Fundamentals of experimental design for cDNA microarrays

Variation in gene expression within and among natural populations

Oleksiak, M. F., Churchill, G. A., & Crawford, D. L. (2002) · Nature Genetics · doi:10.1038/ng983 · Cited by 736

Microarray data normalization and transformation

Quackenbush, J. (2002) · Nature Genetics · doi:10.1038/ng1032 · Cited by 1,975

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

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., et al. (2016) · RNA · doi:10.1261/rna.053959.115 · Cited by 966

Gateways to the FANTOM5 promoter level mammalian expression atlas

Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., et al. (2015) · Genome Biology · doi:10.1186/s13059-014-0560-6 · Cited by 871

Reliability and reproducibility issues in DNA microarray measurements

DRAGHICI, S., KHATRI, P., EKLUND, A., & SZALLASI, Z. (2006) · Trends in Genetics · doi:10.1016/j.tig.2005.12.005 · Cited by 590

Gene Expression Profiles in the Brain Predict Behavior in Individual Honey Bees

Whitfield, C. W., Cziko, A.-M., & Robinson, G. E. (2003) · Science · doi:10.1126/science.1086807 · Cited by 527

Statistical Design and Analysis of RNA Sequencing Data

Auer, P. L., & Doerge, R. W. (2010) · Genetics · doi:10.1534/genetics.110.114983 · Cited by 393

MicroRNA-regulated pathways associated with endometriosis

Ohlsson Teague, E. M. C., Van der Hoek, K. H., Van der Hoek, M. B., Perry, N., Wagaarachchi, P., Robertson, S. A., Print, C. G., & Hull, L. M. (2009) · Molecular Endocrinology · doi:10.1210/me.2008-0387 · Cited by 357

Systems biology: experimental design

Kreutz, C., & Timmer, J. (2009) · The FEBS Journal · doi:10.1111/j.1742-4658.2008.06843.x · Cited by 257

IFNs Modify the Proteome of Legionella-Containing Vacuoles and Restrict Infection Via IRG1-Derived Itaconic Acid

Naujoks, J., Tabeling, C., Dill, B. D., Hoffmann, C., Brown, A. S., Kunze, M., Kempa, S., Peter, A., Mollenkopf, H.-J., Dorhoi, A., et al. (2016) · PLOS Pathogens · doi:10.1371/journal.ppat.1005408 · Cited by 261

Sequencing technology does not eliminate biological variability

Hansen, K. D., Wu, Z., Irizarry, R. A., & Leek, J. T. (2011) · Nature Biotechnology · doi:10.1038/nbt.1910 · Cited by 226

Transcriptional characterizations of differences between eutopic and ectopic endometrium

Wu, Y., Kajdacsy-Balla, A., Strawn, E., Basir, Z., Halverson, G., Jailwala, P., Wang, Y., Wang, X., Ghosh, S., & Guo, S.-W. (2006) · Endocrinology · doi:10.1210/en.2005-0426 · Cited by 208

A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation

Boccuto, L., Aoki, K., Flanagan-Steet, H., Chen, C.-F., Fan, X., Bartel, F., Petukh, M., Pittman, A., Saul, R., Chaubey, A., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddt434 · Cited by 182

Circadian Clocks Are Resounding in Peripheral Tissues

Ptitsyn, A. A., Zvonic, S., Conrad, S. A., Scott, L. K., Mynatt, R. L., & Gimble, J. M. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020016 · Cited by 145

Dictyostelium transcriptional host cell response upon infection with Legionella

Farbrother, P., Wagner, C., Na, J., Tunggal, B., Morio, T., Urushihara, H., Tanaka, Y., Schleicher, M., Steinert, M., & Eichinger, L. (2006) · Cellular Microbiology · doi:10.1111/j.1462-5822.2005.00633.x · Cited by 112

Micro/nano multilayered scaffolds of PLGA and collagen by alternately electrospinning for bone tissue engineering

Kwak, S., Haider, A., Gupta, K. C., Kim, S., & Kang, I.-K. (2016) · Nanoscale Research Letters · doi:10.1186/s11671-016-1532-4 · Cited by 99

Comprehensive comparison of large-scale tissue expression datasets

Santos, A., Tsafou, K., Stolte, C., Pletscher-Frankild, S., O’Donoghue, S. I., & Jensen, L. J. (2015) · PeerJ · doi:10.7717/peerj.1054 · Cited by 92

Gene-expression signatures of Atlantic salmon’s plastic life cycle

Aubin-Horth, N., Letcher, B. H., & Hofmann, H. A. (2009) · General and Comparative Endocrinology · doi:10.1016/j.ygcen.2009.04.021 · Cited by 46

Genomic and Proteomic Analysis of Myocarditis and Dilated Cardiomyopathy

Cooper, L. T., Onuma, O. K., Sagar, S., Oberg, A. L., Mahoney, D. W., Asmann, Y. W., & Liu, P. (2010) · Heart Failure Clinics · doi:10.1016/j.hfc.2009.08.012 · Cited by 30

Differential expression and detection of transcripts in sweetpotato (Ipomoea batatas (L.) Lam.) using cDNA microarrays

McGregor, C. (2022) · doi:10.31390/gradschool_dissertations.3754 · Cited by 15