Single-cell RNA-seq: advances and future challenges

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

The present and future role of microfluidics in biomedical research

(2014) Eric K. Sackmann et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Transcriptional profiling of cells sorted by RNA abundance

(2014) Sandy Klemm et al.   NATURE METHODS

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

(2014) Ditte Lovatt et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Microfluidic, marker-free isolation of circulating tumor cells from blood samples

(2014) Nezihi Murat Karabacak et al.   Nature Protocols

Microfluidic single-cell whole-transcriptome sequencing

(2014) A. M. Streets et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Internalization of Salmonella by Macrophages Induces Formation of Nonreplicating Persisters

(2014) S. Helaine et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

High-Throughput Microfluidic Single-Cell Digital Polymerase Chain Reaction

(2013) A. K. White et al.   ANALYTICAL CHEMISTRY

Homopolymer tail-mediated ligation PCR: a streamlined and highly efficient method for DNA cloning and library construction

(2013) David W. Lazinski et al.   BIOTECHNIQUES

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

(2013) Schraga Schwartz et al.   CELL

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

(2013) Jean-Michel Fustin et al.   CELL

Microfluidic genome-wide profiling of intrinsic electrical properties in Saccharomyces cerevisiae

(2013) Michael D. Vahey et al.   LAB ON A CHIP

Translocating Kilobase RNA through the Staphylococcal α-Hemolysin Nanopore

(2013) James A. Cracknell et al.   NANO LETTERS

Nanopore-Based Identification of Individual Nucleotides for Direct RNA Sequencing

(2013) Mariam Ayub et al.   NANO LETTERS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments

(2013) Quin F Wills et al.   NATURE BIOTECHNOLOGY

Unfoldase-mediated protein translocation through an α-hemolysin nanopore

(2013) Jeff Nivala et al.   NATURE BIOTECHNOLOGY

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Identification of a population of blood circulating tumor cells from breast cancer patients that initiates metastasis in a xenograft assay

(2013) Irène Baccelli et al.   NATURE BIOTECHNOLOGY

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

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

(2013) Simone Picelli et al.   NATURE METHODS

Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells

(2013) Lixin Wang et al.   Nature Protocols

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-Sequence Retaining Transcripts in Mouse and Rat Neurons

(2013) Mugdha Khaladkar et al.   PLoS One

RNA-sequencing from single nuclei

(2013) R. V. Grindberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Determinants and Cellular Constraints in Noisy Gene Expression

(2013) A. Sanchez et al.   SCIENCE

Functional Roles of Pulsing in Genetic Circuits

(2013) J. H. Levine et al.   SCIENCE

Circulating Breast Tumor Cells Exhibit Dynamic Changes in Epithelial and Mesenchymal Composition

(2013) M. Yu et al.   SCIENCE

Going with the Flow: From Circulating Tumor Cells to DNA

(2013) F.-C. Bidard et al.   Science Translational Medicine

Inertial Focusing for Tumor Antigen-Dependent and -Independent Sorting of Rare Circulating Tumor Cells

(2013) E. Ozkumur et al.   Science Translational Medicine

Quantitative Diagnosis of Malignant Pleural Effusions by Single-Cell Mechanophenotyping

(2013) H. T. K. Tse et al.   Science Translational Medicine

An automated system for high-throughput single cell-based breeding

(2013) Nobuo Yoshimoto et al.   Scientific Reports

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing

(2013) Hagen Tilgner et al.   G3-Genes Genomes Genetics

Single cell expression quantitative trait loci and complex traits

(2013) Enrico Petretto   Genome Medicine

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

(2013) Gaurav Dugar et al.   PLoS Genetics

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

CD147-Dependent Heterogeneity in Malignant and Chemoresistant Properties of Cancer Cells

(2012) Lu Dai et al.   AMERICAN JOURNAL OF PATHOLOGY

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

RNA editing in the human ENCODE RNA-seq data

(2012) E. Park et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Mechanosensitive mechanisms in transcriptional regulation

(2012) Akiko Mammoto et al.   JOURNAL OF CELL SCIENCE

Quantitative biology of single neurons

(2012) J. Eberwine et al.   Journal of the Royal Society Interface

Cytometry: Today’s technology and tomorrow’s horizons

(2012) Pratip K. Chattopadhyay et al.   METHODS

Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells

(2012) Kenneth J. Livak et al.   METHODS

Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

(2012) Omri Wurtzel et al.   Molecular Systems Biology

Individual RNA Base Recognition in Immobilized Oligonucleotides Using a Protein Nanopore

(2012) Mariam Ayub et al.   NANO LETTERS

RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis

(2012) Min Yu et al.   NATURE

Clonally dominant cardiomyocytes direct heart morphogenesis

(2012) Vikas Gupta et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

From single cells to deep phenotypes in cancer

(2012) Sean C Bendall et al.   NATURE BIOTECHNOLOGY

Oxford Nanopore announcement sets sequencing sector abuzz

(2012) Michael Eisenstein   NATURE BIOTECHNOLOGY

DNA sequencing with nanopores

(2012) Grégory F Schneider et al.   NATURE BIOTECHNOLOGY

Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

(2012) Saiful Islam et al.   Nature Protocols

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Microfluidics separation reveals the stem-cell-like deformability of tumor-initiating cells

(2012) W. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two methods for full-length RNA sequencing for low quantities of cells and single cells

(2012) X. Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrodynamic stretching of single cells for large population mechanical phenotyping

(2012) D. R. Gossett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput single-microparticle imaging flow analyzer

(2012) K. Goda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

(2012) C. Kroger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Genomic Analysis at the Single-Cell Level

(2011) Tomer Kalisky et al.   Annual Review of Genetics

An imaging flow cytometric method for measuring cell division history and molecular symmetry during mitosis

(2011) Andrew Filby et al.   CYTOMETRY PART A

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Transcript amplification from single bacterium for transcriptome analysis

(2011) Y. Kang et al.   GENOME RESEARCH

cis-Antisense RNA, Another Level of Gene Regulation in Bacteria

(2011) J. Georg et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

A human memory T cell subset with stem cell–like properties

(2011) Luca Gattinoni et al.   NATURE MEDICINE

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Comprehensive qPCR profiling of gene expression in single neuronal cells

(2011) Ami Citri et al.   Nature Protocols

Bacterial transcriptomics: what is beyond the RNA horiz-ome?

(2011) Marc Güell et al.   NATURE REVIEWS MICROBIOLOGY

The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages

(2011) Mobarak A. Mraheil et al.   NUCLEIC ACIDS RESEARCH

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres

(2011) Fuchou Tang et al.   PLoS One

High-throughput microfluidic single-cell RT-qPCR

(2011) A. K. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

The transcriptional landscape of Chlamydia pneumoniae

(2011) Marco Albrecht et al.   GENOME BIOLOGY

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Identifying single-cell molecular programs by stochastic profiling

(2010) Kevin A Janes et al.   NATURE METHODS

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Digital MDA for enumeration of total nucleic acid contamination

(2010) P. C. Blainey et al.   NUCLEIC ACIDS RESEARCH

An RNA degradosome assembly in Caulobacter crescentus

(2010) S. W. Hardwick et al.   NUCLEIC ACIDS RESEARCH

Identification of regulatory RNAs in Bacillus subtilis

(2010) Irnov Irnov et al.   NUCLEIC ACIDS RESEARCH

Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays

(2010) A.-E. Saliba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

mRNA Localization: Gene Expression in the Spatial Dimension

(2009) Kelsey C. Martin et al.   CELL

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

A global view of protein expression in human cells, tissues, and organs

(2009) Fredrik Pontén et al.   Molecular Systems Biology

Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

(2009) Yanmei Shi et al.   NATURE

Population context determines cell-to-cell variability in endocytosis and virus infection

(2009) Berend Snijder et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Novel mutations in Moloney Murine Leukemia Virus reverse transcriptase increase thermostability through tighter binding to template-primer

(2008) Bahram Arezi et al.   NUCLEIC ACIDS RESEARCH

A microfluidics approach for the isolation of nucleated red blood cells (NRBCs) from the peripheral blood of pregnant women

(2008) R. Huang et al.   PRENATAL DIAGNOSIS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE