Waner DA, Horie T, Li SL, Horie R, Abid KB, Schroeder JI. Microarray-based rapid cloning of an ion accumulation deletion mutant in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15404-9. [PubMed]
3. Armstrong JI, Yuan S, Dale JM, Tanner VN, Theologis A. Identification of inhibitors of auxin transcriptional activation by means of chemical genetics in Arabidopsis. Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14978-83. Epub 2004 Oct 04. [PubMed]
4. Waters DL, Holton TA, Ablett EM, Lee LS, Henry RJ. cDNA microarray analysis of developing grape ( Vitis vinifera cv. Shiraz) berry skin. Funct Integr Genomics. 2004 Oct 5;. [Epub ahead of print] [PubMed]

Microbiology

1. Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 2004;5(11):R87. [PubMed]
   

Genome scale studies

1. Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 2004;5(11):R87. [PubMed]
2. Yamashita T, Honda M, Takatori H, Nishino R, Hoshino N, Kaneko S. Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes. Genomics. 2004 Nov;84(5):867-75. [PubMed]
3. Adjaye J, Herwig R, Herrmann D, Wruck W, Benkahla A, Brink TC, Nowak M, Carnwath JW, Hultschig C, Niemann H, Lehrach H. Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays. BMC Genomics. 2004 Oct 28;5(1):83 [Epub ahead of print] [PubMed]
4. Carter NP, Vetrie D. Applications of genomic microarrays to explore human chromosome structure and function. Hum Mol Genet. 2004 Oct 1;13 Spec No 2:R297-302. [PubMed]
5. Messina DN, Glasscock J, Gish W, Lovett M. An ORFeome-based Analysis of Human Transcription Factor Genes and the Construction of a Microarray to Interrogate Their Expression. Genome Res. 2004 Oct;14(10B):2041-7. [PubMed]

Comparative Genomics

1. Huminiecki L, Wolfe KH. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res. 2004 Oct;14(10):1870-9. [PubMed]
   

Network/pathway reconstruction and analysis

1. Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol. 2004;5(11):R90. [PubMed]

Genetic analysis

1. Daruwala RS, Rudra A, Ostrer H, Lucito R, Wigler M, Mishra B. A versatile statistical analysis algorithm to detect genome copy number variation. Proc Natl Acad Sci U S A. 2004 Nov 8;. [Epub ahead of print][PubMed]
2. Bang-Ce Y, Peng Z, Bincheng Y, Songyang L. Estimation of relative allele frequencies of single-nucleotide polymorphisms in different populations by microarray hybridization of pooled DNA. Anal Biochem. 2004 Oct 1;333(1):72-8. [PubMed]
3. Belosludtsev YY, Bowerman D, Weil R, Marthandan N, Balog R, Luebke K, Lawson J, Johnston SA, Lyons CR, Obrien K, Garner HR, Powdrill TF.  Organism identification using a genome sequence-independent universal microarray probe set. Biotechniques. 2004 Oct;37(4):654-8, 660. [PubMed]

ArrayCGH

1. Cardoso J, Molenaar L, de Menezes RX, Rosenberg C, Morreau H, Moslein G, Fodde R, Boer JM. Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH. Nucleic Acids Res. 2004 Oct 28;32(19):e146. [PubMed]
   

Pharmacogenomics and pharmacogenetics

Toxicogenomics

Technical development

1. Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, Bennett H, Rigault P, Barker D, McDaniel TK, Chee MS. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res. 2004 Nov;14(11):2347-56. [PubMed]
   

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

1. Stoyanova R, Upson JJ, Patriotis C, Ross EA, Henske EP, Datta K, Boman B, Clapper ML, Knudson AG, Bellacosa A. Use of RNA amplification in the optimal characterization of global gene expression using cDNA microarrays. J Cell Physiol. 2004 Dec;201(3):359-365. [PubMed]
2. Upson JJ, Stoyanova R, Cooper HS, Patriotis C, Ross EA, Boman B, Clapper ML, Knudson AG, Bellacosa A. Optimized procedures for microarray analysis of histological specimens processed by laser capture microdissection. J Cell Physiol. 2004 Dec;201(3):366-73. [PubMed]
   
3. Feezor RJ, Baker HV, Mindrinos M, Hayden D, Tannahill CL, Brownstein BH, Fay A, MacMillan S, Laramie J, Xiao W, Moldawer LL, Cobb JP, Laudanski K, Miller-Graziano CL, Maier RV, Schoenfeld D, Davis RW, Tompkins RG; Inflammation and Host Response to Injury, Large-Scale Collaborative Research Program. Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol Genomics. 2004 Nov 17;19(3):247-54. [PubMed]
4. Bengtsson H, Jonsson G, Vallon-Christersson J. Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. BMC Bioinformatics. 2004 Nov 12;5(1):177. [Epub ahead of print][PubMed]
5. Wang G, Maher E, Brennan C, Chin L, Leo C, Kaur M, Zhu P, Rook M, Wolfe JL, Makrigiorgos GM. DNA amplification method tolerant to sample degradation. Genome Res. 2004 Nov;14(11):2357-66. [PubMed]
6. Gadgil C, Yeckel A, Derby JJ, Hu WS. A diffusion-reaction model for DNA microarray assays. J Biotechnol. 2004 Oct 19;114(1-2):31-45. [PubMed]
7. Goff LA, Bowers J, Schwalm J, Howerton K, Getts RC, Hart RP. Evaluation of sense-strand mRNA amplification by comparative quantitative PCR. BMC Genomics. 2004 Oct 6;5(1):76. [Epub ahead of print] [PubMed]
8. Van Bakel H, Holstege FC. In control: systematic assessment of microarray performance. EMBO Rep. 2004 Oct;5(10):964-9. [PubMed]
9. Kaposi-Novak P, Lee JS, Mikaelyan A, Patel V, Thorgeirsson SS. Oligonucleotide microarray analysis of aminoallyl-labeled cDNA targets from linear RNA amplification. Biotechniques. 2004 Oct;37(4):580, 582-6, 588.[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 Nov 1;20(16):2821-8. [ PubMed]
   

Data analysis

1. Li KC, Liu CT, Sun W, Yuan S, Yu T. A system for enhancing genome-wide coexpression dynamics study. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15561-6. [PubMed]
2. Ji L, Tan KL. Mining gene expression data for positive and negative co-regulated gene clusters. Bioinformatics. 2004 Nov 1;20(16):2711-8. [PubMed]
3. Yang ZR. Mining gene expression data based on template theory. Bioinformatics. 2004 Nov 1;20(16):2759-66. [PubMed]
4. Dodd LE, Korn EL, McShane LM, Chandramouli GV, Chuang EY. Correcting log ratios for signal saturation in cDNA microarrays. Bioinformatics. 2004 Nov 1;20(16):2685-93. [PubMed]
5. Bar-Joseph Z. Analyzing time series gene expression data. Bioinformatics. 2004 Nov 1;20(16):2493-503. [PubMed]
6. Pasquier C, Girardot F, Jevardat de Fombelle K, Christen R. THEA: ontology-driven analysis of microarray data. Bioinformatics. 2004 Nov 1;20(16):2636-43. [PubMed]
7. Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N; Microarray Gene Expression Data (MGED) Society. An open letter on microarray data from the MGED Society. Microbiology. 2004 Nov;150(Pt 11):3522-4. [PubMed]
8. Dozmorov I, Knowlton N, Tang Y, Shields A, Pathipvanich P, Jarvis JN, Centola M. Hypervariable genes--experimental error or hidden dynamics. Nucleic Acids Res. 2004 Oct 28;32(19):e147. [PubMed]
9. Wang Z, Lewis MG, Nau ME, Arnold A, Vahey MT. Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip(R) platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples. BMC Bioinformatics. 2004 Oct 26;5(1):165. [Epub ahead of print][PubMed]
10. Hwang KB, Kong SW, Greenberg SA, Park PJ. Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics. 2004 Oct 25;5(1):159. [PubMed]

Oligo design for array manufacturing

1. Rimour S, Hill D, Militon C, Peyret P. GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics. 2004 Nov 5;. [Epub ahead of print][PubMed]
   

   Image analysis

Affymetrix probe level analysis

1. Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP. Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics. 2004 Nov 1;20(16):2534-44. [PubMed]
   

Normalization

1. Ballman KV, Grill DE, Oberg AL, Therneau TM. Faster cyclic loess: normalizing RNA arrays via linear models. Bioinformatics. 2004 Nov 1;20(16):2778-86. [PubMed]
2. Eckel JE, Gennings C, Therneau TM, Burgoon LD, Boverhof DR, Zacharewski TR.  Normalization of two-channel microarray experiments: a semiparametric approach. Bioinformatics. 2004 Oct 28; [Epub ahead of print] [PubMed]

Pattern recognition, classification & data mining by unsupervised methods

1. Swift S, Tucker A, Vinciotti V, Martin N, Orengo C, Liu X, Kellam P. Consensus clustering and functional interpretation of gene-expression data. Genome Biol. 2004;5(11):R94. [PubMed]
2. Adryan B, Schuh R. Gene-Ontology-based clustering of gene expression data. Bioinformatics. 2004 Nov 1;20(16):2851-2. [PubMed]
3. Bidaut G, Ochs MF. ClutrFree: cluster tree visualization and interpretation. Bioinformatics. 2004 Nov 1;20(16):2869-71. [PubMed]
4. Luo F, Khan L, Bastani F, Yen IL, Zhou J. A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles. Bioinformatics. 2004 Nov 1;20(16):2605-17.  [PubMed]
5. Balasubramaniyan R, Hullermeier E, Weskamp N, Kamper J. Clustering of gene expression data using a local shape-based similarity measure. Bioinformatics. 2004 Oct 28; [Epub ahead of print] [PubMed]
6. Lu Y, Lu S, Fotouchi F, Deng Y, Brown SJ. Incremental genetic K-means algorithm and its application in gene expression data analysis. BMC Bioinformatics. 2004 Oct 28;5(1):172 [Epub ahead of print] [PubMed]
7. Taguchi YH, Oono Y.  Relational patterns of gene expression via nonmetric multidimensional scaling analysis. Bioinformatics. 2004 Oct 27; [Epub ahead of print][PubMed]

Pattern recognition, classification & data mining by supervised methods

1. Fort G, Lambert-Lacroix S. Classification using Partial Least Squares with penalized logistic regression. Bioinformatics. 2004 Nov 5; [Epub ahead of print] [PubMed]
2. Alexandridis R, Lin S, Irwin M. Class discovery and classification of tumor samples using mixture modeling of gene expression data--a unified approach. Bioinformatics. 2004 Nov 1;20(16):2545-52.  [PubMed]
3. 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 Oct 12;20(15):2429-37. [PubMed]
4. Dettling M, Zurich ET. BagBoosting for tumor classification with gene expression data. Bioinformatics. 2004 Oct 5 [Epub ahead of print][PubMed]
   

Network/pathway reconstruction and analysis

1. Kyoda K, Baba K, Onami S, Kitano H. DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. Bioinformatics. 2004 Nov 1;20(16):2662-75. [PubMed]
2. Kiryu H, Oshima T, Asai K. Extracting relations between promoter sequences and their strengths from microarray data. Bioinformatics. 2004 Oct 28; [Epub ahead of print] [PubMed]
3. Liu Y, Zhao H. A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. BMC Bioinformatics. 2004 Oct 25;5(1):158. [PubMed]
4. Schafer J, Strimmer K. An empirical bayes approach to inferring large-scale gene association networks. Bioinformatics. 2004 Oct 12;. [Epub ahead of print] [PubMed]
   

Statistical significance of analysis

1. Wei C, Li J, Bumgarner RE. Sample size for detecting differentially expressed genes in microarray experiments. BMC Genomics. 2004 Nov 8;5(1):87. [Epub ahead of print][PubMed]
2. Zhang SD, Gant TW.  A statistical framework for the design of microarray experiments and effective detection of differential gene expression. Bioinformatics. 2004 Nov 1;20(16):2821-8. [ PubMed]
3. Mansourian R, Mutch DM, Antille N, Aubert J, Fogel P, Le Goff JM, Moulin J, Petrov A, Rytz A, Voegel JJ, Roberts MA. The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data. Bioinformatics. 2004 Nov 1;20(16):2726-37. [PubMed]
4. Liao JG, Lin Y, Selvanayagam ZE, Shih WJ. A mixture model for estimating the local false discovery rate in DNA microarray analysis. Bioinformatics. 2004 Nov 1;20(16):2694-701. [PubMed]
5. 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 Nov 1;20(16):2562-71. [PubMed]
6. Attoor S, Dougherty ER, Chen Y, Bittner ML, Trent JM. Which is better for cDNA-microarray-based classification: ratios or direct intensities. Bioinformatics. 2004 Nov 1;20(16):2513-20. [PubMed]
7. Yang YH, Xiao Y, Segal MR. Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics. 2004 Oct 28; [Epub ahead of print] [PubMed]
8. Xiao Y, Frisina R, Gordon A, Klebanov L, Yakovlev A. Multivariate Search for Differentially Expressed Gene Combinations. BMC Bioinformatics. 2004 Oct 26;5(1):164. [Epub ahead of print][PubMed]
9. Kim KY, Kim BJ, Yi GS. Reuse of imputed data in microarray analysis increases imputation efficiency. BMC Bioinformatics. 2004 Oct 26;5(1):160. [PubMed]
10. Qin LX, Kerr KF; Contributing Members of the Toxicogenomics Research Consortium. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res. 2004 Oct 12;32(18):5471-9. [PubMed]
11. Dalmasso C, Broet P, Moreau T. A simple procedure for estimating the false discovery rate. Bioinformatics. 2004 Oct 12;. [Epub ahead of print] [PubMed]
12. Martin DE, Demougin P, Hall MN, Bellis M. Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data. BMC Bioinformatics. 2004 Oct 11;5(1):148 [Epub ahead of print] [PubMed]

Software

1. Lingjaerde OC, Baumbusch LO, Liestol K, Glad IK, Borresen-Dale AL.CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics. 2004 Nov 5;. [Epub ahead of print][PubMed]
2. Smid M, Dorssers LC. GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics. 2004 Nov 1;20(16):2618-25. [PubMed]
3. Adryan B, Schuh R. Gene-Ontology-based clustering of gene expression data. Bioinformatics. 2004 Nov 1;20(16):2851-2. [PubMed]
4. Bidaut G, Ochs MF. ClutrFree: cluster tree visualization and interpretation. Bioinformatics. 2004 Nov 1;20(16):2869-71. [PubMed]
5. Kok Ng JK, Liu WT. LabArray: real-time imaging and analytical tool for microarrays. Bioinformatics. 2004 Oct 27; [Epub ahead of print] [PubMed]
6. Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G. Caryoscope: An Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics. 2004 Oct 15;5(1):151. [PubMed]
7. Le Meur N, Lamirault G, Bihouee A, Steenman M, Bedrine-Ferran H, Teusan R, Ramstein G, Leger JJ.  A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. Nucleic Acids Res. 2004 Oct 08;32(18):5349-58. [PubMed]
8. Sharma A, Srivastava GP, Sharma VK, Ramachandran S. ArrayD: A general purpose software for Microarray design. BMC Bioinformatics. 2004 Oct 2;5(1):142 [Epub ahead of print] [PubMed]
9. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80. [PubMed]
10. Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G. GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics. 2004 Oct 01;5(1):141. [PubMed]

Database

Tissue microarray

1. Gulmann C, Loring P, O'grady A, Kay E. Miniature tissue microarrays for HercepTest(R) standardisation and analysis. J Clin Pathol. 2004 Nov;57(11):1229-31. [PubMed]
2. Fedor HL, De Marzo AM.Practical methods for tissue microarray construction. Methods Mol Med. 2004;103:89-102. [PubMed]

Protein array

1. Quintana FJ, Hagedorn PH, Elizur G, Merbl Y, Domany E, Cohen IR. Functional immunomics: Microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes. Proc Natl Acad Sci U S A. 2004 Oct 5;101 Suppl 2:14615-21. [PubMed]
2. Kwon Y, Han Z, Karatan E, Mrksich M, Kay BK. Antibody arrays prepared by cutinase-mediated immobilization on self-assembled monolayers. Anal Chem. 2004 Oct 1;76(19):5713-20. [PubMed]

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

1. Gu W, Zhu X, Futai N, Cho BS, Takayama S. Computerized microfluidic cell culture using elastomeric channels and Braille displays. Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15861-6. [PubMed]
2. Huang Y, Shirajian J, Schroder A, Yao Z, Summers T, Hodko D, Sosnowski R. Multiple sample amplification and genotyping integrated on a single electronic microarray. Electrophoresis. 2004 Oct;25(18-19):3106-16.  [PubMed]
   

Cell microarray

1. Delehanty JB, Shaffer KM, Lin B. A comparison of microscope slide substrates for use in transfected cell microarrays. Biosens Bioelectron. 2004 Nov 15;20(4):773-9.[PubMed]
2. Bailey SN, Sabatini DM, Stockwell BR. Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens. Proc Natl Acad Sci U S A. 2004 Nov 8;. [Epub ahead of print][PubMed]

Other array platforms

1. Sauvaigo S, Guerniou V, Rapin D, Gasparutto D, Caillat S, Favier A. An oligonucleotide microarray for the monitoring of repair enzyme activity toward different DNA base damage. Anal Biochem. 2004 Oct 1;333(1):182-92. [PubMed]