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Journal articles on the topic 'Long-read RNA-seq'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

Lin, Kuan-Ting, and Adrian R. Krainer. "PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis." Bioinformatics 35, no. 23 (2019): 5048–54. http://dx.doi.org/10.1093/bioinformatics/btz438.

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Abstract Motivation Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data. We developed PSI-Sigma, which uses a new PSI index, and we employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins) to benchmark its performance (i.e. precision, recall, false positive rate and correlation) in comparison with three leading tools (rMATS, SUPPA2 and Whippet). Results PSI-Sigma outperformed these tools, especially in th

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Kim, Yewon, Anvith Kakkera, Asher Bryant, et al. "Abstract 995: Leveraging RNA and long-read DNA to improve genetic etiology identification in individuals with elevated cancer risk: A pilot study in individuals with Li-Fraumeni-like phenotype." Cancer Research 85, no. 8_Supplement_1 (2025): 995. https://doi.org/10.1158/1538-7445.am2025-995.

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Abstract Individuals with clinical Li-Fraumeni Syndrome (LFS) are at hereditary risk of developing multiple cancers in their lifetime. Among those meeting classic LFS criteria, about 10% do not have a germline mutation identified in TP53. Long-read DNA sequencing identifies complex and structural variants missed on short-read sequencing. Clinical germline testing labs also recently began using short-read RNA-seq to characterize alternative splicing events. This project aims to explore underlying genetic etiology of those with LFS and no identifiable germline TP53 variant using long-read DNA-se

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Križanović, Krešimir, Amina Echchiki, Julien Roux, and Mile Šikić. "Evaluation of tools for long read RNA-seq splice-aware alignment." Bioinformatics 34, no. 5 (2017): 748–54. http://dx.doi.org/10.1093/bioinformatics/btx668.

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Solaiman, Morjina. "The Quick Guide to RNA-Seq: From Data Acquisition to Functional Analysis." Journal of Scientific Reports 10, no. 1 (2025): 37–51. https://doi.org/10.58970/jsr.1114.

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RNA sequencing (RNA-Seq) has revolutionized transcriptomics by enabling comprehensive and unbiased gene expression profiling across diverse biological contexts. This review summarizes the key stages of RNA-Seq, from RNA isolation and library preparation to sequencing technologies and computational analyses. We discuss the evolution of sequencing platforms, including second-generation short-read and third-generation long-read technologies, highlighting their applications and limitations. Critical steps such as quality control, read alignment, transcript assembly, normalization, and differential

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Wong, Kwong-Kwok, Yvonne Tsang, and David M. Gershenson. "Abstract 4081: Analysis of low-grade serous ovarian cancer by long-read full length transcripts sequencing." Cancer Research 85, no. 8_Supplement_1 (2025): 4081. https://doi.org/10.1158/1538-7445.am2025-4081.

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Abstract Low grade serous ovarian carcinoma is a rare epithelial ovarian cancer that occurs more frequently in younger women. RNA sequencing (RNAseq) has been playing a pivotal role in understanding the molecular pathogenesis of the low-grade ovarian serous carcinoma (LGSOC). The quantification of gene expression with enough sequencing depth can be fairly accurate. However, the current short-read RNAseq approach is not very accurate in measuring individual transcript activity. This is because multiple transcripts from the same gene share high sequence similarity, which complicates the transcri

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Broseus, Lucile, Aubin Thomas, Andrew J. Oldfield, Dany Severac, Emeric Dubois, and William Ritchie. "TALC: Transcript-level Aware Long-read Correction." Bioinformatics 36, no. 20 (2020): 5000–5006. http://dx.doi.org/10.1093/bioinformatics/btaa634.

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Abstract Motivation Long-read sequencing technologies are invaluable for determining complex RNA transcript architectures but are error-prone. Numerous ‘hybrid correction’ algorithms have been developed for genomic data that correct long reads by exploiting the accuracy and depth of short reads sequenced from the same sample. These algorithms are not suited for correcting more complex transcriptome sequencing data. Results We have created a novel reference-free algorithm called Transcript-level Aware Long-Read Correction (TALC) which models changes in RNA expression and isoform representation

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Bell, Bryan, Lisa Welter, Kazuo Tori, et al. "Abstract LB316: Enabling long-read mRNA-seq for oncology biomarker discovery using limited clinical sample inputs." Cancer Research 85, no. 8_Supplement_2 (2025): LB316. https://doi.org/10.1158/1538-7445.am2025-lb316.

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Abstract RNAs serve a central role in cellular biology by converting genomic information into effector molecules, either as mRNAs or directly functional RNAs. Measurement of RNA through RNA Sequencing has become an important method to understand biological processes. While it has been long appreciated that a vast diversity of RNA transcripts can be produced through alternative splicing, more recent work has defined a significant contribution of alternate and aberrant splicing to diseases like cancer, neurodegeneration, and autoimmunity. Thus, understanding the diversity of RNA transcripts is a

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Hazzard, Brittany, Juliana M. Sá, Angela C. Ellis, et al. "Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts." PLOS Neglected Tropical Diseases 16, no. 12 (2022): e0010991. http://dx.doi.org/10.1371/journal.pntd.0010991.

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Plasmodium vivax infections often consist of heterogenous populations of parasites at different developmental stages and with distinct transcriptional profiles, which complicates gene expression analyses. The advent of single cell RNA sequencing (scRNA-seq) enabled disentangling this complexity and has provided robust and stage-specific characterization of Plasmodium gene expression. However, scRNA-seq information is typically derived from the end of each mRNA molecule (usually the 3’-end) and therefore fails to capture the diversity in transcript isoforms documented in bulk RNA-seq data. Here

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Liu, Yanling, Bensheng Ju, Li Dong, et al. "Abstract 2617: Uncovering genomic complexity of PAX5 internal tandem duplication using short-read and long-read sequencing." Cancer Research 85, no. 8_Supplement_1 (2025): 2617. https://doi.org/10.1158/1538-7445.am2025-2617.

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Abstract PAX5 is known to be frequently mutated in childhood B-cell precursor acute lymphoblastic leukemia (B-ALL) via several molecular mechanisms, including chimeric fusion, focal deletion, and point mutations. Among these, patients with PAX5 internal tandem duplication (PAX5-ITD) are reported to have a poor outcome. Unlike other common ITDs (e.g., FLT3), PAX5-ITD often involves gain of more than one copy of involved exons, and the exact nature of these alterations remain elusive. Here we aim to investigate the following questions: 1) what are the typical copy number gains in DNA and RNA amo

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Mitsuhashi, Satomi, So Nakagawa, Mitsuru Sasaki-Honda, Hidetoshi Sakurai, Martin C. Frith, and Hiroaki Mitsuhashi. "Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells." Human Molecular Genetics 30, no. 7 (2021): 552–63. http://dx.doi.org/10.1093/hmg/ddab063.

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Abstract Facioscapulohumeral muscular dystrophy (FSHD) is an inherited muscle disease caused by misexpression of the DUX4 gene in skeletal muscle. DUX4 is a transcription factor, which is normally expressed in the cleavage-stage embryo and regulates gene expression involved in early embryonic development. Recent studies revealed that DUX4 also activates the transcription of repetitive elements such as endogenous retroviruses (ERVs), mammalian apparent long terminal repeat (LTR)-retrotransposons and pericentromeric satellite repeats (Human Satellite II). DUX4-bound ERV sequences also create alt

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Carmen, Silvina del, Prashant Singh, Pulak Nath, et al. "Isoform repertoire of Blood mononuclear cells from SLE patients." Journal of Immunology 204, no. 1_Supplement (2020): 218.12. http://dx.doi.org/10.4049/jimmunol.204.supp.218.12.

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Abstract Systemic Lupus Erythematosus (SLE) is characterized by numerous immunological alterations, including increased expression of immune activators, such as IFNa, along with alterations in cell composition, such as expansion of plasma cells that produce autoantibodies. Alternative Splicing (AS) is a biological process that regulates post-transcriptional alterations of the RNA. Pathogenic AS events have been associated to several diseases. Furthermore, the description of SLE autoantibodies that target components of the spliceosome such as anti-Sm/RNP, anti-Ro/La, and anti-dsDNA has led us t

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Tang, Jinyang, and Fei Wang. "Detecting differentially expressed genes by smoothing effect of gene length on variance estimation." Journal of Bioinformatics and Computational Biology 13, no. 06 (2015): 1542004. http://dx.doi.org/10.1142/s0219720015420044.

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Next-generation sequencing technologies are widely used in genome research, and RNA sequencing (RNA-Seq) is becoming the main application for gene expression profiling. A large number of computational methods have been developed for analyzing differentially expressed (DE) genes in RNA-Seq data. However, most existing algorithms prefer to call long genes as DE. Short DE genes are rarely detected. In this work, we set out to gain insight into the influence of gene length on RNA-Seq data analysis and to figure out the effect of gene length on variance estimation of RNA-Seq read counts, which is i

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Massaiu, Ilaria, Paola Songia, Mattia Chiesa, et al. "Evaluation of Oxford Nanopore MinION RNA-Seq Performance for Human Primary Cells." International Journal of Molecular Sciences 22, no. 12 (2021): 6317. http://dx.doi.org/10.3390/ijms22126317.

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Transcript sequencing is a crucial tool for gaining a deep understanding of biological processes in diagnostic and clinical medicine. Given their potential to study novel complex eukaryotic transcriptomes, long-read sequencing technologies are able to overcome some limitations of short-read RNA-Seq approaches. Oxford Nanopore Technologies (ONT) offers the ability to generate long-read sequencing data in real time via portable protein nanopore USB devices. This work aimed to provide the user with the number of reads that should be sequenced, through the ONT MinION platform, to reach the desired

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Yuan, Yubai, Qi Xu, Agaz Wani, et al. "Differentially expressed heterogeneous overdispersion genes testing for count data." PLOS ONE 19, no. 7 (2024): e0300565. http://dx.doi.org/10.1371/journal.pone.0300565.

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The mRNA-seq data analysis is a powerful technology for inferring information from biological systems of interest. Specifically, the sequenced RNA fragments are aligned with genomic reference sequences, and we count the number of sequence fragments corresponding to each gene for each condition. A gene is identified as differentially expressed (DE) if the difference in its count numbers between conditions is statistically significant. Several statistical analysis methods have been developed to detect DE genes based on RNA-seq data. However, the existing methods could suffer decreasing power to

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Van den Berge, Koen, Katharina M. Hembach, Charlotte Soneson, et al. "RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis." Annual Review of Biomedical Data Science 2, no. 1 (2019): 139–73. http://dx.doi.org/10.1146/annurev-biodatasci-072018-021255.

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Gene expression is the fundamental level at which the results of various genetic and regulatory programs are observable. The measurement of transcriptome-wide gene expression has convincingly switched from microarrays to sequencing in a matter of years. RNA sequencing (RNA-seq) provides a quantitative and open system for profiling transcriptional outcomes on a large scale and therefore facilitates a large diversity of applications, including basic science studies, but also agricultural or clinical situations. In the past 10 years or so, much has been learned about the characteristics of the RN

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Uapinyoying, Prech, Jeremy Goecks, Susan M. Knoblach, et al. "A long-read RNA-seq approach to identify novel transcripts of very large genes." Genome Research 30, no. 6 (2020): 885–97. http://dx.doi.org/10.1101/gr.259903.119.

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Lackey, Lela, Aaztli Coria, Auyon J. Ghosh та ін. "Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease". PLOS Genetics 17, № 11 (2021): e1009912. http://dx.doi.org/10.1371/journal.pgen.1009912.

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α1-anti-trypsin (A1AT), encoded by SERPINA1, is a neutrophil elastase inhibitor that controls the inflammatory response in the lung. Severe A1AT deficiency increases risk for Chronic Obstructive Pulmonary Disease (COPD), however, the role of A1AT in COPD in non-deficient individuals is not well known. We identify a 2.1-fold increase (p = 2.5x10-6) in the use of a distal poly-adenylation site in primary lung tissue RNA-seq in 82 COPD cases when compared to 64 controls and replicate this in an independent study of 376 COPD and 267 controls. This alternative polyadenylation event involves two sit

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Li, Zhigang, Jiankun Fan, Yuanze Zhou, and Yu Hou. "The RNA Helicase DHX16 Is Required for the Maintenance of Hematopoietic Stem Cells." Blood 142, Supplement 1 (2023): 2683. http://dx.doi.org/10.1182/blood-2023-184623.

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Lifelong hematopoiesis relies on the homeostasis of hematopoietic stem cells(HSCs), but the underlying mechanisms remain incompletely understood. Here, we identified a critical role for DHX16, a member of DEAH-box RNA helicase, in the maintenance of HSCs. After inducing deletion of Dhx16 gene in mice, the knockout animals developed pancytopenia within 5-7 days and died within two weeks. Flow cytometric analyses demonstrated that Dhx16-deficient mice had significantly reduced hematopoietic stem and progenitor cells, altered cell cycle dynamics with decreased G0 phase and increased G2/M phase, a

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Hu, Yu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li, and Kai Wang. "LIQA: long-read isoform quantification and analysis." Genome Biology 22, no. 1 (2021). http://dx.doi.org/10.1186/s13059-021-02399-8.

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AbstractLong-read RNA sequencing (RNA-seq) technologies can sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression over short-read RNA-seq. We present LIQA to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read direct mRNA sequencing or cDNA sequencing data. LIQA incorporates base pair quality score and isoform-specific read length information in a survival model to assign different weights across reads, and uses an expectation-maximization algorithm for parameter estimation. We apply LIQA to long-rea

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Liu, Zhiheng, Giovanni Quinones-Valdez, Ting Fu, et al. "L-GIREMI uncovers RNA editing sites in long-read RNA-seq." Genome Biology 24, no. 1 (2023). http://dx.doi.org/10.1186/s13059-023-03012-w.

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AbstractAlthough long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in si

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You, Yupei, Yair D. J. Prawer, Ricardo De Paoli-Iseppi, et al. "Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE." Genome Biology 24, no. 1 (2023). http://dx.doi.org/10.1186/s13059-023-02907-y.

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AbstractLong-read single-cell RNA sequencing (scRNA-seq) enables the quantification of RNA isoforms in individual cells. However, long-read scRNA-seq using the Oxford Nanopore platform has largely relied upon matched short-read data to identify cell barcodes. We introduce BLAZE, which accurately and efficiently identifies 10x cell barcodes using only nanopore long-read scRNA-seq data. BLAZE outperforms the existing tools and provides an accurate representation of the cells present in long-read scRNA-seq when compared to matched short reads. BLAZE simplifies long-read scRNA-seq while improving

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Masuda, Keigo, Yoshiaki Sota, and Hideo Matsuda. "Gene Fusion Detection in Long-Read Transcriptome Datasets from Multiple Cancer Cell Lines." Frontiers in Bioscience-Landmark 29, no. 12 (2024). https://doi.org/10.31083/j.fbl2912413.

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Background: Fusion genes are important biomarkers in cancer research because their expression can produce abnormal proteins with oncogenic properties. Long-read RNA sequencing (long-read RNA-seq), which can sequence full-length mRNA transcripts, facilitates the detection of such fusion genes. Several tools have been proposed for detecting fusion genes in long-read RNA-seq datasets derived from cancer cells. However, the high sequencing error rate in long-read RNA-seq makes fusion gene detection challenging. Methods: To address this issue, additional steps were incorporated into the fusion dete

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Ren, Yan, Elizabeth Tseng, Timothy P. L. Smith, Stefan Hiendleder, John L. Williams, and Wai Yee Low. "Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies." BMC Genomics 24, no. 1 (2023). http://dx.doi.org/10.1186/s12864-023-09212-9.

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AbstractThe Iso-Seq method of full-length cDNA sequencing is suitable to quantify differentially expressed genes (DEGs), transcripts (DETs) and transcript usage (DTU). However, the higher cost of Iso-Seq relative to RNA-seq has limited the comparison of both methods. Transcript abundance estimated by RNA-seq and deep Iso-Seq data for fetal liver from two cattle subspecies were compared to evaluate concordance. Inter-sample correlation of gene- and transcript-level abundance was higher within technology than between technologies. Identification of DEGs between the cattle subspecies depended on

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Liu, Qian, Yu Hu, Andres Stucky, Li Fang, Jiang F. Zhong, and Kai Wang. "LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing." BMC Genomics 21, S11 (2020). http://dx.doi.org/10.1186/s12864-020-07207-4.

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Abstract Background Long-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that typically generate < 150 bp reads. However, there is a general lack of software tools for gene fusion detection from long-read RNA-seq data, which takes into account the high basecalling error rates and the presence of alignment errors. Results In this study, we developed a fast computational tool, LongGF, to efficiently detect candidate gene fusions from long-read

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Carbonell-Sala, Sílvia, Tamara Perteghella, Julien Lagarde, et al. "CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing." Nature Communications 15, no. 1 (2024). http://dx.doi.org/10.1038/s41467-024-49523-3.

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AbstractLong-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we develop CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5’ capped, full-length transcripts. In our study, we evaluate the performance of CapTrap-seq alongside other widely used RNA-seq library preparation protocol

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Qin, Qian, Victoria Popic, Kirsty Wienand, et al. "Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution." Genome Research, March 14, 2025. https://doi.org/10.1101/gr.279200.124.

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Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics and prognostics and for guiding therapeutic development. Most currently available methods for fusion transcript detection are compatible with Illumina RNA-seq involving highly accurate short-read sequences. Recent advances in long-read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single-cell samples. Here, we developed a new computational tool, CTAT-LR-Fusion, to detect fusi

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Wang, Feng, Yang Xu, Robert Wang, et al. "TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing." Nature Communications 14, no. 1 (2023). http://dx.doi.org/10.1038/s41467-023-40083-6.

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AbstractLong-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially

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Kovaka, Sam, Aleksey V. Zimin, Geo M. Pertea, Roham Razaghi, Steven L. Salzberg, and Mihaela Pertea. "Transcriptome assembly from long-read RNA-seq alignments with StringTie2." Genome Biology 20, no. 1 (2019). http://dx.doi.org/10.1186/s13059-019-1910-1.

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AbstractRNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads. StringTie2 includes new methods to handle the high error rate of long reads and offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of short-read assemblies. StringTie2 is more accurate

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Gong, Binsheng, Dan Li, Paweł P. Łabaj, et al. "Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing." Scientific Data 11, no. 1 (2024). http://dx.doi.org/10.1038/s41597-024-03741-y.

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AbstractNext-generation sequencing (NGS) has revolutionized genomic research by enabling high-throughput, cost-effective genome and transcriptome sequencing accelerating personalized medicine for complex diseases, including cancer. Whole genome/transcriptome sequencing (WGS/WTS) provides comprehensive insights, while targeted sequencing is more cost-effective and sensitive. In comparison to short-read sequencing, which still dominates the field due to high speed and cost-effectiveness, long-read sequencing can overcome alignment limitations and better discriminate similar sequences from altern

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Nguyen, Manh Hung, Ha-Nam Nguyen, and Trung Nghia Vu. "Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data." BMC Genomics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12864-022-08329-7.

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Abstract Background Circular RNA (circRNA), a class of RNA molecule with a loop structure, has recently attracted researchers due to its diverse biological functions and potential biomarkers of human diseases. Most of the current circRNA detection methods from RNA-sequencing (RNA-Seq) data utilize the mapping information of paired-end (PE) reads to eliminate false positives. However, much of the practical RNA-Seq data such as cross-linking immunoprecipitation sequencing (CLIP-Seq) data usually contain single-end (SE) reads. It is not clear how well these tools perform on SE RNA-Seq data. Resul

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Miller, Rachel, Ben Jordan, Madison Mehlferber, et al. "Enhanced Protein Isoform Characterization Through Long-Read Proteogenomics - Jurkat Samples and Reference Data." July 5, 2021. https://doi.org/10.5281/zenodo.5703754.

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  The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine.  Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal.  Long-read RNA sequencing (e.g. PacBio, Oxford Nanopore) provide full-length transcript sequencing, which can be used to predict full-length proteins.  Here, we describe a long-read proteogenomics approach for integrating

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Meleshko, Dmitry, Andrey D. Prjbelski, Mikhail Raiko, Alexandru I. Tomescu, Hagen Tilgner, and Iman Hajirasouliha. "cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data." Bioinformatics, January 23, 2024. http://dx.doi.org/10.1093/bioinformatics/btad781.

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Abstract Motivation Recent advancements in long-read RNA sequencing have enabled the examination of full-length isoforms, previously uncaptured by short-read sequencing methods. An alternative powerful method for studying isoforms is through the use of barcoded short-read RNA reads, for which a barcode indicates whether two short-reads arise from the same molecule or not. Such techniques included the 10x Genomics linked-read based SParse Isoform Sequencing (SPIso-seq), as well as Loop-Seq, or Tell-Seq. Some applications, such as novel-isoform discovery, require very high coverage. Obtaining hi

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Bizuayehu, Teshome Tilahun, Kornel Labun, Martin Jakubec, Kirill Jefimov, Adnan Muhammad Niazi, and Eivind Valen. "Long-read single-molecule RNA structure sequencing using nanopore." Nucleic Acids Research, September 27, 2022. http://dx.doi.org/10.1093/nar/gkac775.

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Abstract RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that onl

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Yamamoto, Ryo, Zhiheng Liu, Mudra Choudhury, and Xinshu Xiao. "dsRID: in silico identification of dsRNA regions using long-read RNA-seq data." Bioinformatics, October 23, 2023. http://dx.doi.org/10.1093/bioinformatics/btad649.

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Abstract Motivation Double-stranded RNAs (dsRNAs) are potent triggers of innate immune responses upon recognition by cytosolic dsRNA sensor proteins. Identification of endogenous dsRNAs helps to better understand the dsRNAome and its relevance to innate immunity related to human diseases. Results Here, we report dsRID (double-stranded RNA identifier), a machine learning-based method to predict dsRNA regions in silico, leveraging the power of long-read RNA-sequencing (RNA-seq) and molecular traits of dsRNAs. Using models trained with PacBio long-read RNA-seq data derived from Alzheimer’s diseas

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Hijikata, Minako, Kozo Morimoto, Masashi Ito, Keiko Wakabayashi, Akiko Miyabayashi, and Naoto Keicho. "Robust detection of pathogenicHYDINvariants that cause primary ciliary dyskinesia using RNA-seq of nasal mucosa." Journal of Medical Genetics, January 13, 2025, jmg—2024–110400. https://doi.org/10.1136/jmg-2024-110400.

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Primary ciliary dyskinesia (PCD, OMIM 244400) is a rare genetic disorder that affects motile cilia and is characterised by impaired mucociliary clearance of the airway epithelium, which results in chronic upper and lower airway infections. While short-read next-generation sequencing technology has been used for the genetic testing of PCD, its effectiveness is limited in identifying variants in theHYDINgene because of the nearly identical pseudogeneHYDIN2. As we confirmed that theHYDIN2gene was not expressed in airway cells, we obtained nasal mucosa biopsy specimens for total RNA sequencing (RN

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Liu, Christine S., Chris Park, Tony Ngo, et al. "RNA isoform diversity in human neurodegenerative diseases." eneuro, December 10, 2024, ENEURO.0296–24.2024. https://doi.org/10.1523/eneuro.0296-24.2024.

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Single-nucleus RNA-sequencing (snRNA-seq) has revealed new levels of cellular organization and diversity within the human brain. However, full-length mRNA isoforms are not resolved in typical snRNA-seq analyses using short-read sequencing that cannot capture full-length transcripts. Here we combine standard 10X Genomics short-read snRNA-seq with targeted PacBio long-read snRNA-seq to examine isoforms of genes associated with neurological diseases at the single-cell level from prefrontal cortex samples of diseased and non-diseased human brain, assessing over 165,000 cells. Samples from 25 post-

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de Souza, Vladimir B. C., Ben T. Jordan, Elizabeth Tseng, et al. "Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data." Genome Biology 24, no. 1 (2023). http://dx.doi.org/10.1186/s13059-023-02923-y.

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AbstractLong-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms. Furthermore, there is an opportunity to call variants directly from lrRNA-seq data. However, most state-of-the-art variant callers have been developed for genomic DNA. Here, there are two objectives: first, we perform a mini-benchmark on GATK, DeepVariant, Clair3, and NanoCaller primarily on PacBio Iso-Seq, data, but also on Nanopore and Illumina RNA-seq data; second, we propose a pipeline to process spliced-alignment files, making them suitabl

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Hardwick, Simon A., Wen Hu, Anoushka Joglekar, et al. "Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue." Nature Biotechnology, March 7, 2022. http://dx.doi.org/10.1038/s41587-022-01231-3.

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AbstractSingle-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhib

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Tanaka, Yoshihisa, Naohiro Sunamura, Rei Kajitani, Marie Ikeguchi, and Ryo Kunimoto. "Long-read RNA sequencing unveils a novel cryptic exon in MNAT1 along with its full-length transcript structure in TDP-43 proteinopathy." Communications Biology 8, no. 1 (2025). https://doi.org/10.1038/s42003-025-08463-4.

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Abstract Understanding the role of transcript isoforms is essential for elucidating disease mechanisms. TDP-43 regulates RNA splicing, and its dysfunction in neurons is a hallmark of some neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). While an association between TDP-43-dependent cryptic exons and disease pathogenesis has been suggested, an approach to investigate how cryptic exons disrupt transcript isoforms has yet to be established. In this study, we developed IsoRefiner, a novel method for identifying full-length transcript

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Abood, Abdullah, Larry L. Mesner, Erin D. Jeffery, et al. "Long read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors in disease." March 1, 2023. https://doi.org/10.5281/zenodo.7603851.

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A major fraction of loci identified by genome-wide association studies (GWASs) lead to alterations in alternative splicing, but interpretation of how such alterations impact proteins is hindered by the technical limitations of short-read RNA-seq, which cannot directly link splicing events to full-length transcript or protein isoforms. Long-read RNA-seq represents a powerful tool to define and quantify transcript isoforms, and, recently, infer protein isoform existence. Here we present a novel approach that integrates information from GWAS, splicing QTL (sQTL), and PacBio long-read RNA-seq in a

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Tang, Alison D., Colette Felton, Eva Hrabeta-Robinson, Roger Volden, Christopher Vollmers, and Angela N. Brooks. "Detecting haplotype-specific transcript variation in long reads with FLAIR2." Genome Biology 25, no. 1 (2024). http://dx.doi.org/10.1186/s13059-024-03301-y.

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Abstract Background RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme that mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung adenocarcinoma cells and associated with splicing regulation. Despite the functional importance of studying splicing and S

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Gao, Yuan, Feng Wang, Robert Wang, et al. "ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data." Science Advances 9, no. 3 (2023). http://dx.doi.org/10.1126/sciadv.abq5072.

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Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing platforms poses a major challenge. We present ESPRESSO, a computational tool for robust discovery and quantification of transcript isoforms from error-prone long reads. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoform

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Rebboah, Elisabeth, Fairlie Reese, Katherine Williams, et al. "Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq." Genome Biology 22, no. 1 (2021). http://dx.doi.org/10.1186/s13059-021-02505-w.

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AbstractThe rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation includ

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Pardo-Palacios, Francisco J., Dingjie Wang, Fairlie Reese, et al. "Systematic assessment of long-read RNA-seq methods for transcript identification and quantification." Nature Methods, June 7, 2024. http://dx.doi.org/10.1038/s41592-024-02298-3.

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AbstractThe Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more a

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Woolley, Cassandra R., Julia H. Chariker, Eric C. Rouchka, et al. "Reference long-read isoform-aware transcriptomes of 4 human peripheral blood lymphocyte subsets." G3 Genes|Genomes|Genetics, September 26, 2022. http://dx.doi.org/10.1093/g3journal/jkac253.

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Abstract Long-read sequencing technologies such as isoform sequencing can generate highly accurate sequences of full-length mRNA transcript isoforms. Such long-read transcriptomics may be especially useful in investigations of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes are readily available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified 4 lymphocyte populations (CD4+ T, CD8+ T, NK, and Pan B cells) fr

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Hamraoui, Ali, Laurent Jourdren, and Morgane Thomas-Chollier. "AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow." Bioinformatics, February 22, 2025. https://doi.org/10.1093/bioinformatics/btaf087.

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Abstract Motivation The combination of long-read sequencing technologies like Oxford Nanopore with single-cell RNA sequencing (scRNAseq) assays enables the detailed exploration of transcriptomic complexity, including isoform detection and quantification, by capturing full-length cDNAs. However, challenges remain, including the lack of advanced simulation tools that can effectively mimic the unique complexities of scRNAseq long-read datasets. Such tools are essential for the evaluation and optimization of isoform detection methods dedicated to single-cell long read studies. Results We developed

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Liu, Zhen, Chenchen Zhu, Lars M. Steinmetz, and Wu Wei. "Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data." Nucleic Acids Research, October 16, 2023. http://dx.doi.org/10.1093/nar/gkad810.

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Abstract Small exons are pervasive in transcriptomes across organisms, and their quantification in RNA isoforms is crucial for understanding gene functions. Although long-read RNA-seq based on Oxford Nanopore Technologies (ONT) offers the advantage of covering transcripts in full length, its lower base accuracy poses challenges for identifying individual exons, particularly microexons (≤ 30 nucleotides). Here, we systematically assess small exons quantification in synthetic and human ONT RNA-seq datasets. We demonstrate that reads containing small exons are often not properly aligned, affectin

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Kishi-Kaboshi, Mitsuko, Tsuyoshi Tanaka, Katsutomo Sasaki, Naonobu Noda, and Ryutaro Aida. "Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization." Scientific Reports 12, no. 1 (2022). http://dx.doi.org/10.1038/s41598-022-22589-z.

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AbstractChrysanthemum morifolium is one of the most popular ornamental plants globally. Owing to its large and complex genome (around 10 Gb, segmental hexaploid), it has been difficult to obtain comprehensive transcriptome, which will promote to perform new breeding technique, such as genome editing, in C. morifolium. In this study, we used single-molecule real-time (SMRT) sequencing and RNA-seq technologies, combined them with an error-correcting process, and obtained high-coverage ray-floret transcriptome. The SMRT-seq data increased the ratio of long mRNAs containing complete open-reading f

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Dong, Xueyi, Luyi Tian, Quentin Gouil, et al. "The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools." NAR Genomics and Bioinformatics 3, no. 2 (2021). http://dx.doi.org/10.1093/nargab/lqab028.

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Abstract Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such analysis can be challenging due to the high sequence error and small library sizes, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore RNA-seq datasets with the goal of obtaining gene- and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs (‘sequins’) as well as a mouse neural stem cell dataset from samples with a null m

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Mock, Andreas, Melissa Braun, Claudia Scholl, Stefan Fröhling, and Cihan Erkut. "Transcriptome profiling for precision cancer medicine using shallow nanopore cDNA sequencing." Scientific Reports 13, no. 1 (2023). http://dx.doi.org/10.1038/s41598-023-29550-8.

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AbstractTranscriptome profiling is a mainstay of translational cancer research and is increasingly finding its way into precision oncology. While bulk RNA sequencing (RNA-seq) is widely available, high investment costs and long data return time are limiting factors for clinical applications. We investigated a portable nanopore long-read sequencing device (MinION, Oxford Nanopore Technologies) for transcriptome profiling of tumors. In particular, we investigated the impact of lower coverage than that of larger sequencing devices by comparing shallow nanopore RNA-seq data with short-read RNA-seq

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