Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells

Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer

(2020) Matthew G. Costales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems

(2020) Fabian Kern et al.   NUCLEIC ACIDS RESEARCH

Quo vadis microRNAs?

(2020) Bastian Fromm et al.   TRENDS IN GENETICS

A low-bias and sensitive small RNA library preparation method using randomized splint ligation

(2020) Sean Maguire et al.   NUCLEIC ACIDS RESEARCH

Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation

(2019) Nayi Wang et al.   Nature Communications

High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing

(2019) Cassandra D. Belair et al.   Scientific Reports

An estimate of the total number of true human miRNAs

(2019) Julia Alles et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries

(2019) Andrew A Hardigan et al.   NUCLEIC ACIDS RESEARCH

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

(2019) Carrie Wright et al.   BMC GENOMICS

Systematic assessment of commercially available low-input miRNA library preparation kits

(2019) Fatima Heinicke et al.   RNA Biology

Liquid Biopsy in Non-Small Cell Lung Cancer: Highlights and Challenges

(2019) Erika Rijavec et al.   Cancers

Systematic comparison of small RNA library preparation protocols for next-generation sequencing

(2018) Cloelia Dard-Dascot et al.   BMC GENOMICS

Role of miRNAs in lung cancer

(2018) Arif Uddin et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling

(2018) Maria D Giraldez et al.   NATURE BIOTECHNOLOGY

Small-seq for single-cell small-RNA sequencing

(2018) Michael Hagemann-Jensen et al.   Nature Protocols

miRWalk: An online resource for prediction of microRNA binding sites

(2018) Carsten Sticht et al.   PLoS One

piRBase: a comprehensive database of piRNA sequences

(2018) Jiajia Wang et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

An integrated expression atlas of miRNAs and their promoters in human and mouse

(2017) Derek de Rie et al.   NATURE BIOTECHNOLOGY

Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs

(2017) Tobias Fehlmann et al.   NUCLEIC ACIDS RESEARCH

miRCarta: a central repository for collecting miRNA candidates

(2017) Christina Backes et al.   NUCLEIC ACIDS RESEARCH

Single-cell sequencing of the small-RNA transcriptome

(2016) Omid R Faridani et al.   NATURE BIOTECHNOLOGY

Distribution of miRNA expression across human tissues

(2016) Nicole Ludwig et al.   NUCLEIC ACIDS RESEARCH

Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation

(2016) Sabrina Shore et al.   PLoS One

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods

(2015) Jeanette Baran-Gale et al.   Frontiers in Genetics

Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure

(2015) Ryan T. Fuchs et al.   PLoS One

Capture and Amplification by Tailing and Switching (CATS)

(2014) Andrey Turchinovich et al.   RNA Biology

MicroRNAs in Cancer

(2013) Gianpiero Di Leva et al.   Annual Review of Pathology-Mechanisms of Disease

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

RazerS 3: Faster, fully sensitive read mapping

(2012) David Weese et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Unfolding communities in large complex networks: Combining defensive and offensive label propagation for core extraction

(2011) Lovro Šubelj et al.   PHYSICAL REVIEW E

Cell Surface Tetraspanin CD9 Mediates Chemoresistance in Small Cell Lung Cancer

(2010) S. Kohmo et al.   CANCER RESEARCH

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL