Single-cell genome sequencing: current state of the science

Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications

(2015) Lei Huang et al.   Annual Review of Genomics and Human Genetics

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

(2015) Evan Z. Macosko et al.   CELL

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

ProDeGe: a computational protocol for fully automated decontamination of genomes

(2015) Kristin Tennessen et al.   ISME Journal

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

Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification

(2015) Yohei Nishikawa et al.   PLoS One

Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification

(2015) Yusi Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Calibrating genomic and allelic coverage bias in single-cell sequencing

(2015) Cheng-Zhong Zhang et al.   Nature Communications

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

SNES: single nucleus exome sequencing

(2015) Marco L Leung et al.   GENOME BIOLOGY

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

(2015) Yong Hou et al.   GigaScience

Microfluidic Whole Genome Amplification Device for Single Cell Sequencing

(2014) Zhilong Yu et al.   ANALYTICAL CHEMISTRY

On-Chip Separation and Analysis of RNA and DNA from Single Cells

(2014) Hirofumi Shintaku et al.   ANALYTICAL CHEMISTRY

Modeling genome coverage in single-cell sequencing

(2014) Timothy Daley et al.   BIOINFORMATICS

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

(2014) Kyung Kim et al.   BMC BIOINFORMATICS

Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing

(2014) Chang Yu et al.   CELL RESEARCH

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Genome sequencing of normal cells reveals developmental lineages and mutational processes

(2014) Sam Behjati et al.   NATURE

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

(2014) Jens G Lohr et al.   NATURE BIOTECHNOLOGY

RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia

(2014) Elli Papaemmanuil et al.   NATURE GENETICS

Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics

(2014) Christian Rinke et al.   Nature Protocols

Recent advances in genomic DNA sequencing of microbial species from single cells

(2014) Roger S. Lasken et al.   NATURE REVIEWS GENETICS

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

Single cell sequencing reveals low levels of aneuploidy across mammalian tissues

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

Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics

(2014) Charles Gawad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

(2014) Xuyu Cai et al.   Cell Reports

Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing

(2014) Andrew E. O. Hughes et al.   PLoS Genetics

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

An estimation of the number of cells in the human body

(2013) Eva Bianconi et al.   ANNALS OF HUMAN BIOLOGY

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Genome Analyses of Single Human Oocytes

(2013) Yu Hou et al.   CELL

Single-cell mutational profiling and clonal phylogeny in cancer

(2013) N. E. Potter et al.   GENOME RESEARCH

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

(2013) M. S. Fitzsimons et al.   GENOME RESEARCH

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

(2013) Jeff Gole et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

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

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Evolution and dynamics of pancreatic cancer progression

(2013) S Yachida et al.   ONCOGENE

A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing

(2013) Chunlei Zhang et al.   PLoS One

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

(2013) X. Ni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

(2013) J. S. McLean et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mosaic Copy Number Variation in Human Neurons

(2013) M. J. McConnell et al.   SCIENCE

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

(2013) Jeremy A. Dodsworth et al.   Nature Communications

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

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

(2012) Yong Hou et al.   CELL

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

(2012) Jianbin Wang et al.   CELL

Quantitative PCR Analysis of DNA, RNAs, and Proteins in the Same Single Cell

(2012) A. Stahlberg et al.   CLINICAL CHEMISTRY

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

Postzygotic HRAS and KRAS mutations cause nevus sebaceous and Schimmelpenning syndrome

(2012) Leopold Groesser et al.   NATURE GENETICS

Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA

(2012) Marjorie J Lindhurst et al.   NATURE GENETICS

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

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

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

(2012) C. Zong et al.   SCIENCE

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

Clonal Evolution of Preleukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia

(2012) M. Jan et al.   Science Translational Medicine

Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

(2012) Yingrui Li et al.   GigaScience

Partial Genome Assembly for a Candidate Division OP11 Single Cell from an Anoxic Spring (Zodletone Spring, Oklahoma)

(2011) Noha H. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

First births after preimplantation genetic diagnosis of structural chromosome abnormalities using comparative genomic hybridization and microarray analysis

(2011) S. Alfarawati et al.   HUMAN REPRODUCTION

Polar body array CGH for prediction of the status of the corresponding oocyte. Part I: clinical results

(2011) J. Geraedts et al.   HUMAN REPRODUCTION

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing

(2011) Manuel Martinez-Garcia et al.   ISME Journal

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

A Mosaic Activating Mutation inAKT1Associated with the Proteus Syndrome

(2011) Marjorie J. Lindhurst et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Single-cell copy number variation detection

(2011) Jiqiu Cheng et al.   GENOME BIOLOGY

Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis

(2010) Laura K. Conlin et al.   HUMAN MOLECULAR GENETICS

Digital MDA for enumeration of total nucleic acid contamination

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

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

Somatic mosaicism for copy number variation in differentiated human tissues

(2008) Arkadiusz Piotrowski et al.   HUMAN MUTATION

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

McKusick's Online Mendelian Inheritance in Man (OMIM(R))

(2008) J. Amberger et al.   NUCLEIC ACIDS RESEARCH