A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

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

(2020) Molly B. Reilly et al.   NATURE

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

(2019) Adam D. Warner et al.   GENOME RESEARCH

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

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

(2019) Jonathan S. Packer et al.   SCIENCE

A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes

(2019) Joo Lee et al.   eLife

AceTree: a major update and case study in the long term maintenance of open-source scientific software

(2018) Braden Katzman et al.   BMC BIOINFORMATICS

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

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

(2018) Neda Masoudi et al.   PLOS BIOLOGY

A transcription factor collective defines the HSN serotonergic neuron regulatory landscape

(2018) Carla Lloret-Fernández et al.   eLife

FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

(2018) Brittany Z. Suggs et al.   DEVELOPMENTAL BIOLOGY

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds ofDrosophilaandCaenorhabditis elegansTranscription Factors

(2017) Michelle M. Kudron et al.   GENETICS

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

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

(2017) Sze Yen Kerk et al.   NEURON

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

The Bright Fluorescent Protein mNeonGreen Facilitates Protein Expression Analysis In Vivo

(2017) Lola Hostettler et al.   G3-Genes Genomes Genetics

Nanos promotes epigenetic reprograming of the germline by down-regulation of the THAP transcription factor LIN-15B

(2017) Chih-Yung Sean Lee et al.   eLife

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds ofDrosophilaandCaenorhabditis elegansTranscription Factors

(2017) Michelle M. Kudron et al.   GENETICS

In vivo mapping of tissue- and subcellular-specific proteomes in Caenorhabditis elegans

(2017) Aaron W. Reinke et al.   Science Advances

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

The Paired-box protein PAX-3 regulates the choice between lateral and ventral epidermal cell fates in C. elegans

(2016) Kenneth W. Thompson et al.   DEVELOPMENTAL BIOLOGY

A Transcriptional Lineage of the Early C. elegans Embryo

(2016) Sophia C. Tintori et al.   DEVELOPMENTAL CELL

A microRNA program in theC. eleganshypodermis couples to intestinal mTORC2/PQM-1 signaling to modulate fat transport

(2016) Robert H. Dowen et al.   GENES & DEVELOPMENT

The time-resolved transcriptome ofC. elegans

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

MED GATA factors promote robust development of the C. elegans endoderm

(2015) Morris F. Maduro et al.   DEVELOPMENTAL BIOLOGY

The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo

(2015) Zhuo Du et al.   DEVELOPMENTAL CELL

The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development

(2015) Travis Walton et al.   PLoS Genetics

A semi-local neighborhood-based framework for probabilistic cell lineage tracing

(2014) Anthony Santella et al.   BMC BIOINFORMATICS

Cellular Differences in Protein Synthesis Regulate Tissue Homeostasis

(2014) Michael Buszczak et al.   CELL

De Novo Inference of Systems-Level Mechanistic Models of Development from Live-Imaging-Based Phenotype Analysis

(2014) Zhuo Du et al.   CELL

Scalable and Versatile Genome Editing Using Linear DNAs with Microhomology to Cas9 Sites in Caenorhabditis elegans

(2014) Alexandre Paix et al.   GENETICS

Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer

(2014) Tamar Hashimshony et al.   NATURE

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

(2014) Carlos L. Araya et al.   NATURE

Conservation of mRNA and Protein Expression during Development of C. elegans

(2014) Dominic Grün et al.   Cell Reports

BLMP-1/Blimp-1 Regulates the Spatiotemporal Cell Migration Pattern in C. elegans

(2014) Tsai-Fang Huang et al.   PLoS Genetics

Germline Signals Deploy NHR-49 to Modulate Fatty-Acid β-Oxidation and Desaturation in Somatic Tissues of C. elegans

(2014) Ramesh Ratnappan et al.   PLoS Genetics

PQM-1 Complements DAF-16 as a Key Transcriptional Regulator of DAF-2-Mediated Development and Longevity

(2013) Ronald G. Tepper et al.   CELL

Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis

(2013) J. L. Moore et al.   DEVELOPMENT

Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination

(2013) Daniel J Dickinson et al.   NATURE METHODS

A High-Fidelity Cell Lineage Tracing Method for Obtaining Systematic Spatiotemporal Gene Expression Patterns in Caenorhabditis elegans

(2013) Daniel L Mace et al.   G3-Genes Genomes Genetics

A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans

(2012) Mihail Sarov et al.   CELL

Multidimensional regulation of gene expression in the C. elegans embryo

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

Clonally related visual cortical neurons show similar stimulus feature selectivity

(2012) Ye Li et al.   NATURE

Preferential electrical coupling regulates neocortical lineage-dependent microcircuit assembly

(2012) Yong-Chun Yu et al.   NATURE

Cell Architecture: Surrounding Muscle Cells Shape Gland Cell Morphology in theCaenorhabditis elegansPharynx

(2011) Wahyu Hendrati Raharjo et al.   GENETICS

A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D

(2010) Anthony Santella et al.   BMC BIOINFORMATICS

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Dynamic Chromatin Organization during Foregut Development Mediated by the Organ Selector Gene PHA-4/FoxA

(2010) Tala H. I. Fakhouri et al.   PLoS Genetics

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

(2009) Xiao Liu et al.   CELL

The NK-2 class homeodomain factor CEH-51 and the T-box factor TBX-35 have overlapping function in C. elegans mesoderm development

(2009) G. Broitman-Maduro et al.   DEVELOPMENT

The C. elegans Tailless/TLX transcription factor nhr-67 controls neuronal identity and left/right asymmetric fate diversification

(2009) S. Sarin et al.   DEVELOPMENT

A 3D digital atlas of C. elegans and its application to single-cell analyses

(2009) Fuhui Long et al.   NATURE METHODS

Control of cell cycle timing during C. elegans embryogenesis

(2008) Zhirong Bao et al.   DEVELOPMENTAL BIOLOGY

Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression

(2008) Itai Yanai et al.   Molecular Systems Biology

Automated analysis of embryonic gene expression with cellular resolution in C. elegans

(2008) John Isaac Murray et al.   NATURE METHODS

Behavioral and synaptic defects inC. eleganslacking the NK-2 homeobox geneceh-28

(2007) Paramita Ray et al.   Developmental Neurobiology