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

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

(2016) Charles Girardot et al.   BMC BIOINFORMATICS

Genetic variants regulating expression levels and isoform diversity during embryogenesis

(2016) Enrico Cannavò et al.   NATURE

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

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

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

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps

(2015) Manu Setty et al.   PLoS Computational Biology

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

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

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Multiple regulatory safeguards confine the expression of the GATA factor Serpent to the hemocyte primordium within the Drosophila mesoderm

(2013) Philipp Spahn et al.   DEVELOPMENTAL BIOLOGY

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

Spatial expression of transcription factors in Drosophila embryonic organ development

(2013) Ann S Hammonds et al.   GENOME BIOLOGY

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Stefan Bonn et al.   Nature Protocols

Sequential Signaling Crosstalk Regulates Endomesoderm Segregation in Sea Urchin Embryos

(2012) A. J. Sethi et al.   SCIENCE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

(2011) Sean Thomas et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape

(2010) Erwin Frise et al.   Molecular Systems Biology

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Conservation and divergence in developmental networks: a view from Drosophila myogenesis

(2009) Lucia Ciglar et al.   CURRENT OPINION IN CELL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY