Molecular topography of an entire nervous system

Structural and developmental principles of neuropil assembly in C. elegans

(2021) Mark W. Moyle et al.   NATURE

A multi-scale brain map derived from whole-brain volumetric reconstructions

(2021) Christopher A. Brittin et al.   NATURE

A head-to-head comparison of ribodepletion and polyA selection approaches for C. elegans low input RNA-sequencing libraries

(2021) Alec Barrett et al.   G3-Genes Genomes Genetics

A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord

(2020) Aaron M Allen et al.   eLife

Unique homeobox codes delineate all the neuron classes of C. elegans

(2020) Molly B. Reilly et al.   NATURE

NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans

(2020) Eviatar Yemini et al.   CELL

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

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

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Plasticity of the Electrical Connectome of C. elegans

(2019) Abhishek Bhattacharya et al.   CELL

Similarity regression predicts evolution of transcription factor sequence specificity

(2019) Samuel A. Lambert et al.   NATURE GENETICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Whole-animal connectomes of both Caenorhabditis elegans sexes

(2019) Steven J. Cook et al.   NATURE

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

(2019) Stefan Siebert et al.   SCIENCE

Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors

(2019) Morgan Thompson et al.   eLife

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development

(2019) Li Li et al.   PLoS Genetics

Single-cell transcriptomic evidence for dense intracortical neuropeptide networks

(2019) Stephen J Smith et al.   eLife

A Genetic Model of the Connectome

(2019) Dániel L. Barabási et al.   NEURON

Molecular Architecture of Genetically-Tractable GABA Synapses in C. elegans

(2019) Xin Zhou et al.   Frontiers in Molecular Neuroscience

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

Tetraspanins shape the synapse

(2018) Luca Murru et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity

(2018) Neda Masoudi et al.   PLOS BIOLOGY

An atlas of Caenorhabditis elegans chemoreceptor expression

(2018) Berta Vidal et al.   PLOS BIOLOGY

The CeNGEN Project: The Complete Gene Expression Map of an Entire Nervous System

(2018) Marc Hammarlund et al.   NEURON

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Spatiotemporal transcriptomic divergence across human and macaque brain development

(2018) Ying Zhu et al.   SCIENCE

Quantitative RNA-seq meta-analysis of alternative exon usage inC. elegans

(2017) Nicolas J. Tourasse et al.   GENOME RESEARCH

C. elegans neurons jettison protein aggregates and mitochondria under neurotoxic stress

(2017) Ilija Melentijevic et al.   NATURE

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Diversification of C. elegans Motor Neuron Identity via Selective Effector Gene Repression

(2017) Sze Yen Kerk et al.   NEURON

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

DSCAM promotes axon fasciculation and growth in the developing optic pathway

(2017) Freyja M. Bruce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Multiple conserved cell adhesion protein interactions mediate neural wiring of a sensory circuit in C. elegans

(2017) Byunghyuk Kim et al.   eLife

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data

(2016) André Kahles et al.   BIOINFORMATICS

The genome-wide role of HSF-1 in the regulation of gene expression in Caenorhabditis elegans

(2016) Jessica Brunquell et al.   BMC GENOMICS

Revisiting Neuronal Cell Type Classification in Caenorhabditis elegans

(2016) Oliver Hobert et al.   CURRENT BIOLOGY

De novo discovery of neuropeptides in the genomes of parasitic flatworms using a novel comparative approach

(2016) Uriel Koziol et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions

(2016) Juan I Fuxman Bass et al.   Molecular Systems Biology

Disentangling neural cell diversity using single-cell transcriptomics

(2016) Jean-Francois Poulin et al.   NATURE NEUROSCIENCE

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

The neurogenetics of alternative splicing

(2016) Celine K. Vuong et al.   NATURE REVIEWS NEUROSCIENCE

Splicing factors control C. elegans behavioural learning in a single neuron by producing DAF-2c receptor

(2016) Masahiro Tomioka et al.   Nature Communications

A cellular and regulatory map of the GABAergic nervous system of C. elegans

(2016) Marie Gendrel et al.   eLife

Morphologically defined sub-stages of C. elegans vulval development in the fourth larval stage

(2015) Darren Z. L. Mok et al.   BMC DEVELOPMENTAL BIOLOGY

Global Brain Dynamics Embed the Motor Command Sequence of Caenorhabditis elegans

(2015) Saul Kato et al.   CELL

L1CAM/Neuroglian controls the axon–axon interactions establishing layered and lobular mushroom body architecture

(2015) Dominique Siegenthaler et al.   JOURNAL OF CELL BIOLOGY

The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators

(2015) Rachel Kaletsky et al.   NATURE

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

(2015) Nikolaos Stefanakis et al.   NEURON

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

(2015) Bushra Raj et al.   NEURON

Pan-neuronal imaging in roamingCaenorhabditis elegans

(2015) Vivek Venkatachalam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-brain calcium imaging with cellular resolution in freely behavingCaenorhabditis elegans

(2015) Jeffrey P. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) A. Zeisel et al.   SCIENCE

A cellular and regulatory map of the cholinergic nervous system of C. elegans

(2015) Laura Pereira et al.   eLife

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A Pair of RNA-Binding Proteins Controls Networks of Splicing Events Contributing to Specialization of Neural Cell Types

(2014) Adam D. Norris et al.   MOLECULAR CELL

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling

(2014) W. Clay Spencer et al.   PLoS One

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Modular Control of Glutamatergic Neuronal Identity in C. elegans by Distinct Homeodomain Proteins

(2013) Esther Serrano-Saiz et al.   CELL

Molecular evolution of peptidergic signaling systems in bilaterians

(2013) O. Mirabeau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Compendium of Caenorhabditis elegans RNA Binding Proteins Predicts Extensive Regulation at Multiple Levels

(2013) Alex M. Tamburino et al.   G3-Genes Genomes Genetics

A Transcriptional Program Promotes Remodeling of GABAergic Synapses in Caenorhabditis elegans

(2011) S. C. Petersen et al.   JOURNAL OF NEUROSCIENCE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Isolation and Culture of Larval Cells from C. elegans

(2011) Sihui Zhang et al.   PLoS One

Six and Eya promote apoptosis through direct transcriptional activation of the proapoptotic BH3-only gene egl-1 in Caenorhabditis elegans

(2010) T. Hirose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Conversion of C. elegans Germ Cells into Specific Neuron Types

(2010) B. Tursun et al.   SCIENCE

Poly(C)-binding proteins as transcriptional regulators of gene expression

(2009) Hack Sun Choi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

(2009) Christian A. Grove et al.   CELL

Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

(2009) Xiao Liu et al.   CELL

Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans

(2009) B. J. Lesch et al.   GENES & DEVELOPMENT

Secreted semaphorins control spine distribution and morphogenesis in the postnatal CNS

(2009) Tracy S. Tran et al.   NATURE

Semaphorin 5B mediates synapse elimination in hippocampal neurons

(2009) Timothy P O'Connor et al.   Neural Development

Comparison of Caenorhabditis elegans NLP peptides with arthropod neuropeptides

(2009) Steven J. Husson et al.   TRENDS IN PARASITOLOGY

Trafficking and function of the tetraspanin CD63

(2008) Maaike S. Pols et al.   EXPERIMENTAL CELL RESEARCH

UNC-6/netrin and its receptor UNC-5 locally exclude presynaptic components from dendrites

(2008) Vivian Y. Poon et al.   NATURE

Using Expression Profiles of Caenorhabditis elegans Neurons To Identify Genes That Mediate Synaptic Connectivity

(2008) Leehod Baruch et al.   PLoS Computational Biology