High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Larval body patterning and apical organs are conserved in animal evolution

(2014) Heather Marlow et al.   BMC BIOLOGY

Melatonin Signaling Controls Circadian Swimming Behavior in Marine Zooplankton

(2014) Maria Antonietta Tosches et al.   CELL

Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution

(2014) Robert Durruthy-Durruthy et al.   CELL

Conservation and evolutionary modifications of neuroblast expression patterns in insects

(2014) Lucia Biffar et al.   DEVELOPMENTAL BIOLOGY

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

(2014) Ditte Lovatt et al.   NATURE METHODS

Cell-type-based model explaining coexpression patterns of genes in the brain

(2014) P. Grange et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets

(2014) Jean-Baptiste Pettit et al.   PLoS Computational Biology

Expression Dynamics and Protein Localization of Rhabdomeric Opsins in Platynereis Larvae

(2013) Nadine Randel et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

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

(2013) Nico Battich et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps

(2013) Swee Jin Tan et al.   PLoS One

Stable transgenesis in the marine annelid Platynereis dumerilii sheds new light on photoreceptor evolution

(2013) B. Backfisch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved MIP receptor-ligand pair regulates Platynereis larval settlement

(2013) M. Conzelmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global view of the evolution and diversity of metazoan neuropeptide signaling

(2013) G. Jekely   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary crossroads in developmental biology: annelids

(2012) D. E. K. Ferrier   DEVELOPMENT

Ancient deuterostome origins of vertebrate brain signalling centres

(2012) Ariel M. Pani et al.   NATURE

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

Whole-body gene expression pattern registration in Platynereis larvae

(2012) Albina Asadulina et al.   EvoDevo

Antibodies against conserved amidated neuropeptide epitopes enrich the comparative neurobiology toolbox

(2012) Markus Conzelmann et al.   EvoDevo

The segmental pattern of otx, gbx, and Hox genes in the annelid Platynereis dumerilii

(2011) Patrick R. H. Steinmetz et al.   EVOLUTION & DEVELOPMENT

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Neuropeptides regulate swimming depth of Platynereis larvae

(2011) M. Conzelmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images

(2010) Kriti Puniyani et al.   BIOINFORMATICS

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

(2010) Raju Tomer et al.   CELL

A systematic analysis of the gap gene system in the moth midge Clogmia albipunctata

(2010) Mónica García-Solache et al.   DEVELOPMENTAL BIOLOGY

Ancient animal microRNAs and the evolution of tissue identity

(2010) Foteini Christodoulou et al.   NATURE

Hedgehog Signaling Regulates Segment Formation in the Annelid Platynereis

(2010) N. Dray et al.   SCIENCE

Orthologs of key vertebrate neural genes are expressed during neurogenesis in the annelidPlatynereis dumerilii

(2009) Pierre Kerner et al.   EVOLUTION & DEVELOPMENT

atonal- and achaete-scute-related genes in the annelid Platynereis dumerilii: insights into the evolution of neural basic-Helix-Loop-Helix genes

(2008) Elena Simionato et al.   BMC EVOLUTIONARY BIOLOGY

Mechanism of phototaxis in marine zooplankton

(2008) Gáspár Jékely et al.   NATURE

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS