Bioinformatics approaches to single-cell analysis in developmental biology

Considerations when quantitating protein abundance by immunoblot

(2015) Alicia A. McDonough et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Normalization and noise reduction for single cell RNA-seq experiments

(2015) Bo Ding et al.   BIOINFORMATICS

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu 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

The Technology and Biology of Single-Cell RNA Sequencing

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

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Modeling genome coverage in single-cell sequencing

(2014) Timothy Daley et al.   BIOINFORMATICS

Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data

(2014) Florian Buettner et al.   BIOINFORMATICS

Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development

(2014) Haifen Chen et al.   BIOINFORMATICS

MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data

(2014) Justin Feigelman et al.   BMC BIOINFORMATICS

Using single cell sequencing data to model the evolutionary history of a tumor

(2014) Kyung Kim et al.   BMC BIOINFORMATICS

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Single-cell analysis of the transcriptome and its application in the characterization of stem cells and early embryos

(2014) Na Liu et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Applications of imaging fluorescence correlation spectroscopy

(2014) Anand P Singh et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Single cell sequencing approaches for complex biological systems

(2014) Timour Baslan et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The workflow of single-cell expression profiling using quantitative real-time PCR

(2014) Anders Ståhlberg et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Bioinformatics approaches to single-blastomere transcriptomics

(2014) Leila Taher et al.   MOLECULAR HUMAN REPRODUCTION

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

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

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

(2014) Q. Deng et al.   SCIENCE

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Robust image registration of biological microscopic images

(2014) Ching-Wei Wang et al.   Scientific Reports

Current Challenges in the Bioinformatics of Single Cell Genomics

(2014) Luwen Ning et al.   Frontiers in Oncology

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

(2013) Shintaro Katayama et al.   BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Monitoring and quantifying dynamic physiological processes in live neurons using fluorescence recovery after photobleaching

(2013) Kevin Staras et al.   JOURNAL OF NEUROCHEMISTRY

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

(2013) Zhigang Xue et al.   NATURE

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

(2013) Jeff Gole et al.   NATURE BIOTECHNOLOGY

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

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

(2013) Philip Brennecke et al.   NATURE METHODS

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

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

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

(2013) Jong Kim et al.   GENOME BIOLOGY

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst

(2012) F. Buettner et al.   BIOINFORMATICS

Fast and robust optical flow for time-lapse microscopy using super-voxels

(2012) Fernando Amat et al.   BIOINFORMATICS

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

(2012) Andrew McDavid et al.   BIOINFORMATICS

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

Dissecting ensemble networks in ES cell populations reveals micro-heterogeneity underlying pluripotency

(2012) Jamie Trott et al.   Molecular BioSystems

Advanced Fluorescence Microscopy Techniques—FRAP, FLIP, FLAP, FRET and FLIM

(2012) Hellen C. Ishikawa-Ankerhold et al.   MOLECULES

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong 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

Gene expression heterogeneities in embryonic stem cell populations: origin and function

(2011) Alfonso Martinez Arias et al.   CURRENT OPINION IN CELL BIOLOGY

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

(2011) S. Islam et al.   GENOME RESEARCH

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells

(2011) Kazim H. Narsinh et al.   JOURNAL OF CLINICAL INVESTIGATION

Performance of optical flow techniques for motion analysis of fluorescent point signals in confocal microscopy

(2011) José Delpiano et al.   MACHINE VISION AND APPLICATIONS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Single-cell genomics

(2011) Tomer Kalisky et al.   NATURE METHODS

What's New Is Old: Resolving the Identity of Leptothrix ochracea Using Single Cell Genomics, Pyrosequencing and FISH

(2011) Emily J. Fleming et al.   PLoS One

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

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

Single Virus Genomics: A New Tool for Virus Discovery

(2011) Lisa Zeigler Allen 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

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

(2011) A. D. Tadmor et al.   SCIENCE

SmashCell: a software framework for the analysis of single-cell amplified genome sequences: Fig. 1.

(2010) Eoghan D. Harrington et al.   BIOINFORMATICS

ExprEssence - Revealing the essence of differential experimental data in the context of an interaction/regulation net-work

(2010) Gregor Warsow et al.   BMC Systems Biology

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

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Capturing diversity of marine heterotrophic protists: one cell at a time

(2010) Jane L Heywood et al.   ISME Journal

Whole-genome molecular haplotyping of single cells

(2010) H Christina Fan et al.   NATURE BIOTECHNOLOGY

The PluriNetWork: An Electronic Representation of the Network Underlying Pluripotency in Mouse, and Its Applications

(2010) Anup Som et al.   PLoS One

High throughput single cell bioinformatics

(2009) Kenneth L. Roach et al.   BIOTECHNOLOGY PROGRESS

Evaluation of genome coverage and fidelity of multiple displacement amplification from single cells by SNP array

(2009) J. Ling et al.   MOLECULAR HUMAN REPRODUCTION

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes

(2009) Shaoqiang Zhang et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One

Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States

(2008) Katsuhiko Hayashi et al.   Cell Stem Cell

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

(2008) Erik K Binga et al.   ISME Journal

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS