Normalization of cDNA microarray data

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.

Yang, Y., Dudoit, S., Luu, P., Lin, D., Peng, V., Ngai, J., & Speed, T. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.4.e15 · Cited by 3,722 · see citing works

Statistical Models in S

Chambers, J. M., Hastie, T., & Pregibon, D. (1990) · Physica-Verlag eBooks · doi:10.1007/978-3-642-50096-1_48 · Cited by 1,763 · see citing works

STATISTICAL METHODS FOR IDENTIFYING DIFFERENTIALLY EXPRESSED GENES IN REPLICATED cDNA MICROARRAY EXPERIMENTS

Dudoit, S., Yang, J. Y. H., Callow, M. J., & Speed, T. P. (2002) · Cited by 1,392 · see citing works

Replicated microarray data

Lönnstedt, I. M. (2001) · Cited by 670 · see citing works

The Analysis of Gene Expression Data: Methods and Software

Boyle, T. (2005) · Journal of Statistical Software · doi:10.18637/jss.v014.b01 · Cited by 514 · see citing works

Normalization for cDNA microarry data

Yang, J. Y. H., Dudoit, S., Luu, P., & Speed, T. P. (2001) · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · doi:10.1117/12.427982 · Cited by 442 · see citing works

Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient MicePreprint

Callow, M. J. (2000) · Genome Research · doi:10.1101/gr.10.12.2022 · Cited by 228 · see citing works

Bioconductor R Packages for Exploratory Analysis and Normalization of cDNA Microarray Data

Dudoit, S., & Yang, J. Y. H. (2003) · Statistics for biology and health · doi:10.1007/0-387-21679-0_3 · Cited by 73 · see citing works

limma powers differential expression analyses for RNA-sequencing and microarray studies

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458 · see citing works

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829 · see citing works

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771 · see citing works

Microarray data analysis: from disarray to consolidation and consensus

Allison, D. B., Cui, X., Page, G. P., & Sabripour, M. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1749 · Cited by 1,339 · see citing works

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

Tran, H. T. N., Ang, K. S., Chevrier, M., Zhang, X., Lee, N. Y. S., Goh, M., & Chen, J. (2020) · Genome Biology · doi:10.1186/s13059-019-1850-9 · Cited by 1,113 · see citing works

INTERFEROME v2.0: an updated database of annotated interferon-regulated genes

Rusinova, I., Forster, S., Yu, S., Kannan, A., Masse, M., Cumming, H., Chapman, R., & Hertzog, P. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1215 · Cited by 878 · see citing works

Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations

Soldner, F., Laganière, J., Cheng, A. W., Hockemeyer, D., Gao, Q., Alagappan, R., Khurana, V., Golbe, L. I., Myers, R. H., Lindquist, S., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.019 · Cited by 728 · see citing works

Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development

Dawlaty, M. M., Ganz, K., Powell, B. E., Hu, Y.-C., Markoulaki, S., Cheng, A. W., Gao, Q., Kim, J., Choi, S.-W., Page, D. C., et al. (2011) · Cell stem cell · doi:10.1016/j.stem.2011.07.010 · Cited by 508 · see citing works

Normalizing single-cell RNA sequencing data: challenges and opportunities

Vallejos, C. A., Risso, D., Scialdone, A., Dudoit, S., & Marioni, J. C. (2017) · Nature Methods · doi:10.1038/nmeth.4292 · Cited by 436 · see citing works

METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation

Pandolfini, L., Barbieri, I., Bannister, A. J., Hendrick, A., Andrews, B., Webster, N., Murat, P., Mach, P., Brandi, R., Robson, S. C., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.03.040 · Cited by 491 · see citing works

Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity

Henegar, C., Tordjman, J., Achard, V., Lacasa, D., Cremer, I., Guerre-Millo, M., Poitou, C., Basdevant, A., Stich, V., Viguerie, N., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-1-r14 · Cited by 471 · see citing works

Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways

Lim, E., Wu, D., Pal, B., Bouras, T., Asselin-Labat, M.-L., Vaillant, F., Yagita, H., Lindeman, G. J., Smyth, G. K., & Visvader, J. E. (2010) · Breast Cancer Research · doi:10.1186/bcr2560 · Cited by 440 · see citing works

The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing

Barry, G., Briggs, J. A., Vanichkina, D. P., Poth, E. M., Beveridge, N. J., Ratnu, V. S., Nayler, S. P., Nones, K., Hu, J., Bredy, T. W., et al. (2014) · Molecular Psychiatry · doi:10.1038/mp.2013.45 · Cited by 394 · see citing works

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

Wang, X., Wei, X., Thijssen, B., Das, J., Lipkin, S. M., & Yu, H. (2012) · Nature Biotechnology · doi:10.1038/nbt.2106 · Cited by 385 · see citing works

Empirical array quality weights in the analysis of microarray data

Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, A., Holloway, A., & Smyth, G. K. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-261 · Cited by 312 · see citing works

<i>BRANCHED1</i> Promotes Axillary Bud Dormancy in Response to Shade in <i>Arabidopsis</i>

González-Grandío, E., Poza-Carrión, C., Sorzano, C. O. S., & Cubas, P. (2013) · The Plant Cell · doi:10.1105/tpc.112.108480 · Cited by 272 · see citing works

The Key Sigma Factor of Transition Phase, SigH, Controls Sporulation, Metabolism, and Virulence Factor Expression in Clostridium difficile

Saujet, L., Monot, M., Dupuy, B., Soutourina, O., & Martin-Verstraete, I. (2011) · Journal of Bacteriology · doi:10.1128/jb.00272-11 · Cited by 173 · see citing works

MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy

Patterson, E. E., Holloway, A. K., Weng, J., Fojo, T., & Kebebew, E. (2011) · Cancer · doi:10.1002/cncr.25724 · Cited by 171 · see citing works

Progress in the use of microarray technology to study the neurobiology of disease

Mirnics, K., & Pevsner, J. (2004) · Nature Neuroscience · doi:10.1038/nn1230 · Cited by 150 · see citing works

Regulation of the Hypoxic Response in Candida albicans

Synnott, J. M., Guida, A., Mulhern-Haughey, S., Higgins, D. G., & Butler, G. (2010) · Eukaryotic Cell · doi:10.1128/ec.00159-10 · Cited by 132 · see citing works

DNA Methylation Patterns Separate Senescence from Transformation Potential and Indicate Cancer Risk

Xie, W., Kagiampakis, I., Pan, L., Zhang, Y. W., Murphy, L., Tao, Y., Kong, X., Kang, B., Xia, L., Carvalho, F. L. F., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.01.008 · Cited by 122 · see citing works

Regulation of a Truncated Form of Tropomyosin-Related Kinase B (TrkB) by Hsa-miR-185* in Frontal Cortex of Suicide Completers

Maussion, G., Yang, J., Yerko, V., Barker, P., Mechawar, N., Ernst, C., & Turecki, G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039301 · Cited by 91 · see citing works

Conserved and Divergent Roles of Bcr1 and CFEM Proteins in Candida parapsilosis and Candida albicans

Ding, C., Vidanes, G. M., Maguire, S. L., Guida, A., Synnott, J. M., Andes, D. R., & Butler, G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028151 · Cited by 93 · see citing works

Transcriptional profiling of azole-resistant Candida parapsilosis strains

Silva, A. P., Miranda, I. M., Guida, A., Synnott, J., Rocha, R., Silva, R., Amorim, A., Pina-Vaz, C., Butler, G., & Rodrigues, A. G. (2011) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01127-10 · Cited by 86 · see citing works

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease

Wu, D., Hu, Y., Tong, S., Williams, B. R. G., Smyth, G. K., & Gantier, M. P. (2013) · RNA · doi:10.1261/rna.035055.112 · Cited by 71 · see citing works

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes

Oshlack, A., Emslie, D., Corcoran, L. M., & Smyth, G. K. (2007) · Genome biology · doi:10.1186/gb-2007-8-1-r2 · Cited by 69 · see citing works

Integrative “Omics”-Approach Discovers Dynamic and Regulatory Features of Bacterial Stress Responses

Berghoff, B. A., Konzer, A., Mank, N. N., Looso, M., Rische, T., Förstner, K. U., Krüger, M., & Klug, G. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003576 · Cited by 54 · see citing works

Matrigel Basement Membrane Matrix influences expression of microRNAs in cancer cell lines

Price, K. J., Tsykin, A., Giles, K. M., Sladic, R. T., Epis, M. R., Ganss, R., Goodall, G. J., & Leedman, P. J. (2012) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2012.09.059 · Cited by 49 · see citing works

An Antifungal Benzimidazole Derivative Inhibits Ergosterol Biosynthesis and Reveals Novel Sterols

Keller, P., Müller, C., Engelhardt, I., Hiller, E., Lemuth, K., Eickhoff, H., Wiesmüller, K.-H., Burger-Kentischer, A., Bracher, F., & Rupp, S. (2015) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00640-15 · Cited by 50 · see citing works

Endometrial vezatin and its association with endometriosis risk

Holdsworth-Carson, S. J., Fung, J. N., Luong, H. T. T., Sapkota, Y., Bowdler, L. M., Wallace, L., Teh, W. T., Powell, J. E., Girling, J. E., Healey, M., et al. (2016) · Human Reproduction · doi:10.1093/humrep/dew047 · Cited by 41 · see citing works

A novel strategy to dissect multifaceted macrophage function in human diseases

Karlinsey, K., Qu, L., Matz, A. J., & Zhou, B. (2022) · Journal of Leukocyte Biology · doi:10.1002/jlb.6mr0522-685r · Cited by 23 · see citing works

Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool

Yu, H., Nguyen, K., Royce, T., Qian, J., Nelson, K., Snyder, M., & Gerstein, M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl871 · Cited by 13 · see citing works

FACE RECOGNITION BASED ON GPPBTF AND LBP WITH CLASSIFIER FUSION

Xu, G., Lu, H., & Wang, Z. (2012) · International Journal of Image and Graphics · doi:10.1142/s0219467812500118

Gradient feature extraction for classification-based face detection

Huang, L.-L., Shimizu, A., Hagihara, Y., & Kobatake, H. (2003) · Pattern Recognition · doi:10.1016/s0031-3203(03)00130-4 · Cited by 45 · see citing works

Data Normalization

Priddy, K. L., & Keller, P. E. (2009) · SPIE eBooks · doi:10.1117/3.633187.ch3

NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data

Heckmann, L., Sørensen, P. B., Krogh, P. H., & Sørensen, J. G. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-250 · Cited by 151 · see citing works

Normalization of Biological Expression Data Based on Selection of a Stable Element Set

Bouki, Y., Yoshihiro, T., Inoue, E., et al. (2011) · Lecture notes in computer science · doi:10.1007/978-3-642-23854-3_17