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Sequencing technology does not eliminate biological variability
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“Biological variability is particular to each experimental system and is harder to control [189].”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [189]
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“The accurate and abundant Illumina reads can be used both to correct long-read sequencing errors and to quantify transcript levels [189].”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [189]
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Cites
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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
Tackling the widespread and critical impact of batch effects in high-throughput data
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Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes
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Self-citationUnderstanding mechanisms underlying human gene expression variation with RNA sequencing
Pickrell, J. K., Marioni, J. C., Pai, A. A., Degner, J. F., Engelhardt, B. E., Nkadori, E., Veyrieras, J.-B., Stephens, M., Gilad, Y., & Pritchard, J. K. (2010) · Nature · doi:10.1038/nature08872 · Cited by 1,256
Fundamentals of experimental design for cDNA microarrays
Churchill, G. A. (2002) · Nature Genetics · doi:10.1038/ng1031 · Cited by 1,049
Multiple-laboratory comparison of microarray platforms
Irizarry, R. A., Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., Gabrielson, E., Garcia, J. G. N., Geoghegan, J., Germino, G., et al. (2005) · Nature Methods · doi:10.1038/nmeth756 · Cited by 862
Self-citationTranscriptome genetics using second generation sequencing in a Caucasian population
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Individuality and variation in gene expression patterns in human blood
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Choy, E., Yelensky, R., Bonakdar, S., Plenge, R. M., Saxena, R., Jager, P. L. D., Shaw, S. Y., Wolfish, C. S., Slavik, J. M., Cotsapas, C. J., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000287 · Cited by 211
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Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,145
McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks042 · Cited by 5,195
A survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794
Shen, S., Park, J. W., Lu, Z.-X., Lin, L., Henry, M. D., Wu, Y. N., Zhou, Q., & Xing, Y. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419161111 · Cited by 2,713
RNA sequencing: the teenage years
Stark, R., Grzelak, M., & Hadfield, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0150-2 · Cited by 2,041
Metadata
- Authors
- Hansen, K. D., Wu, Z., Irizarry, R. A., & Leek, J. T.
- Affiliations
- Johns Hopkins University (US)
- Brown University (US)
- Corresponding author
- Irizarry, Rafael A
- Leek, Jeffrey T
- Venue
- Nature Biotechnology
- Published
- 2011-07
- Volume
- 29
- Issue
- 7
- Pages
- 572-573
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC3137276
- OpenAlex
- W1974611660
- Cited by
- 226
- References
- 16
- Citations by year
- 2026: 2 · 2025: 10 · 2024: 7 · 2023: 10 · 2022: 15 · 2021: 26 · 2020: 16 · 2019: 14 · 2018: 16 · 2017: 13 · 2016: 12 · 2015: 10 · 2014: 21 · 2013: 36 · 2012: 15
- FWCI
- 9.75
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Human Genome Research Institute (R01HG005220)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- biological variation, autosomal dominant polycystic kidney disease, gene expression differences
- MeSH terms
- Biotechnology, DNA, Genetic Variation, Sequence Analysis, DNA
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