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Landscape of transcription in human cells

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Characterization of Full-Length Transcriptome Sequences and Splice Variants of Lateolabrax maculatus by Single-Molecule Long-Read Sequencing and Their Involvement in Salinity Regulation

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Computing the Role of Alternative Splicing in Cancer

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The dynamic landscape of fission yeast meiosis alternative-splice isoformsPreprint

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Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organismsPreprint

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Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events

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Single-molecule real-time transcript sequencing identified flowering regulatory genes in Crocus sativus

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PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes

Ali, A., Thorgaard, G. H., & Salem, M. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.683408 · Cited by 40

Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patternsPreprint

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De novo clustering of long reads by gene from transcriptomics data

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Single cell expression analysis of primate-specific retroviruses-derived HPAT lincRNAs in viable human blastocysts identifies embryonic cells co-expressing genetic markers of multiple lineages

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Informed kmer selection for de novo transcriptome assembly

Durai, D. A., & Schulz, M. H. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw217 · Cited by 35

Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii)

Zhang, X., Zhou, J., Li, L., Huang, W., Ahmad, H. I., Li, H., Jiang, H., & Chen, J. (2020) · Frontiers in Zoology · doi:10.1186/s12983-020-00355-z · Cited by 35

IsoTools: a flexible workflow for long-read transcriptome sequencing analysis

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The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing

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Direct transposition of native DNA for sensitive multimodal single-molecule sequencing

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RNA sequencing: from tag-based profiling to resolving complete transcript structure

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PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq

Gao, Y., Wang, H., Zhang, H., Wang, Y., Chen, J., & Gu, L. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx830 · Cited by 32

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts

Babarinde, I. A., Li, Y., & Hutchins, A. P. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.04.012 · Cited by 30

Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings

Xu, J., Zheng, Y., Pu, S., Zhang, X., Li, Z., & Chen, J. (2020) · BMC Genomics · doi:10.1186/s12864-020-06979-z · Cited by 33

Transcriptome and metabolome analyses reveal a key role of the anthocyanin biosynthetic pathway cascade in the pigmentation of a Cinnamomum camphora red bark mutant (‘Gantong 1’)

Zhong, Y., Chen, C., Gong, X., Luan, X., Wu, Z., Li, H., Liu, Q., Xu, M., & Yu, F. (2021) · Industrial Crops and Products · doi:10.1016/j.indcrop.2021.114236 · Cited by 33

SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus

Ma, J., Xiang, Y., Xiong, Y., Lin, Z. Y., Xue, Y., Mao, M., Sun, L., Zhou, Y., Li, X., & Huang, Z. (2019) · PeerJ · doi:10.7717/peerj.7062 · Cited by 32

The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing

Zhang, Y., Nyong’a, T. M., Shi, T., & Yang, P. (2019) · DNA Research · doi:10.1093/dnares/dsz010 · Cited by 33

Long-read sequencing reveals oncogenic mechanism of HPV-human fusion transcripts in cervical cancer

Liu, M., Han, Z., Zhi, Y., Ruan, Y., Cao, G., Wang, G., Xu, X., Mu, J., Kang, J., Dai, F., et al. (2022) · Translational research · doi:10.1016/j.trsl.2022.09.004 · Cited by 32

Thymus cDNA library survey uncovers novel features of immune molecules in Chinese giant salamander Andrias davidianus

Zhu, R., Chen, Z., Wang, J., Yuan, J.-D., Liao, X., Gui, J., & Zhang, Q.-Y. (2014) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2014.05.019 · Cited by 30

Study of the whole genome, methylome and transcriptome of Cordyceps militaris

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Application of third-generation sequencing in cancer research

Chen, Z., & He, X. (2021) · Medical Review · doi:10.1515/mr-2021-0013 · Cited by 35

Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos

Yin, Z., Zhang, F., Smith, J., Kuo, R. I., & Hou, Z. (2019) · Scientific Data · doi:10.1038/s41597-019-0293-1 · Cited by 27

LSCplus: a fast solution for improving long read accuracy by short read alignment

Hu, R., Sun, G., & Sun, X. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1316-y · Cited by 28

On the design and prospects of direct RNA sequencing

Marinov, G. K. (2017) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw043 · Cited by 29

Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome

Ning, G., Cheng, X., Luo, P., Liang, F., Wang, Z., Yu, G., Li, X., Wang, D., & Bao, M. (2017) · Scientific Reports · doi:10.1038/srep43793 · Cited by 27

Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing

Piriyapongsa, J., Kaewprommal, P., Vaiwsri, S., Anuntakarun, S., Wirojsirasak, W., Punpee, P., Klomsa-ard, P., Shaw, P. J., Pootakham, W., Yoocha, T., et al. (2018) · PeerJ · doi:10.7717/peerj.5818 · Cited by 27

ScisorWiz: visualizing differential isoform expression in single-cell long-read data

Stein, A. N., Joglekar, A., Poon, C.-L., & Tilgner, H. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac340 · Cited by 24

Investigating the Mechanism of Metabolic Resistance to Tribenuron-Methyl in Capsella bursa-pastoris (L.) Medik. by Full-Length Transcriptome Assembly Combined with RNA-Seq

Zhang, X., Wang, D., Bei, F., Wu, C., Zhang, L., Jia, S., Wang, J., & Liu, W. (2021) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c07512 · Cited by 26

SMRT sequencing of the full-length transcriptome of the Sunda pangolin (Manis javanica)

Ma, J., Jiang, H., Li, L., Zhang, X., Li, H., Li, G.-Y., Mo, D.-Y., & Chen, J.-P. (2019) · Gene · doi:10.1016/j.gene.2019.01.008 · Cited by 25

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng

Zhang, D., Li, W., Chen, Z., Wei, F., Liu, Y.-L., & Gao, L. (2020) · Scientific Reports · doi:10.1038/s41598-020-72291-1 · Cited by 25

A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis

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FLAS: fast and high-throughput algorithm for PacBio long-read self-correction

Bao, E., Xie, F., Song, C., & Song, D. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz206 · Cited by 25

Contrasting and combining transcriptome complexity captured by short and long RNA sequencing readsPreprint

Han, S. W., Jewell, S., Thomas‐Tikhonenko, A., & Barash, Y. (2024) · Genome Research · doi:10.1101/gr.278659.123 · Cited by 25

Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomicsPreprint

Belchikov, N., Hsu, J., Li, X. J., Jarroux, J., Hu, W., Joglekar, A., & Tilgner, H. (2024) · Genome Research · doi:10.1101/gr.279640.124 · Cited by 26

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat

Yuan, Z., Ge, L., Sun, J., Zhang, W., Wang, S., Cao, X., & Sun, W. (2021) · PeerJ · doi:10.7717/peerj.12454 · Cited by 23

Identification of essential genes involved in metabolism‐based resistance mechanism to fenoxaprop‐ P ‐ethyl in Polypogon fugax

Zhao, N., Yang, J., Jiang, M., Liao, M., & Cao, H. (2021) · Pest Management Science · doi:10.1002/ps.6733 · Cited by 24

Genome-wide analysis of methyl jasmonate-regulated isoform expression in the medicinal plant Andrographis paniculata

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

Pardo-Palacios, F. J., Wang, D., Reese, F., Diekhans, M., Sala, S. C., Williams, B. A., Loveland, J. E., María, M. D., Adams, M. S., Balderrama-Gutierrez, G., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.25.550582 · Cited by 24

Challenges in identifying mRNA transcript starts and ends from long-read sequencing dataPreprint

Calvo-Roitberg, E., Daniels, R. F., & Pai, A. A. (2024) · Genome Research · doi:10.1101/gr.279559.124 · Cited by 24

A full-length transcriptome of Sepia esculenta using a combination of single-molecule long-read (SMRT) and Illumina sequencing

Zhang, J., Liu, C., He, M., Xiang, Z., Yin, Y., Liu, S., & Zhuang, Z. (2018) · Marine Genomics · doi:10.1016/j.margen.2018.08.008 · Cited by 23

Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

Meng, X., Xu, J., Zhang, M., Du, R., Zhao, W., Zeng, Q. H., Tu, Z., Chen, J., & Chen, B. (2021) · BMC Genomics · doi:10.1186/s12864-021-07873-y · Cited by 24

Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale

He, L., Fu, S., Xu, Z., Yan, J., Xu, J., Zhou, H. Y., Zhou, J., Chen, X., Li, Y., Au, K. F., et al. (2017) · Genes · doi:10.3390/genes8100257 · Cited by 23

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads

Tung, L. H., Shao, M., & Kingsford, C. (2019) · Genome biology · doi:10.1186/s13059-019-1883-0 · Cited by 23

SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

Yang, H., Xu, D., Zhuo, Z., Hu, J., & Lu, B. (2020) · PeerJ · doi:10.7717/peerj.9133 · Cited by 22

PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome

Zhang, H., Xu, H., Liu, H., Pan, X., Xu, M., Zhang, G., & He, M. (2020) · BMC Genomics · doi:10.1186/s12864-020-06894-3 · Cited by 22

Targeting alternative splicing in cancer immunotherapy

Han, N., & Liu, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1232146 · Cited by 21

Identification and visualization of differential isoform expression in RNA-seq time series

Nueda, M. J., Martorell‐Marugán, J., Martí, C., Tarazona, S., & Conesa, A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx578 · Cited by 22

Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis

Gao, X. M., Guo, F., Yuan, C., Bai, G., Liu, Y., Jin, J., & Wang, Q. (2021) · Scientific Reports · doi:10.1038/s41598-021-92494-4 · Cited by 22

Hybrid-Transcriptome Sequencing and Associated Metabolite Analysis Reveal Putative Genes Involved in Flower Color Difference in Rose Mutants

Huang, P., Lin, F., Li, B., & Zheng, Y. (2019) · Plants · doi:10.3390/plants8080267 · Cited by 21

RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition

Mao, S., Pachter, L. S., Tse, D. N. C., & Kannan, S. (2020) · PLoS ONE · doi:10.1371/journal.pone.0232946 · Cited by 20

Transcriptome and gene expression analysis ofRhynchophorus ferrugineus(Coleoptera: Curculionidae) during developmental stages

Yang, H., Xu, D., Zhuo, Z., Hu, J., & Lu, B. (2020) · PeerJ · doi:10.7717/peerj.10223 · Cited by 19

From words to complete phrases: insight into single-cell isoforms using short and long reads

Joglekar, A., Foord, C., Jarroux, J., Pollard, S., & Tilgner, H. (2023) · Transcription · doi:10.1080/21541264.2023.2213514 · Cited by 20

Long Read Single-Molecule Real-Time Sequencing Elucidates Transcriptome-Wide Heterogeneity and Complexity in Esophageal Squamous Cells

Cheng, Y., Chen, Y., Zhao, Q., Zhao, X., Wu, Y.-R., Chen, D., Liao, L., Chen, Y., Yang, Q., Xu, L., et al. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00915 · Cited by 18

Prospects for the use of third generation sequencers for quantitative profiling of transcriptome

Radko, S. P., Kurbatov, L. K., Ptitsyn, K. G., Kiseleva, Y. Y., Ponomarenko, E. A., Лисица, А. В., & Арчаков, А. И. (2018) · Biomedical Chemistry Research and Methods · doi:10.18097/bmcrm00086 · Cited by 19

Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome utilizing PacBio long reads combined with Illumina short reads

Chen, D., Du, Y., Fan, X., Zhu, Z., Jiang, H., Wang, J., Fan, Y., Chen, H., Zhou, D., Xiong, C., et al. (2020) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2020.107475 · Cited by 17

Towards next generation CHO cell biology: Bioinformatics methods for RNA‐Seq‐based expression profiling

Monger, C., Kelly, P. S., Gallagher, C., CLYNES, M. M., Barron, N., & Clarke, C. (2015) · Biotechnology Journal · doi:10.1002/biot.201500107 · Cited by 20

Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies

Yeh, H.-S., Zhang, W., & Yong, J. (2017) · BMB Reports · doi:10.5483/bmbrep.2017.50.4.019 · Cited by 18

Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity

Gao, Y., Xi, F., Zhang, H., Liu, X., Wang, H., Zhao, L., Reddy, A. S. N., & Gu, L. (2019) · Current Bioinformatics · doi:10.2174/1574893614666190204151746 · Cited by 18

Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response

Xu, J., Fang, M., Li, Z., Zhang, M., Liu, X., Peng, Y., Wan, Y., & Chen, J. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00249 · Cited by 18

Alternative mRNA Processing of Innate Response Pathways in Respiratory Syncytial Virus (RSV) Infection

Xu, X., Mann, M. W., Qiao, D., & Brasier, A. R. (2021) · Viruses · doi:10.3390/v13020218 · Cited by 18

Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing Reveals Novel and Distinct mRNA Isoforms in Human Bone Marrow Cell Subpopulations

Mays, A. D., Schmidt, M. O., Graham, G. T., Tseng, E., Baybayan, P. A., Sebra, R., Šanda, M., Mazarati, J.-B., Riegel, A. T., & Wellstein, A. (2019) · Genes · doi:10.3390/genes10040253 · Cited by 18

Single-molecule real-time (SMRT) sequencing facilitates Tachypleus tridentatus genome annotation

Lou, F., Song, N., Han, Z., & Gao, T. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.01.029 · Cited by 17

Accurate transcriptome assembly by Nanopore RNA sequencing reveals novel functional transcripts in hepatocellular carcinoma

Fang, Y., Chen, G., Chen, F., Hu, E., Dong, X., Li, Z., He, L., Sun, Y., Qiu, L., Xu, H., et al. (2021) · Cancer Science · doi:10.1111/cas.15058 · Cited by 17

Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State

Pells, S., Koutsouraki, E., Morfopoulou, S., Valencia-Cadavid, S., Tomlinson, S. R., Kalathur, R. K. R., Futschik, M. E., & Sousa, P. A. D. (2015) · PLoS ONE · doi:10.1371/journal.pone.0131102 · Cited by 17

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

One-two punch mechanism of gene repression: a fresh perspective on gene regulation

Tresenrider, A. M., & Ünal, E. (2017) · Current Genetics · doi:10.1007/s00294-017-0793-5 · Cited by 17

Transcriptome Survey of a Marine Food Fish: Asian Seabass (Lates calcarifer)

Thevasagayam, N. M., Sridatta, P. S. R., Jiang, J., Tong, A. H. Y., Saju, J. M., Purushothaman, K., Kwan, H. Y., Ngoh, S. Y., Liew, W. C., Kuznetsova, I. S., et al. (2015) · Journal of Marine Science and Engineering · doi:10.3390/jmse3020382 · Cited by 16

Identifying Candidate Genes Involved in the Regulation of Early Growth Using Full-Length Transcriptome and RNA-Seq Analyses of Frontal and Parietal Bones and Vertebral Bones in Bighead Carp (Hypophthalmichthys nobilis)

Luo, W., Zhou, Y., Wang, J., Yu, X., & Tong, J. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2020.603454 · Cited by 16

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidomePreprint

Maeng, J. H., Jang, H. J., Du, A. Y., Tzeng, S., & Wang, T. (2023) · Genome Research · doi:10.1101/gr.277061.122 · Cited by 16

Phosphate-Modified Nucleotides for Monitoring Enzyme Activity

Ermert, S., Marx, A., & Hacker, S. M. (2017) · Topics in Current Chemistry · doi:10.1007/s41061-017-0117-8 · Cited by 15

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Mueller, R. C., Ellström, P., Howe, K., Uliano‐Silva, M., Kuo, R. I., Miedzinska, K., Warr, A., Fedrigo, O. D., Haase, B., Mountcastle, J., et al. (2021) · GigaScience · doi:10.1093/gigascience/giab081 · Cited by 15

Full-length transcriptome sequencing provides insights into flavonoid biosynthesis in Camellia nitidissima Petals

Liu, H., Liu, Q., Chen, Y., Zhu, Y., Zhou, X., & Li, B. (2022) · Gene · doi:10.1016/j.gene.2022.146924 · Cited by 15

Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data

Newman, J. R. B., CONCANNON, P. J., Tardáguila, M., Conesa, A., & McIntyre, L. M. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200373 · Cited by 14

Full-length transcriptome sequencing on PacBio platform

Bu, W., Liu, G., He, B., Gao, S., ZHANG, J., Wu, Z., Ren, Y., Ruan, J., & Sun, Y. (2016) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/n972015-01384 · Cited by 14

Characterization and analysis of the transcriptome in Opisina arenosella from different developmental stages using single-molecule real-time transcript sequencing and RNA-seq

Xu, D., Yang, H., Zhuo, Z., Lu, B., Hu, J., & Yang, F. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.12.098 · Cited by 15

The Value and Significance of Metagenomics of Marine Environments

Zhao, F., & Bajić, V. B. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.10.002 · Cited by 15

Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L.

Ma, T., Gao, H., Zhang, D., Sun, W., Yin, Q., Wu, L., Zhang, T., Xu, Z., Wei, J., Su, Y., et al. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.733505 · Cited by 12

Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing

Gong, B., Li, D., Łabaj, P. P., Pan, B., Novoradovskaya, N., Thierry‐Mieg, D., Thierry‐Mieg, J., Chen, G., Lucas, A. B., LoCoco, J. S., et al. (2024) · Scientific Data · doi:10.1038/s41597-024-03741-y · Cited by 15

Genomic variability and protein species — Improving sequence coverage for proteogenomics

Bischoff, R., Permentier, H. P., Guryev, V., & Horvatovich, P. L. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.09.021 · Cited by 14

Embryonic Stem Cells Exhibit mRNA Isoform Specific Translational Regulation

Wong, Q. W.-L., Vaz, C., Lee, Q. Y., Zhao, T. Y., Luo, R., Archer, S. K., Preiß, T., Tanavde, V., & Vardy, L. A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0143235 · Cited by 13

Finding function in mystery transcripts

Chi, K. R. (2016) · Nature · doi:10.1038/529423a · Cited by 13

Differential Expression Analysis of Olfactory Genes Based on a Combination of Sequencing Platforms and Behavioral Investigations in Aphidius gifuensis

Fan, J., Zhang, Q. Y., Xu, Q., Xue, W., Han, Z., Sun, J., & Chen, J. (2018) · Frontiers in Physiology · doi:10.3389/fphys.2018.01679 · Cited by 13

Alternative Splicing Landscape of Small Brown Planthopper and Different Response of JNK2 Isoforms to Rice Stripe Virus Infection

Tong, L., Chen, X., Wang, W., Xiao, Y., Yu, J., Lu, H., & Cui, F. (2021) · Journal of Virology · doi:10.1128/jvi.01715-21 · Cited by 11

Improving gene isoform quantification with miniQuant

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In silico read normalization using set multi-cover optimization

Durai, D. A., & Schulz, M. H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty307 · Cited by 12

Combined transcriptome sequencing reveals the photoperiod insensitivity mechanism of oats

An, J., Yu, D., Yang, X., Rong, X., Han, B., Cai, Y., Yang, Y., Zhou, H., & Li, T. (2019) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2019.11.015 · Cited by 12

Performance difference of graph-based and alignment-based hybrid error correction methods for error-prone long reads

Wang, A., & Au, K. F. (2020) · Genome biology · doi:10.1186/s13059-019-1885-y · Cited by 11

Draft genome of Meyerozyma guilliermondii strain vka1: a yeast strain with composting potential

Valsalan, R., & Mathew, D. (2020) · Journal of Genetic Engineering and Biotechnology · doi:10.1186/s43141-020-00074-2 · Cited by 11

Transcriptome profiling of Capsicum annuum using Illumina- and PacBio SMRT-based RNA-Seq for in-depth understanding of genes involved in trichome formation

Gao, S., Li, N., Juntawong, N., Wang, F., Yin, Y., Yu, C., Jiao, C., Yang, C., & Yao, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-89619-0 · Cited by 12

Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica

Guan, J., Yin, S., Yue, Y., Liu, L., Guo, Y., Zhang, H., Fan, X., & Teng, K. (2022) · BMC Plant Biology · doi:10.1186/s12870-022-03640-7 · Cited by 12

Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola

Jia, M., Ni, Y., Zhao, H. J., Liu, X., Yan, W., Zhao, X., Wang, J., He, B., & Liu, H. (2024) · BMC Plant Biology · doi:10.1186/s12870-024-04728-y · Cited by 11

Generation and comparative analysis of full-length transcriptomes in sweetpotato and its putative wild ancestor I. trifidaPreprint

Luo, Y., Ding, N., Shi, X., Wu, Y., Wang, R., Pei, L., Xu, R., Cheng, S., Lian, Y., Gao, J., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/112425 · Cited by 11

The non-coding genome in early human development – Recent advancements

Paloviita, P., & Vuoristo, S. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.02.010 · Cited by 12

Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens

Hovhannisyan, H., & Gabaldón, T. (2018) · Current topics in microbiology and immunology · doi:10.1007/82_2018_122 · Cited by 11

Computational Approaches for Transcriptome Assembly Based on Sequencing Technologies

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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