Comprehensive single-cell transcriptional profiling of a multicellular organism

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

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

Batch effects and the effective design of single-cell gene expression studies

(2017) Po-Yuan Tung et al.   Scientific Reports

Revisiting Neuronal Cell Type Classification in Caenorhabditis elegans

(2016) Oliver Hobert et al.   CURRENT BIOLOGY

The time-resolved transcriptome ofC. elegans

(2016) Max E. Boeck et al.   GENOME RESEARCH

Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity

(2016) Weihua Zeng et al.   NUCLEIC ACIDS RESEARCH

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

(2016) Graham Heimberg et al.   Cell Systems

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

A germ cell determinant reveals parallel pathways for germ line development inCaenorhabditis elegans

(2015) Rana Mainpal et al.   DEVELOPMENT

The DREAM complex promotes gene body H2A.Z for target repression

(2015) Isabel Latorre et al.   GENES & DEVELOPMENT

A glial K+/Cl−cotransporter modifies temperature-evoked dynamics inCaenorhabditis eleganssensory neurons

(2015) A. Yoshida et al.   GENES BRAIN AND BEHAVIOR

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

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

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

DRE-1/FBXO11-Dependent Degradation of BLMP-1/BLIMP-1 Governs C. elegans Developmental Timing and Maturation

(2014) Moritz Horn et al.   DEVELOPMENTAL CELL

Two Classes of Gap Junction Channels Mediate Soma-Germline Interactions Essential for Germline Proliferation and Gametogenesis in Caenorhabditis elegans

(2014) T. A. Starich et al.   GENETICS

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

Extensive Oscillatory Gene Expression during C. elegans Larval Development

(2014) Gert-Jan Hendriks et al.   MOLECULAR CELL

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

(2014) Carlos L. Araya et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen 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

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals

(2014) Giovanni Strona et al.   Nature Communications

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

(2013) Alex K. Shalek et al.   NATURE

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

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

(2013) Quin F Wills et al.   NATURE BIOTECHNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

(2013) Simone Picelli et al.   NATURE METHODS

RNA-sequencing from single nuclei

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

Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs

(2013) Michelle Kudron et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Multidimensional regulation of gene expression in the C. elegans embryo

(2012) J. I. Murray et al.   GENOME RESEARCH

Transcriptional regulation of HLH-6-independent and subtype-specific genes expressed in the Caenorhabditis elegans pharyngeal glands

(2012) Vikas Ghai et al.   MECHANISMS OF DEVELOPMENT

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

An N-Myristoylated Globin with a Redox-Sensing Function That Regulates the Defecation Cycle in Caenorhabditis elegans

(2012) Lesley Tilleman et al.   PLoS One

Neuroblast migration along the anteroposterior axis of C. elegans is controlled by opposing gradients of Wnts and a secreted Frizzled-related protein

(2011) M. Harterink et al.   DEVELOPMENT

Specific insulin-like peptides encode sensory information to regulate distinct developmental processes

(2011) A. Cornils et al.   DEVELOPMENT

Transposase mediated construction of RNA-seq libraries

(2011) J. Gertz et al.   GENOME RESEARCH

OrthoList: A Compendium of C. elegans Genes with Human Orthologs

(2011) Daniel D. Shaye et al.   PLoS One

Isolation and Culture of Larval Cells from C. elegans

(2011) Sihui Zhang et al.   PLoS One

Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex

(2011) Tomoko M. Tabuchi et al.   PLoS Genetics

xnd-1 regulates the global recombination landscape in Caenorhabditis elegans

(2010) Cynthia R. Wagner et al.   NATURE

Olfactory Plasticity Is Regulated by Pheromonal Signaling in Caenorhabditis elegans

(2010) K. Yamada et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

A neuromedin-pyrokinin-like neuropeptide signaling system in Caenorhabditis elegans

(2009) Marleen Lindemans et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

C. elegans mig-6 encodes papilin isoforms that affect distinct aspects of DTC migration, and interacts genetically with mig-17 and collagen IV

(2009) T. Kawano et al.   DEVELOPMENT

FLR-2, the glycoprotein hormone alpha subunit, is involved in the neural control of intestinal functions inCaenorhabditis elegans

(2009) Akane Oishi et al.   GENES TO CELLS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Single-cell transcriptional analysis of taste sensory neuron pair in Caenorhabditis elegans

(2009) Jun Takayama et al.   NUCLEIC ACIDS RESEARCH

Caenorhabditis elegans BAH-1 Is a DUF23 Protein Expressed in Seam Cells and Required for Microbial Biofilm Binding to the Cuticle

(2009) Kevin Drace et al.   PLoS One

Discovery of a Cholecystokinin-Gastrin-Like Signaling System in Nematodes

(2008) Tom Janssen et al.   ENDOCRINOLOGY

TheC. elegansL1CAM homologue LAD-2 functions as a coreceptor in MAB-20/Sema2–mediated axon guidance

(2008) Xuelin Wang et al.   JOURNAL OF CELL BIOLOGY

Glia Are Essential for Sensory Organ Function in C. elegans

(2008) T. Bacaj et al.   SCIENCE

OSM-11 Facilitates LIN-12 Notch Signaling during Caenorhabditis elegans Vulval Development

(2008) Hidetoshi Komatsu et al.   PLOS BIOLOGY