Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Bursty Gene Expression in the Intact Mammalian Liver

(2015) Keren Bahar Halpern et al.   MOLECULAR CELL

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Whole-mount single molecule FISH method for zebrafish embryo

(2015) Yuma Oka et al.   Scientific Reports

Systematic imaging reveals features and changing localization of mRNAs in Drosophila development

(2015) Helena Jambor et al.   eLife

Simultaneous high-resolution detection of multiple transcripts combined with localization of proteins in whole-mount embryos

(2014) Theresa Gross-Thebing et al.   BMC BIOLOGY

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

A Predictive Model of Bifunctional Transcription Factor Signaling during Embryonic Tissue Patterning

(2014) Jan Philipp Junker et al.   DEVELOPMENTAL CELL

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization

(2013) Jean Ollion et al.   BIOINFORMATICS

Precise Developmental Gene Expression Arises from Globally Stochastic Transcriptional Activity

(2013) Shawn C. Little et al.   CELL

Gene transcription is coordinated with, but not dependent on, cell divisions during C. elegans embryonic fate specification

(2013) G. Nair et al.   DEVELOPMENT

Dampening of expression oscillations by synchronous regulation of a microRNA and its target

(2013) Dong hyun Kim et al.   NATURE GENETICS

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

(2013) Nico Battich et al.   NATURE METHODS

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

(2013) Marshall J Levesque et al.   NATURE METHODS

FISH-quant: automatic counting of transcripts in 3D FISH images

(2013) Florian Mueller et al.   NATURE METHODS

Single-molecule mRNA detection and counting in mammalian tissue

(2013) Anna Lyubimova et al.   Nature Protocols

Transcript processing and export kinetics are rate-limiting steps in expressing vertebrate segmentation clock genes

(2013) N. P. Hoyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Transcription Fosters Coordinate snail Expression in the Drosophila Embryo

(2013) Alistair Nicol Boettiger et al.   Cell Reports

Optimality in the Development of Intestinal Crypts

(2012) Shalev Itzkovitz et al.   CELL

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning

(2012) K. A. Peterson et al.   GENES & DEVELOPMENT

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

(2012) Johannes Schindelin et al.   NATURE METHODS

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Single-molecule transcript counting of stem-cell markers in the mouse intestine

(2011) Shalev Itzkovitz et al.   NATURE CELL BIOLOGY

no tail integrates two modes of mesoderm induction

(2010) S. A. Harvey et al.   DEVELOPMENT

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

Auto-Context and Its Application to High-Level Vision Tasks and 3D Brain Image Segmentation

(2009) Zhuowen Tu et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Visualisation and Quantification of Morphogen Gradient Formation in the Zebrafish

(2009) Steven A Harvey et al.   PLOS BIOLOGY

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Translational control of localized mRNAs: restricting protein synthesis in space and time

(2008) Florence Besse et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

High-resolution in situ hybridization to whole-mount zebrafish embryos

(2007) Christine Thisse et al.   Nature Protocols