The DOI matches its Crossref record; 33 of the 34 references it cites were found in a registry or an index.
Characterization of the human ESC transcriptome by hybrid sequencing
Open accessAbstract
Significance: Isoform identification and discovery are an important goal for transcriptome analysis because the majority of human genes express multiple isoforms with context- and tissue-specific functions. Better annotation of isoforms will also benefit downstream analysis such as expression quantification. Current RNA-Seq methods based on short-read sequencing are not reliable for isoform discovery. In this study we developed a new method based on the combined analysis of short reads and long reads generated, respectively, by second- and third-generation sequencing and applied this method to obtain a comprehensive characterization of the transcriptome of the human embryonic stem cell. The results showed that large gain in sensitivity and specificity can be achieved with this strategy.
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“The technology has proven useful for unraveling isoform diversity at complex loci [186], and for determining allele-specific expression from single reads [187].”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [186]
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Cites
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Self-citationRNA-Seq: a revolutionary tool for transcriptomics
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Sorted by citations
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
Opportunities and challenges in long-read sequencing data analysis
Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530
PacBio Sequencing and its Applications
Rhoads, A., & Au, K. F. (2015) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.08.002 · Cited by 2,135
Self-citationTranscriptome assembly from long-read RNA-seq alignments with StringTie2
Kovaka, S., Zimin, A. V., Pertea, G. M., Razaghi, R., Salzberg, S. L., & Pertea, M. (2019) · Genome biology · doi:10.1186/s13059-019-1910-1 · Cited by 2,041
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
- Au, K. F., Sebastiano, V., Afshar, P. T., Durruthy, J. D., Lee, L., Williams, B. A., van Bakel, H., Schadt, E. E., Reijo-Pera, R. A., Underwood, J. G., & Wong, W. H.
- Affiliations
- Stanford University (US)
- Stanford Medicine (US)
- Center for Human Pluripotent Stem Cell Research and Education, Department of Obstetrics and Gynecology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305;
- Invitae (United States) (US)
- California Institute of Technology (US)
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029-6574; and
- Icahn School of Medicine at Mount Sinai (US)
- University of Washington (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2013-11-26
- Volume
- 110
- Issue
- 50
- Pages
- E4821-30
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3864310
- OpenAlex
- W2054841963
- Cited by
- 341
- References
- 34
- Citations by year
- 2026: 8 · 2025: 8 · 2024: 19 · 2023: 17 · 2022: 34 · 2021: 49 · 2020: 33 · 2019: 48 · 2018: 28 · 2017: 31 · 2016: 24 · 2015: 21 · 2014: 19
- FWCI
- 9.56
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- National Heart, Lung, and Blood Institute (U01HL100397)
- National Human Genome Research Institute (U54HG004576, R01HG005717, U54HG006998)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD068158)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- human embryonic stem cells, transcriptome, isoform identification, novel transcripts, pluripotency genes, gene expression profiling, hybrid sequencing, transcriptome completeness
- MeSH terms
- Humans, Male, Alternative Splicing, Protein Isoforms, Gene Expression Profiling, Embryonic Stem Cells, High-Throughput Nucleotide Sequencing, Transcriptome
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