SNPs matter: impact on detection of differential expression.
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Alignment of RNA-seq reads to a reference genome can result in biased transcript abundance estimates.
“We have demonstrated that alignment of RNA-seq reads to a reference genome can result in biased transcript abundance estimates, much in the same way that a reference-based probe design can bias hybridization of genetically diverse samples to microarrays (Walter et al. 2007).”
From RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations (2014) · cites this paper as Walter et al. 2007
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Comparative analysis of proteome and transcriptome variation in mouse
Ghazalpour, A., Bennett, B., Petyuk, V. A., Orozco, L., Hagopian, R., Mungrue, I. N., Farber, C. R., Sinsheimer, J., Kang, H. M., Furlotte, N., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001393 · Cited by 624 · see citing works
Genes, behavior and next‐generation <scp>RNA</scp> sequencing
Hitzemann, R., Bottomly, D., Darakjian, P., Walter, N., Iancu, O., Searles, R., Wilmot, B., & McWeeney, S. (2013) · Genes, Brain and Behavior · doi:10.1111/gbb.12007 · Cited by 88 · see citing works
Self-citationMunger, S. C., Raghupathy, N., Choi, K., Simons, A. K., Gatti, D. M., Hinerfeld, D. A., Svenson, K. L., Keller, M. P., Attie, A. D., Hibbs, M. A., et al. (2014) · Genetics · doi:10.1534/genetics.114.165886 · Cited by 85 · see citing works
Introduction to Sequencing the Brain Transcriptome
Hitzemann, R., Darakjian, P., Walter, N., Dan Iancu, O., Searles, R., & McWeeney, S. (2014) · International Review of Neurobiology · doi:10.1016/b978-0-12-801105-8.00001-1 · Cited by 20 · see citing works
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- Authors
- Walter, N. A. R., McWeeney, S. K., Peters, S. T., Belknap, J. K., Hitzemann, R., & Buck, K. J.
- Affiliations
- Oregon Health & Science University (US)
- Venue
- Nature Methods
- Published
- 2007-09
- Volume
- 4
- Issue
- 9
- Pages
- 679-680
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC3410665
- OpenAlex
- W1989212333
- Cited by
- 67
- References
- 0
- Citations by year
- 2022: 1 · 2021: 1 · 2019: 2 · 2018: 2 · 2017: 2 · 2016: 3 · 2015: 3 · 2014: 7 · 2013: 4 · 2012: 7
- FWCI
- 3.31
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute on Alcohol Abuse and Alcoholism (AA010760, AA011114, R01AA011114, P60AA010760)
- National Institute on Drug Abuse (DA05228, R01DA005228)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- single nucleotide polymorphisms, differential gene expression, gene expression regulation, genetic variation, behavioral genetics
- MeSH terms
- Animals, Base Sequence, False Negative Reactions, Mice, Inbred C57BL, Mice, Inbred DBA, Molecular Sequence Data, Sensitivity and Specificity, Species Specificity, Gene Expression, Genome, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Databases, Genetic, Mice
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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