miRSCAPE - inferring miRNA expression from scRNA-seq data

Olgun, Gulden; Gopalan, Vishaka; Hannenhalli, Sridhar

doi:10.1016/j.isci.2022.104962

Cited by 3 publications

(1 citation statement)

References 80 publications

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“…After having demonstrated the capabilities of SingmiR with previously published datasets ( 18 ), the here presented web server is well positioned to serve as a useful tool for upcoming and larger single-cell miRNA-seq studies. Additionally, the development of techniques that aim to predict miRNA activity based on single-cell mRNA data ( 43 ) indicates interest in this field. Recent advancements in sequencing technology ( 44 ) and the need to study miRNA activity in complex tissues contribute to the increasing emergence of single-cell studies ( 45 ).…”

Section: Discussionmentioning

confidence: 99%

SingmiR: a single-cell miRNA alignment and analysis tool

Engel,

Rishik,

Hirsch

et al. 2024

Nucleic Acids Research

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Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic and therapeutic approaches. However, most of the gene regulatory processes on the single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like the established single-cell gene expression analysis, advanced computational expertise is required to comprehensively process newly emerging single-cell miRNA-seq datasets. A web server providing a workflow tailored for single-cell miRNA-seq data with a self-explanatory interface is currently not available. Here, we present SingmiR, enabling the rapid (pre-)processing and quantification of human miRNAs from noncoding single-cell samples. It performs read trimming for different library preparation protocols, generates automated quality control reports and provides feature-normalized count files. Numerous standard and advanced analyses such as dimension reduction, clustered feature heatmaps, sample correlation heatmaps and differential expression statistics are implemented. We aim to speed up the prototyping pipeline for biologists developing single-cell miRNA-seq protocols on small to medium-sized datasets. SingmiR is freely available to all users without the need for a login at https://www.ccb.uni-saarland.de/singmir.

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Section: Discussionmentioning

confidence: 99%

SingmiR: a single-cell miRNA alignment and analysis tool

Engel,

Rishik,

Hirsch

et al. 2024

Nucleic Acids Research

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Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response

Grafanaki

Grammatikakis

Ghosh

et al. 2023

Pharmacology & Therapeutics

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Epigenetic Biomarkers in Thrombophilia-Related Pregnancy Complications: Mechanisms, Diagnostic Potential, and Therapeutic Implications: A Narrative Review

Bardan,

Ioniță,

Iordache

et al. 2024

IJMS

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Pregnancy complications associated with thrombophilia represent significant risks for maternal and fetal health, leading to adverse outcomes such as pre-eclampsia, recurrent pregnancy loss, and intra-uterine growth restriction (IUGR). They are caused by disruptions in key physiological processes, including the coagulation cascade, trophoblast invasion, angiogenesis, and immune control. Recent advancements in epigenetics have revealed that non-coding RNAs, especially microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and extracellular vesicles (EVs) carrying these RNAs, play crucial roles in the regulation of these biological processes. This review aims to identify the epigenetic biomarkers that are the best candidates for evaluating thrombophilia-related pregnancy complications and for assessing the efficacy of anticoagulant and antiaggregant therapies. We emphasize their potential integration into personalized treatment plans, aiming to improve the risk assessment and therapy strategies for thrombophilic pregnancies. Future research should focus on validating these epigenetic biomarkers and establishing standardized protocols to enable their integration into clinical practice, paving the way for a precision medicine approach in obstetric care.

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miRSCAPE - inferring miRNA expression from scRNA-seq data

Cited by 3 publications

References 80 publications

SingmiR: a single-cell miRNA alignment and analysis tool

SingmiR: a single-cell miRNA alignment and analysis tool

Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response

Epigenetic Biomarkers in Thrombophilia-Related Pregnancy Complications: Mechanisms, Diagnostic Potential, and Therapeutic Implications: A Narrative Review

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