The beginning of the end for microarrays?

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696

Stem cell transcriptome profiling via massive-scale mRNA sequencing

Cloonan, N., Forrest, A. R. R., Kolle, G., Gardiner, B. B. A., Faulkner, G. J., Brown, M. K., Taylor, D. F., Steptoe, A. L., Wani, S., Bethel, G., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1223 · Cited by 1,035

Accurate whole human genome sequencing using reversible terminator chemistry

Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684

RNA Sequencing and Analysis

Kukurba, K. R., & Montgomery, S. B. (2015) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top084970 · Cited by 924

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

Manzoni, C., Kia, D. A., Vandrovcova, J., Hardy, J., Wood, N. W., Lewis, P. A., & Ferrari, R. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bbw114 · Cited by 804

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

Xie, C., & Tammi, M. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-80 · Cited by 582

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

Portales-Casamar, E., Thongjuea, S., Kwon, A. T., Arenillas, D., Zhao, X., Valen, E., Yusuf, D., Lenhard, B., Wasserman, W. W., & Sandelin, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp950 · Cited by 577

RNA-Seq analysis to capture the transcriptome landscape of a single cell

Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V. I., Lao, K., & Surani, M. A. (2010) · Nature Protocols · doi:10.1038/nprot.2009.236 · Cited by 498

Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops

Mir, R. R., Zaman-Allah, M., Sreenivasulu, N., Trethowan, R., & Varshney, R. K. (2012) · Theoretical and Applied Genetics · doi:10.1007/s00122-012-1904-9 · Cited by 477

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

Li, J., & Tibshirani, R. (2013) · Statistical Methods in Medical Research · doi:10.1177/0962280211428386 · Cited by 437

A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni

Protasio, A. V., Tsai, I. J., Babbage, A., Nichol, S., Hunt, M., Aslett, M. A., De Silva, N., Velarde, G. S., Anderson, T. J. C., Clark, R. C., et al. (2012) · PLoS Neglected Tropical Diseases · doi:10.1371/journal.pntd.0001455 · Cited by 419

Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds

Shi, C.-Y., Yang, H., Wei, C.-L., Yu, O., Zhang, Z.-Z., Jiang, C.-J., Sun, J., Li, Y.-Y., Chen, Q., Xia, T., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-131 · Cited by 398

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

Li, J., Witten, D. M., Johnstone, I. M., & Tibshirani, R. (2012) · Biostatistics · doi:10.1093/biostatistics/kxr031 · Cited by 369

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

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

Au, K. F., Jiang, H., Lin, L., Xing, Y., & Wong, W. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq211 · Cited by 332

RNA‐Seq: A Method for Comprehensive Transcriptome Analysis

Nagalakshmi, U., Waern, K., & Snyder, M. (2010) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb0411s89 · Cited by 324

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre

Poretsky, R. S., Hewson, I., Sun, S., Allen, A. E., Zehr, J. P., & Moran, M. A. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01863.x · Cited by 313

RNA-seq: technical variability and sampling

McIntyre, L. M., Lopiano, K. K., Morse, A. M., Amin, V., Oberg, A. L., Young, L. J., & Nuzhdin, S. V. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-293 · Cited by 285

Application of 'next-generation' sequencing technologies to microbial genetics

MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2088 · Cited by 293

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

Grattapaglia, D., Vaillancourt, R. E., Shepherd, M., Thumma, B. R., Foley, W., Külheim, C., Potts, B. M., & Myburg, A. A. (2012) · Tree Genetics & Genomes · doi:10.1007/s11295-012-0491-x · Cited by 273

RNA-Seq and human complex diseases: recent accomplishments and future perspectives

Costa, V., Aprile, M., Esposito, R., & Ciccodicola, A. (2013) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.129 · Cited by 269

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

Hegedűs, Z., Zakrzewska, A., Ágoston, V. C., Ordas, A., Rácz, P., Mink, M., Spaink, H. P., & Meijer, A. H. (2009) · Molecular Immunology · doi:10.1016/j.molimm.2009.07.002 · Cited by 216

Understanding Alzheimer Disease at the Interface between Genetics and Transcriptomics

Verheijen, J., & Sleegers, K. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.02.007 · Cited by 192

What would you do if you could sequence everything?

Kahvejian, A., Quackenbush, J., & Thompson, J. F. (2008) · Nature Biotechnology · doi:10.1038/nbt1494 · Cited by 189

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

Łabaj, P. P., Leparc, G. G., Linggi, B. E., Markillie, L. M., Wiley, H. S., & Kreil, D. P. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr247 · Cited by 141

Analyzing Schizophrenia by DNA Microarrays

Horváth, S., Janka, Z., & Mirnics, K. (2011) · Biological Psychiatry · doi:10.1016/j.biopsych.2010.07.017 · Cited by 64

Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples

Kapteyn, J., He, R., McDowell, E. T., & Gang, D. R. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-413 · Cited by 59

RNA-Seq optimization with eQTL gold standards

Ellis, S. E., Gupta, S., Ashar, F. N., Bader, J. S., West, A. B., & Arking, D. E. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-892 · Cited by 30