ArticleGenome biology2018
SQUID: transcriptomic structural variation detection from RNA-seq.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing.Nature communications · 2026Article
- Genetic landscape of pediatric acute myeloid leukemia in Taiwan.Scientific reports · 2026Article
- Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea.Frontiers in plant science · 2025Article
- The landscape of fusion transcripts in plants: a new insight into genome complexity.BMC plant biology · 2024Article
- Article
- Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia.Nature communications · 2024Article
- Article
- SFyNCS detects oncogenic fusions involving non-coding sequences in cancer.Nucleic acids research · 2023Article
- OnACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2023Article
- SFyNCS detects oncogenic fusions involving non-coding sequences in cancer.bioRxiv : the preprint server for biology · 2023Article
- A novel colony-stimulating factor 1 (CSF1) translocation involving human endogenous retroviral element in a tenosynovial giant cell tumor.Genes, chromosomes & cancer · 2023Article
- Longitudinal characterization of primary osteosarcoma and derived subcutaneous and orthotopic relapsed patient-derived xenograft models.Frontiers in oncology · 2023Article
- Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases.Genes · 2022Review
- Frequency and Genomic Aspects of Intrinsic Resistance to Vismodegib in Locally Advanced Basal Cell Carcinoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- A guide for the diagnosis of rare and undiagnosed disease: beyond the exome.Genome medicine · 2022Review
- RNA-seq Fusion Detection in Clinical Oncology.Advances in experimental medicine and biology · 2022Article
- MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data.Genome biology · 2021Article
- Identification and Characterization of Non-Coding RNAs in Thymoma.Medical science monitor : international medical journal of experimental and clinical research · 2021Article
- Full-Length Transcriptome Analysis ofFrontiers in cellular and infection microbiology · 2021Article
- The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome.EMBO molecular medicine · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Transcripts are frequently modified by structural variations, which lead to fused transcripts of either multiple genes, known as a fusion gene, or a gene and a previously non-transcribed sequence. Detecting these modifications, called transcriptomic structural variations (TSVs), especially in cancer tumor sequencing, is an important and challenging computational problem. We introduce SQUID, a novel algorithm to predict both fusion-gene and non-fusion-gene TSVs accurately from RNA-seq alignments. SQUID unifies both concordant and discordant read alignments into one model and doubles the precision on simulation data compared to other approaches. Using SQUID, we identify novel non-fusion-gene TSVs on TCGA samples.
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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.