microarray references

[Schena1995Quantitative] M. Schena, D. Shalon, R. W. Davis, and P. O. Brown. Quantitative monitoring of gene expression patterns with a complementary dna microarray. Science, 270(5235):467-470, Oct 1995. [ bib | DOI | http | .pdf | Abstract ]
[DeRisi1997Exploring] J. L. DeRisi, V. R. Iyer, and P. O. Brown. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278(5338):680-686, 1997. [ bib | .pdf | .pdf ]
[Spellman1998Comprehensive] P.T. Spellman, G. Sherlock, M.Q. Zhang, V.R. Iyer, K. Anders, M.B. Eisen, P.O. Brown, D. Botstein, and B. Futcher. Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Mol. Biol. Cell, 9:3273-3297, 1998. [ bib | .pdf | .pdf ]
[Mukherjee1998Support] S. Mukherjee, P. Tamayo, J. P. Mesirov, D. Slonim, A. Verri, and T. Poggio. Support vector machine classification of microarray data. Technical Report 182, C.B.L.C., 1998. A.I. Memo 1677. [ bib | .html | .pdf ]
[Eisen1998Cluster] M. B. Eisen, P. T. Spellman, P. O. Brown, and D. Botstein. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 95:14863-14868, Dec 1998. [ bib | .pdf | .pdf ]
[Chu1998Transcriptional] S. Chu, J. DeRisi, M. Eisen, J. Mulholland, D. Botstein, P.O. Brown, and I. Herskowitz. The Transcriptional Program of Sporulation in Budding Yeast. Science, 282:699-705, 1998. [ bib | .pdf | .pdf ]
[Tavazoie1999Systematic] S. Tavazoie, J. D. Hughes, M. J. Campbell, R. J. Cho, and G. M. Church. Systematic determination of genetic network architecture. Nat. Genet., 22:281-285, 1999. [ bib | DOI | http | .pdf ]
[Golub1999Molecular] T. R. Golub, D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, and E. S. Lander. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286:531-537, 1999. [ bib | DOI | http | .pdf | Abstract ]
[Ferea1999Systematic] T. L. Ferea, D. Botstein, P. O. Brown, and R. F. Rosenzweig. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. USA, 96(17):9721-9726, 1999. [ bib | .pdf | .pdf ]
[Zhu2000Two] G. Zhu, P. T. Spellman, T. Volpe, P. O. Brown, D. Botstein, T. N. Davis, and B. Futcher. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature, 406:90-94, 2000. [ bib | http | .pdf ]
[Selinger2000RNA] Douglas W. Selinger, Kevin J. Cheung, Rui Mei, Erik M. Johansson, Craig S. Richmond, Frederick R. Blattner, David J. Lockhart, and George M. Church. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol., 18:1262-1268, 2000. [ bib | http | .pdf ]
[Ogawa2000New] Nobuo Ogawa, Joseph DeRisi, and Patrick O. Brown. New Components of a System for Phosphate Accumulation and Polyphosphate Metabolism in Saccharomyces cerevisiae Revealed by Genomic Expression Analysis. Mol. Biol. Cell, 11:4309-4321, Dec 2000. [ bib | .pdf | .pdf ]
[Gross2000Identification] C. Gross, M. Kelleher, V.R. Iyer, P.O. Brown, and D.R. Winge. Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays. J. Biol. Chem., 275(41):32310-32316, 2000. [ bib | http | .pdf ]
[Gasch2000Genomic] A. P. Gasch, P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Mol. Biol. Cell, 11:4241-4257, Dec 2000. [ bib | .pdf | .pdf ]
[Friedman2000Using] N. Friedman, M. Linial, I. Nachman, and D. Pe'er. Using Bayesian networks to analyze expression data. J. Comput. Biol., 7(3-4):601-620, 2000. [ bib | DOI | http | .pdf | Abstract ]
[Brown2000Exploring] P.O. Brown and D. Botstein. Exploring the new world of the genome with DNA microarrays. Nat. Genet., 21:33-37, 2000. [ bib | .html | .pdf ]
[Brown2000Knowledge-based] M. P. Brown, W. N. Grundy, D. Lin, N. Cristianini, C. W. Sugnet, T. S. Furey, M. Ares, and D. Haussler. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl. Acad. Sci. USA, 97(1):262-7, Jan 2000. [ bib | http | .pdf | Abstract ]
[Ben-Dor2000Tissue] A. Ben-Dor, L. Bruhn, N. Friedman, I. Nachman, M. Schummer, and Z. Yakhini. Tissue classification with gene expression profiles. J. Comput. Biol., 7(3-4):559-583, 2000. [ bib | http | .pdf | Abstract ]
[Sherlock2001Stanford] G. Sherlock, T. Hernandez-Boussard, A. Kasarskis, G. Binkley, J.C. Matese, S.S. Dwight, M. Kaloper, S. Weng, H. Jin, C.A. Ball, M.B. Eisen, and P.T. Spellman. The Stanford Microarray Database. Nucleic Acids Res., 29(1):152-155, Jan 2001. [ bib | .pdf | .pdf ]
[Ramaswamy2001Multiclass] S. Ramaswamy, P. Tamayo, R. Rifkin, S. Mukherjee, C.H. Yeang, M. Angelo, C. Ladd, M. Reich, E. Latulippe, J.P. Mesirov, T. Poggio, W. Gerald, M. Loda, E.S. Lander, and T.R. Golub. Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl. Acad. Sci. USA, 98(26):15149-15154, Dec 2001. [ bib | DOI | http | .pdf | Abstract ]
[Pilpel2001Identifying] Y. Pilpel, P. Sudarsanam, and G. M. Church. Identifying regulatory networks by combinatorial analysis of promoter elements. Nature, 29:153-159, 2001. [ bib | http | .pdf ]
[Kuhn2001Global] K. M. Kuhn, J. L. DeRisi, P. O. Brown, and P. Sarnow. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol., 21(3):916-927, 2001. [ bib | http | .pdf ]
[Gasch2001Genomic] A.P. Gasch, M. Huang, S. Metzner, D. Botstein, S.J. Elledge, and P.O. Brown. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol. Biol. Cell, 12(10):2987-3003, 2001. [ bib | http | .pdf ]
[Chiang2001Visualizing] D. Y. Chiang, P. O. Brown, and M. B. Eisen. Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics, 17:49S-55S, 2001. [ bib | .pdf | .pdf ]
[Bussemaker2001Regulatory] H. J. Bussemaker, H. Li, and E. D. Siggia. Regulatory element detection using correlation with expression. Nat. Genet., 27:167-174, 2001. [ bib | http | .pdf ]
[Hanisch2002Co-clustering] D. Hanisch, A. Zien, R. Zimmer, and T. Lengauer. Co-clustering of biological networks and gene expression data. Bioinformatics, 2002. [ bib | .pdf ]
[Bao2002Identifying] L. Bao and Z. Sun. Identifying genes related to drug anticancer mechanisms using support vector machine. FEBS Lett., 521:109-114, 2002. [ bib | .html | .pdf | Abstract ]
[Aliferis2002Machine] C.F. Aliferis, D.P. Hardin, and P. Massion. Machine Learning Models For Lung Cancer Classification Using Array Comparative Genomic Hybridization. In Proceedings of the 2002 American Medical Informatics Association (AMIA) Annual Symposium, pages 7-11, 2002. [ bib | .pdf | Abstract ]
[Peng2003Molecular] S. Peng, Q. Xu, X.B. Ling, X. Peng, W. Du, and L. Chen. Molecular classification of cancer types from microarray data using the combination of genetic algorithms and support vector machines. FEBS Lett., 555(2):358-362, 2003. [ bib | DOI | http | .pdf | Abstract ]
[Meireles2003Differentially] S.I. Meireles, A.F. Carvalho, R. Hirata, A.L. Montagnini, W.K. Martins, F.B. Runza, B.S. Stolf, L. Termini, C.E. Neto, R.L. Silva, F.A. Soares, E.J. Neves, and L.F. Reis. Differentially expressed genes in gastric tumors identified by cDNA array. Cancer Lett., 190(2):199-211, Feb 2003. [ bib | DOI | http | .pdf | Abstract ]
[LeRoch2003Discovery] K. G. Le Roch, Y. Zhou, P. L. Blair, M. Grainger, J. K. Moch, J. D. Haynes, P. De la Vega, A. A. Holder, S. Batalov, D. J. Carucci, and E. A. Winzeler. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science, 301(5639):1503-1508, 2003. [ bib | DOI | http | .pdf | Abstract ]
[Bozdech2003Expression] Z. Bozdech, J. Zhu, M. Joachimiak, F. Cohen, B. Pulliam, and J. DeRisi. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology, 4(2):R9, 2003. [ bib | DOI | http | .pdf | Abstract ]
[Bozdech2003Transcriptome] Z. Bozdech, M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu, and J. L. DeRisi. The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum. PLoS Biology, 1(1):e5, 2003. [ bib | DOI | http | .pdf | Abstract ]
[Tsai2004Gene] C.A. Tsai, C.H. Chen, T.C. Lee, I.C. Ho, U.C. Yang, and J.J. Chen. Gene selection for sample classifications in microarray experiments. DNA Cell Biol., 23(10):607-614, 2004. [ bib | DOI | http | .pdf | Abstract ]
[Pochet2004Systematic] N. Pochet, F. De Smet, J. A. K. Suykens, and B. L. R. De Moor. Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics, 20(17):3185-3195, Nov 2004. [ bib | DOI | http | .pdf | Abstract ]
[Ishkanian2004tiling] A. S. Ishkanian, C. A. Malloff, S. K. Watson, R. J. DeLeeuw, B. Chi, B. P. Coe, A. Snijders, D. G. Albertson, D. Pinkel, M. A. Marra, V. Ling, C. MacAulay, and W. L. Lam. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet., 36(3):299-303, Mar 2004. [ bib | DOI | http | .pdf | Abstract ]
[Bozdech2004Antioxidant] Z. Bozdech and H. Ginsburg. Antioxidant defense in Plasmodium falciparum - data mining of the transcriptome. Malaria Journal, 3(1):23, 2004. [ bib | DOI | http | .pdf | Abstract ]
[Pavey2004Microarray] S. Pavey, P. Johansson, L. Packer, J. Taylor, M. Stark, P.M. Pollock, G.J. Walker, G.M. Boyle, U. Harper, S.J. Cozzi, K. Hansen, L. Yudt, C. Schmidt, P. Hersey, K.A. Ellem, M.G. O'Rourke, P.G. Parsons, P. Meltzer, M. Ringner, and N.K. Hayward. Microarray expression profiling in melanoma reveals a BRAF mutation signature. Oncogene, 23(23):4060-4067, May 2004. [ bib | DOI | http | .pdf | Abstract ]
[Zhou2005LS] Xin Zhou and K. Z. Mao. LS Bound based gene selection for DNA microarray data. Bioinformatics, 21(8):1559-64, Apr 2005. [ bib | DOI | http | .pdf | Abstract ]
[Wang2005Gene] Yu Wang, Igor V Tetko, Mark A Hall, Eibe Frank, Axel Facius, Klaus F X Mayer, and Hans W Mewes. Gene selection from microarray data for cancer classification-a machine learning approach. Comput. Biol. Chem., 29(1):37-46, Feb 2005. [ bib | DOI | http | .pdf | Abstract ]
[Wang2005Gene-expression] Y. Wang, J.G.M. Klijn, Y. Zhang, A.M. Sieuwerts, M.P. Look, F. Yang, D. Talantov, M. Timmermans, M.E. Meijer-van Gelder, J. Yu, T. Jatkoe, E.M.J.J. Berns, D. Atkins, and J.A. Foekens. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancers. Lancet, 365(9460):671-679, 2005. [ bib | DOI | http | .pdf | Abstract ]
[Thukral2005Prediction] Sushil K Thukral, Paul J Nordone, Rong Hu, Leah Sullivan, Eric Galambos, Vincent D Fitzpatrick, Laura Healy, Michael B Bass, Mary E Cosenza, and Cynthia A Afshari. Prediction of nephrotoxicant action and identification of candidate toxicity-related biomarkers. Toxicol Pathol, 33(3):343-55, 2005. [ bib | DOI | http | Abstract ]
[Statnikov2005comprehensive] A. Statnikov, C. F. Aliferis, I. Tsamardinos, D. Hardin, and S. Levy. A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis. Bioinformatics, 2005. To appear. [ bib | http | .pdf | Abstract ]
[Segal2005From] E. Segal, N. Friedman, N. Kaminski, A. Regev, and D. Koller. From signatures to models: understanding cancer using microarrays. Nat Genet, 37(6 Suppl):S38-45, 2005. [ bib | DOI | http | .pdf | Abstract ]
[ODonnell2005Gene] Rebekah K O'Donnell, Michael Kupferman, S. Jack Wei, Sunil Singhal, Randal Weber, Bert O'Malley, Yi Cheng, Mary Putt, Michael Feldman, Barry Ziober, and Ruth J Muschel. Gene expression signature predicts lymphatic metastasis in squamous cell carcinoma of the oral cavity. Oncogene, 24(7):1244-51, Feb 2005. [ bib | DOI | http | .pdf | Abstract ]
[Michiels2005Prediction] S. Michiels, S. Koscielny, and C. Hill. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet, 365(9458):488-492, 2005. [ bib | DOI | http | Abstract ]
[Mavroforakis2005Significance] Michael Mavroforakis, Harris Georgiou, Nikos Dimitropoulos, Dionisis Cavouras, and Sergios Theodoridis. Significance analysis of qualitative mammographic features, using linear classifiers, neural networks and support vector machines. Eur J Radiol, 54(1):80-9, Apr 2005. [ bib | DOI | http | .pdf | Abstract ]
[Ioannidis2005Microarrays] J. P. A. Ioannidis. Microarrays and molecular research: noise discovery? Lancet, 365(9458):454, 2005. [ bib | .pdf ]
[Haferlach2005global] Torsten Haferlach, Alexander Kohlmann, Susanne Schnittger, Martin Dugas, Wolfgang Hiddemann, Wolfgang Kern, and Claudia Schoch. A global approach to the diagnosis of leukemia using gene expression profiling. Blood, 106(4):1189-1198, Aug 2005. [ bib | DOI | http | .pdf | Abstract ]
[Haferlach2005AML] Torsten Haferlach, Alexander Kohlmann, Susanne Schnittger, Martin Dugas, Wolfgang Hiddemann, Wolfgang Kern, and Claudia Schoch. AML M3 and AML M3 variant each have a distinct gene expression signature but also share patterns different from other genetically defined AML subtypes. Genes Chromosomes Cancer, 43(2):113-27, Jun 2005. [ bib | DOI | http | .pdf | Abstract ]
[Haasdonk2005Feature] Bernard Haasdonk. Feature space interpretation of SVMs with indefinite kernels. IEEE Trans Pattern Anal Mach Intell, 27(4):482-92, Apr 2005. [ bib | DOI | http | .pdf | Abstract ]
[Ein-Dor2005Outcome] L. Ein-Dor, I. Kela, G. Getz, D. Givol, and E. Domany. Outcome signature genes in breast cancer: is there a unique set? Bioinformatics, 21(2):171-178, Jan 2005. [ bib | DOI | http | .pdf | Abstract ]
[Dong2005Fast] Jian xiong Dong, Adam Krzyzak, and Ching Y Suen. Fast SVM training algorithm with decomposition on very large data sets. IEEE Trans Pattern Anal Mach Intell, 27(4):603-18, Apr 2005. [ bib | Abstract ]
[Burckin2005Exploring] T. Burckin, R. Nagel, Y. Mandel-Gutfreund, L. Shiue, T. A. Clark, J.-L. Chong, T.-H. Chang, S. Squazzo, G. Hartzog, and M. Ares. Exploring functional relationships between components of the gene expression machinery. Nat. Struct. Mol. Biol., 12(2):175-82, Feb 2005. [ bib | DOI | http | .pdf | Abstract ]
[Tothill2005expression-based] Richard W Tothill, Adam Kowalczyk, Danny Rischin, Alex Bousioutas, Izhak Haviv, Ryan K van Laar, Paul M Waring, John Zalcberg, Robyn Ward, Andrew V Biankin, Robert L Sutherland, Susan M Henshall, Kwun Fong, Jonathan R Pollack, David D L Bowtell, and Andrew J Holloway. An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. Cancer Res., 65(10):4031-40, May 2005. [ bib | DOI | http | .pdf | Abstract ]
[Garnis2006High] C. Garnis, W. W. Lockwood, E. Vucic, Y. Ge, L. Girard, J. D. Minna, A. F. Gazdar, S. Lam, C. MacAulay, and W. L. Lam. High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. Int. J. Cancer, 118(6):1556-1564, 2006. [ bib | DOI | http | Abstract ]
[Fan2006Concordance] C. Fan, D.S. Oh, L. Wessels, B. Weigelt, D.S.A. Nuyten, A.B. Nobel, L.J. van't Veer, and C.M. Perou. Concordance among gene-expression-based predictors for breast cancer. N. Engl. J. Med., 355(6):560, 2006. [ bib | DOI | http | .pdf ]
[Levy2007Diploid] Samuel Levy, Granger Sutton, Pauline C Ng, Lars Feuk, Aaron L Halpern, Brian P Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R MacDonald, Andy Wing Chun Pang, Mary Shago, Timothy B Stockwell, Alexia Tsiamouri, Vineet Bafna, Vikas Bansal, Saul A Kravitz, Dana A Busam, Karen Y Beeson, Tina C McIntosh, Karin A Remington, Josep F Abril, John Gill, Jon Borman, Yu-Hui Rogers, Marvin E Frazier, Stephen W Scherer, Robert L Strausberg, and J. Craig Venter. The diploid genome sequence of an individual human. PLoS Biol, 5(10):e254, Sep 2007. [ bib | DOI | http | Abstract ]
[Wirapati2008Meta-analysis] P. Wirapati, C. Sotiriou, S. Kunkel, P. Farmer, S. Pradervand, B. Haibe-Kains, C. Desmedt, M. Ignatiadis, T. Sengstag, F. Schütz, D. R. Goldstein, M. Piccart, and M. Delorenzi. Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res., 10(4):R65, 2008. [ bib | DOI | http | .pdf | Abstract ]
[Reyal2009Analyse] F. Reyal. Analyse du profil d'expression par la technique des puces à ADN. Application à la caractérisation moléculaire et à la détermination du pronostic des cancers canalaires infiltrants du sein. PhD thesis, Université Paris 11, 2009. [ bib ]
[Chen2011Removing] Chao Chen, Kay Grennan, Judith Badner, Dandan Zhang, Elliot Gershon, Li Jin, and Chunyu Liu. Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS One, 6(2):e17238, 2011. [ bib | DOI | http | Abstract ]

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