ReviewComputational and structural biotechnology journal2019
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts.
Review in Computational and structural biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages.Nature communications · 2025Article
- Transcriptome sequencing reveals the evolutionary histories and gene expression evolution in two related Pagurus species.PloS one · 2025Article
- Splicing inhibition mediated by reduced splicing factors and helicases is associated with the cellular response of lung cancer cells to cisplatin.Computational and structural biotechnology journal · 2024Article
- Bioinformatics for Prohormone and Neuropeptide Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Cell-cell contact-driven EphB1 cis- and trans- signalings regulate cancer stem cells enrichment after chemotherapy.Cell death & disease · 2022Article
- Article
- The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome.BMC genomics · 2022Article
- Noncoding RNAs in apoptosis: identification and function.Turkish journal of biology = Turk biyoloji dergisi · 2022Review
- Exosomes from cisplatin-induced dormant cancer cells facilitate the formation of premetastatic niche in bone marrow through activating glycolysis of BMSCs.Frontiers in oncology · 2022Article
- Celastrol inhibits the proliferation and migration of MCF-7 cells through the leptin-triggered PI3K/AKT pathway.Computational and structural biotechnology journal · 2022Article
- Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells.Nucleic acids research · 2021Article
- SAUTE: sequence assembly using target enrichment.BMC bioinformatics · 2021Article
- Review
- Single cells and transposable element heterogeneity in stem cells and development.Cell regeneration (London, England) · 2021Article
- Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions.Frontiers in cell and developmental biology · 2021Review
- Twelve quick steps for genome assembly and annotation in the classroom.PLoS computational biology · 2020Article
- Transcriptome visualization and data availability at the Saccharomyces Genome Database.Nucleic acids research · 2020Article
- Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation.Computational and structural biotechnology journal · 2020Review
- Computational Oncology in the Multi-Omics Era: State of the Art.Frontiers in oncology · 2020Review
- Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis inComputational and structural biotechnology journal · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The measurement of gene expression has long provided significant insight into biological functions. The development of high-throughput short-read sequencing technology has revealed transcriptional complexity at an unprecedented scale, and informed almost all areas of biology. However, as researchers have sought to gather more insights from the data, these new technologies have also increased the computational analysis burden. In this review, we describe typical computational pipelines for RNA-Seq analysis and discuss their strengths and weaknesses for the assembly, quantification and analysis of coding and non-coding RNAs. We also discuss the assembly of transposable elements into transcripts, and the difficulty these repetitive elements pose. In summary, RNA-Seq is a powerful technology that is likely to remain a key asset in the biologist's toolkit.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.