Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states

Small RNAs are modified with N-glycans and displayed on the surface of living cells

(2021) Ryan A. Flynn et al.   CELL

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

(2020) Susanne C. van den Brink et al.   NATURE

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

(2020) Elisabetta Mereu et al.   NATURE BIOTECHNOLOGY

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

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

(2019) Nayi Wang et al.   Nature Communications

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Oncogenic Biogenesis of pri-miR-17∼92 Reveals Hierarchy and Competition among Polycistronic MicroRNAs

(2019) Ariel O. Donayo et al.   MOLECULAR CELL

SMARTer single cell total RNA sequencing

(2019) Karen Verboom et al.   NUCLEIC ACIDS RESEARCH

Regulation of gene expression by cis-acting long non-coding RNAs

(2019) Noa Gil et al.   NATURE REVIEWS GENETICS

Total RNA extraction from tissues for microRNA and target gene expression analysis: not all kits are created equal

(2018) Rikki A. M. Brown et al.   BMC BIOTECHNOLOGY

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

(2018) Johannes W. Bagnoli et al.   Nature Communications

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

scaRNAs and snoRNAs: Are they limited to specific classes of substrate RNAs?

(2018) Svetlana Deryusheva et al.   RNA

Effective detection of variation in single-cell transcriptomes using MATQ-seq

(2017) Kuanwei Sheng et al.   NATURE METHODS

Cell cycle-targeting microRNAs promote differentiation by enforcing cell-cycle exit

(2017) Tobias Otto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Human Long Noncoding RNA Regulation of Stem Cell Potency and Differentiation

(2017) Seahyoung Lee et al.   Stem Cells International

Single-cell sequencing of the small-RNA transcriptome

(2016) Omid R Faridani et al.   NATURE BIOTECHNOLOGY

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

The miR-17 ∼ 92 microRNA Cluster Is a Global Regulator of Tumor Metabolism

(2016) Said Izreig et al.   Cell Reports

A Biogenesis Step Upstream of Microprocessor Controls miR-17∼92 Expression

(2015) Peng Du et al.   CELL

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

Long Noncoding RNAs in Cell-Fate Programming and Reprogramming

(2014) Ryan A. Flynn et al.   Cell Stem Cell

The multiMiR R package and database: integration of microRNA–target interactions along with their disease and drug associations

(2014) Yuanbin Ru et al.   NUCLEIC ACIDS RESEARCH

Capture and Amplification by Tailing and Switching (CATS)

(2014) Andrey Turchinovich et al.   RNA Biology

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

(2013) Y. Liao et al.   BIOINFORMATICS

The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease

(2013) E Mogilyansky et al.   CELL DEATH AND DIFFERENTIATION

Endogenous miRNA Sponge lincRNA-RoR Regulates Oct4, Nanog, and Sox2 in Human Embryonic Stem Cell Self-Renewal

(2013) Yue Wang et al.   DEVELOPMENTAL CELL

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

ENCODE Project Writes Eulogy for Junk DNA

(2012) E. Pennisi   SCIENCE

MicroRNAs and the cell cycle

(2011) María José Bueno et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Spatial and temporal expression pattern of germ layer markers during human embryonic stem cell differentiation in embryoid bodies

(2010) Mari Pekkanen-Mattila et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Opposing microRNA families regulate self-renewal in mouse embryonic stem cells

(2010) Collin Melton et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

(2008) William F. Marzluff et al.   NATURE REVIEWS GENETICS