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

Mapping transcriptomic vector fields of single cells

(2022) Xiaojie Qiu et al.   CELL

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

(2022) Ao Chen et al.   CELL

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

(2022) Hongjie Li et al.   SCIENCE

Dynamic sex chromosome expression in Drosophila male germ cells

(2021) Sharvani Mahadevaraju et al.   Nature Communications

Hotspot identifies informative gene modules across modalities of single-cell genomics

(2021) David DeTomaso et al.   Cell Systems

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

A single-cell atlas of adult Drosophila ovary identifies transcriptional programs and somatic cell lineage regulating oogenesis

(2020) Allison Jevitt et al.   PLOS BIOLOGY

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

(2020) Wei-Ting Chen et al.   CELL

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics

(2020) Jie Liao et al.   TRENDS IN BIOTECHNOLOGY

Molecular atlas of the adult mouse brain

(2020) Cantin Ortiz et al.   Science Advances

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

(2019) Josephine Bageritz et al.   NATURE METHODS

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development

(2019) Jian Zhou et al.   PLoS Genetics

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

(2019) Evan Witt et al.   eLife

Single cell transcriptome atlas of the Drosophila larval brain

(2019) Clarisse Brunet Avalos et al.   eLife

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

The Cellular Diversity and Transcription Factor Code of Drosophila Enteroendocrine Cells

(2019) Xingting Guo et al.   Cell Reports

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

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

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

(2017) David P Leader et al.   NUCLEIC ACIDS RESEARCH

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

Morphological and Molecular Characterization of Adult Midgut Compartmentalization in Drosophila

(2013) Nicolas Buchon et al.   Cell Reports

Physiological and stem cell compartmentalization within the Drosophila midgut

(2013) Alexis Marianes et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

3D Slicer as an image computing platform for the Quantitative Imaging Network

(2012) Andriy Fedorov et al.   MAGNETIC RESONANCE IMAGING

Drosophila Rbp6 Is an Orthologue of Vertebrate Msi-1 and Msi-2, but Does Not Function Redundantly with dMsi to Regulate Germline Stem Cell Behaviour

(2012) Nicole A. Siddall et al.   PLoS One

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

The tyrosine kinase Stitcher activates Grainy head and epidermal wound healing in Drosophila

(2009) Shenqiu Wang et al.   NATURE CELL BIOLOGY

FlyTED: the Drosophila Testis Gene Expression Database

(2009) Jun Zhao et al.   NUCLEIC ACIDS RESEARCH