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Fusion detection and quantification by pseudoalignment

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The Hallmarks of Cancer

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The cancer genome

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Implications of chimaeric non-co-linear transcripts

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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

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Near-optimal probabilistic RNA-seq quantification

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Erratum: Near-optimal probabilistic RNA-seq quantification

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The Cancer Genome Atlas Pan-Cancer analysis project

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Cancer genomics: from discovery science to personalized medicine

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The emerging complexity of gene fusions in cancer

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RNA sequencing: advances, challenges and opportunities

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Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data

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Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

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FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

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ENCODE whole-genome data in the UCSC genome browser (2011 update)

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Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data

inferredcites →https://doi.org/10.1109/dexa.2015.25openalex-snapshot

The Role of Machine Learning in Finding Chimeric RNAs

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Constitutive Fragile Sites and Cancer

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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Open-access synthetic spike-in mRNA-seq data for cancer gene fusions

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Gene fusions and RNA trans-splicing in normal and neoplastic human cells

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Calculating Relative Chimeric RNA Expression with FusionBlaster

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Overview of Fusion Detection Strategies Using Next-Generation Sequencing

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Computational Tools and Databases for Fusion Transcripts: Therapeutic Targets in Cancer

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Establishment of experimental salivary gland cancer models using organoid culture and patient-derived xenografting

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Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy

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Challenges in neoantigen-directed therapeutics

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Whole transcriptome analysis identifies ALB-EEF1A1 fusion as a novel biomarker in metastatic colorectal cancer

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Molecular Profiling Reveals Novel Gene Fusions and Genetic Markers for Refined Patient Stratification in Pediatric Acute Lymphoblastic Leukemia

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A NUT carcinoma lacking squamous differentiation and expressing TTF1

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The implementation of an RNA-based gene fusion assay into a diagnostic oncology department: an Australian perspective

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Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia

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Functional chimeric mRNAs encode proteins in mammalian immunity

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Genetic landscape of pediatric acute myeloid leukemia in Taiwan

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Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies

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Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing

inferred← citeshttps://doi.org/10.1093/bib/bbae251openalex-snapshot

RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz346openalex-snapshot

Alignment-free filtering for cfNA fusion fragments

inferred← citeshttps://doi.org/10.1093/gigascience/giy079openalex-snapshot

Clinker: visualizing fusion genes detected in RNA-seq data

inferred← citeshttps://doi.org/10.1101/2020.06.02.122150openalex-snapshot

Optimizing nucleic acid extraction and transcriptome evaluation from low-input, fixed clinical samples

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CAR T cell therapy drives endogenous locoregional T cell dynamics in a responding patient with glioblastoma

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FDJD: RNA-Seq Based Fusion Transcript Detection Using Jaccard Distance

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Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis

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Bioinformatic Approaches for the Detection of Fusion Genes and trans-Splicing Products (A Review)

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Spatial profiling reveals association between WNT pathway activation and T-cell exclusion in acquired resistance of synovial sarcoma to NY-ESO-1 transgenic T-cell therapy

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Supplementary Figure from Frequency and Genomic Aspects of Intrinsic Resistance to Vismodegib in Locally Advanced Basal Cell Carcinoma

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Data from Frequency and Genomic Aspects of Intrinsic Resistance to Vismodegib in Locally Advanced Basal Cell Carcinoma

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Frequency and Genomic Aspects of Intrinsic Resistance to Vismodegib in Locally Advanced Basal Cell Carcinoma

inferred← citeshttps://doi.org/10.1186/s12864-020-07207-4openalex-snapshot

LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing

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Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

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MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

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JAFFAL: detecting fusion genes with long-read transcriptome sequencing

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Best practices for bioinformatic characterization of neoantigens for clinical utility

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Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches

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Experimental models of salivary gland cancer established using organoid culture and patient-derived xenografting

inferred← citeshttps://doi.org/10.21203/rs.3.rs-779030/v1openalex-snapshot

Novel Preclinical Human Salivary Gland Cancer Models Established Using Organoid Culture And Patient-Derived Xenografting

inferred← citeshttps://doi.org/10.26508/lsa.202302481openalex-snapshot

A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

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Bioinformatic approaches for detection of fusion genes and trans-splicing products

inferred← citeshttps://doi.org/10.3389/fgene.2023.997383openalex-snapshot

RNA-seq data science: From raw data to effective interpretation

inferred← citeshttps://doi.org/10.3389/fonc.2020.00489openalex-snapshot

Next-Generation Sequencing Approaches for the Identification of Pathognomonic Fusion Transcripts in Sarcomas: The Experience of the Italian ACC Sarcoma Working Group

inferred← citeshttps://doi.org/10.3389/fonc.2023.1166063openalex-snapshot

Longitudinal characterization of primary osteosarcoma and derived subcutaneous and orthotopic relapsed patient-derived xenograft models

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PAX5 Alterations in a Consecutive Childhood B-Cell Acute Lymphoblastic Leukemia Cohort Treated Using the ALL IC-BFM 2009 Protocol

inferred← citeshttps://doi.org/10.5753/bsb.2024.245179openalex-snapshot

Comparison of computational fusion detection methods for short-read RNA-seq data

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Relative Index of Chimeric Expression (RICE) Analysis: A Quantitative Approach for Chimeric RNAs Using FusionBlaster

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