Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis

SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes

(2021) Marc Elosua-Bayes et al.   NUCLEIC ACIDS RESEARCH

SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation

(2020) Joseph Bergenstråhle et al.   BMC BIOINFORMATICS

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

High throughput error corrected Nanopore single cell transcriptome sequencing

(2020) Kevin Lebrigand et al.   Nature Communications

Single-cell multiomics: technologies and data analysis methods

(2020) Jeongwoo Lee et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

DIABLO: an integrative approach for identifying key molecular drivers from multi-omic assays

(2019) Amrit Singh et al.   BIOINFORMATICS

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Spatial transcriptomics coming of age

(2019) Darren J. Burgess   NATURE REVIEWS GENETICS

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

(2019) Geng Chen et al.   Frontiers in Genetics

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Beyond bulk: a review of single cell transcriptomics methodologies and applications

(2019) Ashwinikumar Kulkarni et al.   CURRENT OPINION IN BIOTECHNOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data

(2019) Changde Cheng et al.   NUCLEIC ACIDS RESEARCH

The art of using t-SNE for single-cell transcriptomics

(2019) Dmitry Kobak et al.   Nature Communications

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

(2018) Zhun Miao et al.   BIOINFORMATICS

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets

(2018) Kim Wong et al.   BIOINFORMATICS

Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data

(2018) Vilas Menon   Briefings in Functional Genomics

SigEMD: A powerful method for differential gene expression analysis in single-cell RNA sequencing data

(2018) Tianyu Wang et al.   METHODS

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Identification of spatial expression trends in single-cell gene expression data

(2018) Daniel Edsgärd et al.   NATURE METHODS

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

dropClust: efficient clustering of ultra-large scRNA-seq data

(2018) Debajyoti Sinha et al.   NUCLEIC ACIDS RESEARCH

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis

(2018) Johnny A. Sena et al.   Scientific Reports

Bioinformatics applications on Apache Spark

(2018) Runxin Guo et al.   GigaScience

An Introduction to the Analysis of Single-Cell RNA-Sequencing Data

(2018) Aisha A. AlJanahi et al.   Molecular Therapy-Methods & Clinical Development

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

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

(2017) Tom Smith et al.   GENOME RESEARCH

Approximated and User Steerable tSNE for Progressive Visual Analytics

(2017) Nicola Pezzotti et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Big Data Analytics for Genomic Medicine

(2017) Karen He et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

SCnorm: robust normalization of single-cell RNA-seq data

(2017) Rhonda Bacher et al.   NATURE METHODS

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Linnorm: improved statistical analysis for single cell RNA-seq expression data

(2017) Shun H. Yip et al.   NUCLEIC ACIDS RESEARCH

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

(2017) Chiara Medaglia et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Changes to antiretroviral drug regimens during integrated TB–HIV treatment: results of the SAPiT trial

(2017) Anushka Naidoo et al.   ANTIVIRAL THERAPY

Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

(2016) Mihails Delmans et al.   BMC BIOINFORMATICS

Apache Spark

(2016) Matei Zaharia et al.   COMMUNICATIONS OF THE ACM

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells

(2016) Yurong Xin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell Transcriptome Study as Big Data

(2016) Pingjian Yu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Normalization and noise reduction for single cell RNA-seq experiments

(2015) Bo Ding et al.   BIOINFORMATICS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Technologies for Single-Cell Isolation

(2015) Andre Gross et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Microfluidic cell sorting: a review of the advances in the separation of cells from debulking to rare cell isolation

(2015) C. Wyatt Shields IV et al.   LAB ON A CHIP

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex

(2015) Matthew B Johnson et al.   NATURE NEUROSCIENCE

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

Magnetic-activated cell sorting (MACS) can be used as a large-scale method for establishing zebrafish neuronal cell cultures

(2015) Georg Welzel et al.   Scientific Reports

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

(2015) Catalina A. Vallejos et al.   PLoS Computational Biology

Single cell sequencing: technique, application, and future development

(2015) Ruidong Xue et al.   Science Bulletin

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

(2014) Zhaojun Zhang et al.   BIOINFORMATICS

Indexing Graphs for Path Queries with Applications in Genome Research

(2014) Jouni Siren et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

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

(2014) D. A. Jaitin et al.   SCIENCE

Single cell transcriptional analysis reveals novel innate immune cell types

(2014) Linda E. Kippner et al.   PeerJ

‘Big data’, Hadoop and cloud computing in genomics

(2013) Aisling O’Driscoll et al.   JOURNAL OF BIOMEDICAL INFORMATICS

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

(2013) Quin F Wills et al.   NATURE BIOTECHNOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Detection of histone modifications at specific gene loci in single cells in histological sections

(2013) Delphine Gomez et al.   NATURE METHODS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Overview of available methods for diverse RNA-Seq data analyses

(2012) Geng Chen et al.   Science China-Life Sciences

Cell separation: Terminology and practical considerations

(2012) Matthew J Tomlinson et al.   Journal of Tissue Engineering

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

(2011) Ronald C Taylor   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Comprehensive qPCR profiling of gene expression in single neuronal cells

(2011) Ami Citri et al.   Nature Protocols

The Fourth Paradigm: Data-Intensive Scientific Discovery [Point of View]

(2011) Kristin M. Tolle et al.   PROCEEDINGS OF THE IEEE

Microfluidic Platforms for Single-Cell Analysis

(2010) Richard N. Zare et al.   Annual Review of Biomedical Engineering

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Magnetic activated cell sorting (MACS) - a new immunomagnetic method for megakaryocytic cell isolation: Comparison of different separation techniques

(2010) B. Schmitz et al.   EUROPEAN JOURNAL OF HAEMATOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Single cell analysis: the new frontier in ‘omics’

(2010) Daojing Wang et al.   TRENDS IN BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS