A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis

Comparison of hierarchical cluster analysis methods by cophenetic correlation

(2013) Sinan Saraçli et al.   JOURNAL OF INEQUALITIES AND APPLICATIONS

Assembling models of embryo development: Image analysis and the construction of digital atlases

(2012) Carlos Castro-González et al.   BIRTH DEFECTS RESEARCH PART C-EMBRYO TODAY-REVIEWS

ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains

(2012) Olaf Ronneberger et al.   NATURE METHODS

Icy: an open bioimage informatics platform for extended reproducible research

(2012) Fabrice de Chaumont et al.   NATURE METHODS

Predictive computation of genomic logic processing functions in embryonic development

(2012) I. S. Peter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-body gene expression pattern registration in Platynereis larvae

(2012) Albina Asadulina et al.   EvoDevo

3D Reconstruction and Standardization of the Rat Vibrissal Cortex for Precise Registration of Single Neuron Morphology

(2012) Robert Egger et al.   PLoS Computational Biology

Efficient Reverse-Engineering of a Developmental Gene Regulatory Network

(2012) Anton Crombach et al.   PLoS Computational Biology

Advances in multiphoton microscopy for imaging embryos

(2011) Willy Supatto et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Image analysis for understanding embryo development: a bridge from microscopy to biological insights

(2011) MA Luengo-Oroz et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

BrainAligner: 3D registration atlases of Drosophila brains

(2011) Hanchuan Peng et al.   NATURE METHODS

A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

(2011) Charless C. Fowlkes et al.   PLoS Genetics

Profiling by Image Registration Reveals Common Origin of Annelid Mushroom Bodies and Vertebrate Pallium

(2010) Raju Tomer et al.   CELL

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

(2010) Erwin Frise et al.   Molecular Systems Biology

V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues

(2010) Dmitriy M. Chudakov et al.   PHYSIOLOGICAL REVIEWS

Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy

(2010) N. Olivier et al.   SCIENCE

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

(2009) O. Rubel et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Microscopic marvels: Seeing the system

(2009) Alison Abbott   NATURE

A 3D digital atlas of C. elegans and its application to single-cell analyses

(2009) Fuhui Long et al.   NATURE METHODS

Quantitative approaches in developmental biology

(2009) Andrew C. Oates et al.   NATURE REVIEWS GENETICS

More than a decade of developmental gene expression atlases: where are we now?

(2009) B. A. de Boer et al.   NUCLEIC ACIDS RESEARCH

Developmental gene regulatory networks in the zebrafish embryo

(2008) Tzu-Min Chan et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

(2008) Thouis R Jones et al.   BMC BIOINFORMATICS

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

(2008) Charless C. Fowlkes et al.   CELL

Integrating technologies for comparing 3D gene expression domains in the developing chick limb

(2008) Malcolm E. Fisher et al.   DEVELOPMENTAL BIOLOGY

Defining diversity, specialization, and gene specificity in transcriptomes through information theory

(2008) O. Martinez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA