ArticleBMC genomics2018
A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- PARiS: Probabilistic Assignment and Repartitioning of isomiR Sequences: A data-driven method for denoising isomiR read count data.bioRxiv : the preprint server for biology · 2026Article
- New characteristics of MiRNA and IsomiR interactions with mRNA.Scientific reports · 2025Article
- Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome.Nucleic acids research · 2025Article
- Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression.PLoS genetics · 2025Article
- Protein Functional Effector (pfe) Noncoding RNAS Are Identical to Fragments from Various Noncoding RNAs.International journal of molecular sciences · 2025Article
- Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer.Non-coding RNA · 2025Article
- 5'-Isoforms of miR-1246 Have Distinct Targets and Stronger Functional Impact Compared with Canonical miR-1246 in Colorectal Cancer Cells In Vitro.International journal of molecular sciences · 2024Article
- Interrogating the Role of miR-125b and Its 3'isomiRs in Protection against Hypoxia.International journal of molecular sciences · 2023Article
- 3'IsomiR Species Composition Affects Reliable Quantification of miRNA/isomiR Variants by Poly(A) RT-qPCR: Impact on Small RNA-Seq Profiling Validation.International journal of molecular sciences · 2023Article
- A Review of IsomiRs in Colorectal Cancer.Non-coding RNA · 2023Review
- Obtaining Reliable RT-qPCR Results in Molecular Diagnostics-MIQE Goals and Pitfalls for Transcriptional Biomarker Discovery.Life (Basel, Switzerland) · 2022Review
- miRNome Profiling and Functional Analysis Reveal Involvement of hsa-miR-1246 in Colon Adenoma-Carcinoma Transition by TargetingInternational journal of molecular sciences · 2022Article
- A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids.Frontiers in cell and developmental biology · 2022Article
- Global profiling and annotation of templated isomiRs dynamics acrossRNA biology · 2022Article
- Systems analysis of miRNA biomarkers to inform drug safety.Archives of toxicology · 2021Review
- MicroRNA Isoforms Contribution to Melanoma Pathogenesis.Non-coding RNA · 2021Article
- Review
- Review
- Commercially Available Blocking Oligonucleotides Effectively Suppress Unwanted Hemolysis-Related miRNAs in a Large Whole-Blood RNA Cohort.The Journal of molecular diagnostics : JMD · 2021Article
- Methodological considerations for measuring biofluid-based microRNA biomarkers.Critical reviews in toxicology · 2021Article
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Authors and funding
11 authors.
Funding
Abstract
backgroundMicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation.
resultsWe introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms.
conclusionsStudying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis.
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