Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm

(2019) Marta Bozek et al.   GENOME RESEARCH

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

(2019) Carmen Bravo González-Blas et al.   NATURE METHODS

Spatial transcriptomics coming of age

(2019) Darren J. Burgess   NATURE REVIEWS GENETICS

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

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Multilevel regulation of the glass locus during Drosophila eye development

(2019) Cornelia Fritsch et al.   PLoS Genetics

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

(2018) Shuonan Chen et al.   BMC BIOINFORMATICS

Mapping gene regulatory networks from single-cell omics data

(2018) Mark W E J Fiers et al.   Briefings in Functional Genomics

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

(2018) Jelle Jacobs et al.   NATURE GENETICS

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH

(2018) Eduardo Torre et al.   Cell Systems

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

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

(2018) Darren A. Cusanovich et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

(2018) Thomas Moerman et al.   BIOINFORMATICS

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

REDfly: the transcriptional regulatory element database for Drosophila

(2018) John Rivera et al.   NUCLEIC ACIDS RESEARCH

Single cell RNA-sequencing identifies a metabolic aspect of apoptosis in Rbf mutant

(2018) Majd M. Ariss et al.   Nature Communications

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas

(2018) Shengbao Suo et al.   Cell Reports

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

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar 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

A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster

(2017) Danielle C. Hamm et al.   PLoS Genetics

The legacy of Drosophila imaginal discs

(2016) Jorge V. Beira et al.   CHROMOSOMA

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies Using Drosophila melanogaster

(2016) Janani Iyer et al.   G3-Genes Genomes Genetics

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program

(2015) A. Pataskar et al.   EMBO JOURNAL

The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells

(2015) Francesca Froldi et al.   GENES & DEVELOPMENT

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

(2015) Takashi Nagano et al.   Nature Protocols

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

Eye Selector Logic for a Coordinated Cell Cycle Exit

(2015) Carla S. Lopes et al.   PLoS Genetics

Partially Redundant Enhancers Cooperatively Maintain Mammalian Pomc Expression Above a Critical Functional Threshold

(2015) Daniel D. Lam et al.   PLoS Genetics

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

Dedifferentiation of Neurons Precedes Tumor Formation in lola Mutants

(2014) Tony D. Southall et al.   DEVELOPMENTAL CELL

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference

(2014) Delphine Potier et al.   Cell Reports

Insulinoma-associated 1a (Insm1a) is required for photoreceptor differentiation in the zebrafish retina

(2013) Marie A. Forbes-Osborne et al.   DEVELOPMENTAL BIOLOGY

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

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

Control of Airway Tube Diameter and Integrity by Secreted Chitin-Binding Proteins in Drosophila

(2013) Katarína Tiklová et al.   PLoS One

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Dual transcriptional activities of SIX proteins define their roles in normal and ectopic eye development

(2012) A. M. Anderson et al.   DEVELOPMENT

Regulation of locomotion and motoneuron trajectory selection and targeting by the Drosophila homolog of Olig family transcription factors

(2012) Justine Oyallon et al.   DEVELOPMENTAL BIOLOGY

Hox proteins coordinate peripodial decapentaplegic expression to direct adult head morphogenesis in Drosophila

(2012) Brian G. Stultz et al.   DEVELOPMENTAL BIOLOGY

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

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

(2012) Johannes Schindelin et al.   NATURE METHODS

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

A Survey of 6,300 Genomic Fragments for cis-Regulatory Activity in the Imaginal Discs of Drosophila melanogaster

(2012) Aurélie Jory et al.   Cell Reports

Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

(2011) Scott Barolo   BIOESSAYS

Long- and Short-Range Transcriptional Repressors Induce Distinct Chromatin States on Repressed Genes

(2011) Li M. Li et al.   CURRENT BIOLOGY

Segment-specific regulation of the Drosophila AP-2 gene during leg and antennal development

(2011) Youngwook Ahn et al.   DEVELOPMENTAL BIOLOGY

JAK/STAT and the GATA factor Pannier control hemocyte maturation and differentiation in Drosophila

(2011) Svetlana Minakhina et al.   DEVELOPMENTAL BIOLOGY

Convergent Local Identity and Topographic Projection of Sensory Neurons

(2011) M. R. Karim et al.   JOURNAL OF NEUROSCIENCE

Prospero and Pax2 combinatorially control neural cell fate decisions by modulating Ras- and Notch-dependent signaling

(2011) Mark Charlton-Perkins et al.   Neural Development

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

Expression and function of the empty spiracles gene in olfactory sense organ development of Drosophila melanogaster

(2010) S. Sen et al.   DEVELOPMENT

Genetic interactions of eyes absent, twin of eyeless and orthodenticle regulate sine oculis expression during ocellar development in Drosophila

(2010) Jorge Blanco et al.   DEVELOPMENTAL BIOLOGY

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification

(2010) Stein Aerts et al.   PLOS BIOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Pattern formation in the Drosophila eye disc

(2009) Jean-Yves Roignant et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Two-step selection of a single R8 photoreceptor: a bistable loop between senseless and rough locks in R8 fate

(2008) K. L. Pepple et al.   DEVELOPMENT