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IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing

Fu, S., Ma, Y., Yao, H., Xu, Z., Chen, S., Song, J., & Au, K. F. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty098 · Cited by 54

TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization

Ibrahim, F., Oppelt, J., Maragkakis, M., & Mourelatos, Z. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab713 · Cited by 58

Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system

Zhang, X., Li, G., Jiang, H., Li, L., Ma, J., Li, H., & Chen, J. (2019) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2019.01.023 · Cited by 57

Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

Zuo, C., Blow, M. J., Sreedasyam, A., Kuo, R. C., Ramamoorthy, G., Torres‐Jerez, I., Li, G., Wang, M., Dilworth, D. J., Barry, K., et al. (2018) · Biotechnology for Biofuels · doi:10.1186/s13068-018-1167-z · Cited by 53

Integration of full-length transcriptomics and targeted metabolomics to identify benzylisoquinoline alkaloid biosynthetic genes in Corydalis yanhusuo

Xu, D., Lin, H., Tang, Y., Huang, L., Xu, J., Nian, S., & Zhao, Y. (2021) · Horticulture Research · doi:10.1038/s41438-020-00450-6 · Cited by 58

Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us?

Leblanc, V., & Marra, M. A. (2015) · Cancers · doi:10.3390/cancers7030869 · Cited by 57

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon

Sahlin, K., Tomaszkiewicz, M., Makova, K. D., & Medvedev, P. (2018) · Nature Communications · doi:10.1038/s41467-018-06910-x · Cited by 54

Getting the Entire Message: Progress in Isoform Sequencing

Hardwick, S. A., Joglekar, A., Flicek, P., Frankish, A., & Tilgner, H. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00709 · Cited by 59

IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing

Deonovic, B., Wang, Y., Weirather, J. L., Wang, X., & Au, K. F. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1076 · Cited by 56

PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome

Teng, K., Teng, W., Wen, H., Yue, Y., Guo, W., Wu, J., & Fan, X. (2019) · BMC Genomics · doi:10.1186/s12864-019-6163-6 · Cited by 51

Long-read sequencing reveals the landscape of aberrant alternative splicing and novel therapeutic target in colorectal cancer

Sun, Q., Ye, H., He, J., Wang, J., Ma, X., Ning, Q., Zhao, Q., Jin, Q., Yang, L., Li, S., et al. (2023) · Genome Medicine · doi:10.1186/s13073-023-01226-y · Cited by 52

Systematic assessment of long-read RNA-seq methods for transcript identification and quantificationPreprint

Pardo-Palacios, F. J., Reese, F., Sala, S. C., Diekhans, M., Liang, C., Wang, D., Williams, B. A., Adams, M. S., Behera, A. K., Lagarde, J., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-777702/v1 · Cited by 50

Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq

Feng, X., Jia, Y., Zhu, R., Chen, K., & Chen, Y. (2019) · DNA Research · doi:10.1093/dnares/dsz014 · Cited by 50

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

González‐Ibeas, D., Martínez‐García, P. J., Famula, R. A., Mix, A. D., Stevens, K., Loopstra, C. A., Langley, C. H., Neale, D. B., & Wegrzyn, J. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.032805 · Cited by 51

Full-Length Transcriptome Analysis of the Genes Involved in Tocopherol Biosynthesis inTorreya grandis

Lou, H., Ding, M., Wu, J., Zhang, F., Chen, W., Yang, Y., Suo, J., Yu, W., Xu, C., & Song, L. (2019) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.8b06138 · Cited by 49

The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools

Dong, X., Tian, L., Gouil, Q. A., Kariyawasam, H., Su, S., Paoli‐Iseppi, R. D., Prawer, Y. D. J., Clark, M. B., Breslin, K. A., Iminitoff, M., et al. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab028 · Cited by 43

Single-molecule long-read sequencing facilitates shrimp transcriptome research

Zeng, D., Chen, X., Peng, J., Yang, C., Peng, M., Zhu, W., Xie, D., He, P., Wei, P., Lin, Y., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-35066-3 · Cited by 46

Shannon: An Information-Optimal de Novo RNA-Seq AssemblerPreprint

Kannan, S., Hui, J., Mazooji, K., Pachter, L. S., & Tse, D. N. C. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/039230 · Cited by 47

Computational Identification of Novel Genes: Current and Future Perspectives

Klasberg, S., Bitard‐Feildel, T., & Mallet, L. (2016) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s39950 · Cited by 44

Cloning and annotation of novel transcripts from human embryonic stem cells

Khattra, J. S. (2008) · cIRcle (University of British Columbia) · doi:10.14288/1.0066593

TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencingPreprint

Mercuri, R. L. V., Mombach, D. M., dos Santos, F. R. C., Pérez‐Schindler, J., Huang, Y., Spealman, P., Pintacuda, G., Al’Khafaji, A. M., Donnard, E. R., Claussnitzer, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.08.737305

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cellsPreprint

Kolle, G., Shepherd, J. L., Gardiner, B., Kassahn, K. S., Cloonan, N., Wood, D., Nourbakhsh, E., Taylor, D. F., Wani, S., Chy, H. S., et al. (2011) · Genome Research · doi:10.1101/gr.119321.110 · Cited by 25

The transcriptome of human pluripotent stem cells

Au, K. F., & Sebastiano, V. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.09.012 · Cited by 17

LongSAGE profiling of nine human embryonic stem cell lines

Hirst, M., Delaney, A. D., Rogers, S. A., Schnerch, A., Persaud, D. R., O’Connor, M. D., Zeng, T., Moksa, M., Fichter, K., Mah, D. G., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-6-r113 · Cited by 28