The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Analysis of RNA-Seq Data Using TopHat and Cufflinks
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Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
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
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,116
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,617
Cited by
KBase: The United States Department of Energy Systems Biology Knowledgebase
(2018) · doi:10.1038/nbt.4163 · Cited by 1,624
Kim, S., Min, S., Choi, Y. S., Jo, S.-H., Jung, J. H., Han, K., Kim, J., An, S., Ji, Y. W., Kim, Y.-G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29279-4 · Cited by 375
Kim, S., Park, J., Yeom, S.-I., Kim, Y.-M., Seo, E., Kim, K.-T., Kim, M.-S., Lee, J. M., Cheong, K., Shin, H.-S., et al. (2017) · Genome Biology · doi:10.1186/s13059-017-1341-9 · Cited by 312
Rabanus-Wallace, M. T., Hackauf, B., Mascher, M., Lux, T., Wicker, T., Gundlach, H., Baez, M., Houben, A., Mayer, K. F. X., Guo, L., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00807-0 · Cited by 267
TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
Monat, C., Padmarasu, S., Lux, T., Wicker, T., Gundlach, H., Himmelbach, A., Ens, J., Li, C., Muehlbauer, G. J., Schulman, A. H., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1899-5 · Cited by 251
Metadata
- Authors
- Ghosh, S., & Chan, C.-K. K.
- Venue
- Methods in Molecular Biology
- Publisher
- Springer New York
- Published
- 2016
- Volume
- 1374
- Pages
- 339-361
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W2405688533
- Cited by
- 593
- References
- 39
- FWCI
- 47.65
- Type
- book chapter
- Language
- en
- Open access
- closed
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- CoChat. (2026). Citation check: Analysis of RNA-Seq Data Using TopHat and Cufflinks. https://app.cochat.ai/papers/10.1007/978-1-4939-3167-5_18
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- Ghosh, S., & Chan, C.-K. K. (2016). Analysis of RNA-Seq Data Using TopHat and Cufflinks. Methods in Molecular Biology. https://doi.org/10.1007/978-1-4939-3167-5_18
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
