The continuum of Drosophila embryonic development at single-cell resolution

Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories

(2022) Stefano Secchia et al.   DEVELOPMENTAL CELL

High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae

(2022) Mingyue Wang et al.   DEVELOPMENTAL CELL

Systematic reconstruction of cellular trajectories across mouse embryogenesis

(2022) Chengxiang Qiu et al.   NATURE GENETICS

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

(2022) Hongjie Li et al.   SCIENCE

Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization

(2021) Margarita V. Brovkina et al.   PLoS Genetics

Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila

(2021) Colleen N McLaughlin et al.   eLife

A single-embryo, single-cell time-resolved model for mouse gastrulation

(2021) Markus Mittnenzweig et al.   CELL

Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions

(2021) Nicholas J Everetts et al.   eLife

Molecular architecture of the developing mouse brain

(2021) Gioele La Manno et al.   NATURE

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

(2021) Jingyue Duan et al.   eLife

Single-cyst transcriptome analysis of Drosophila male germline stem cell lineage

(2020) Zhen Shi et al.   DEVELOPMENT

A cell atlas of the adult Drosophila midgut

(2020) Ruei-Jiun Hung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Loss of Pseudouridine Synthases in the RluA Family Causes Hypersensitive Nociception in Drosophila

(2020) Wan Song et al.   G3-Genes Genomes Genetics

Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis

(2020) James P. Reddington et al.   DEVELOPMENTAL CELL

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

(2019) Maxim V Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns

(2019) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Gene expression atlas of a developing tissue by single cell expression correlation analysis

(2019) Josephine Bageritz et al.   NATURE METHODS

Drosophila Snazarus Regulates a Lipid Droplet Population at Plasma Membrane-Droplet Contacts in Adipocytes

(2019) Rupali Ugrankar et al.   DEVELOPMENTAL CELL

The mode of action of Fruitless: Is it an easy matter to switch the sex?

(2019) Kosei Sato et al.   GENES BRAIN AND BEHAVIOR

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

(2019) Jonathan S. Packer et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo

(2018) Jenna E. Haines et al.   PLoS Genetics

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

(2018) Ignacio E. Schor et al.   CURRENT BIOLOGY

REDfly: the transcriptional regulatory element database for Drosophila

(2018) John Rivera et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Michelle M. Kudron et al.   GENETICS

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

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

(2017) Michelle M. Kudron et al.   GENETICS

Fruitless Represses robo1 Transcription to Shape Male-Specific Neural Morphology and Behavior in Drosophila

(2016) Hiroki Ito et al.   CURRENT BIOLOGY

Evolved Repression Overcomes Enhancer Robustness

(2016) Ella Preger-Ben Noon et al.   DEVELOPMENTAL CELL

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

Zygotic Genome Activation Triggers the DNA Replication Checkpoint at the Midblastula Transition

(2015) Shelby A. Blythe et al.   CELL

Drosophilablood cells and their role in immune responses

(2015) Isabella Vlisidou et al.   FEBS Journal

Drosophila Lipophorin Receptors Recruit the Lipoprotein LTP to the Plasma Membrane to Mediate Lipid Uptake

(2015) Míriam Rodríguez-Vázquez et al.   PLoS Genetics

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Organ-specific gene expression: the bHLH protein Sage provides tissue specificity to Drosophila FoxA

(2013) R. M. Fox et al.   DEVELOPMENT

Spatial expression of transcription factors in Drosophila embryonic organ development

(2013) Ann S Hammonds et al.   GENOME BIOLOGY

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

(2012) Stefan Bonn et al.   Nature Protocols

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY