Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Elementary nervous systems

(2021) Detlev Arendt   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

(2021) Alexander J Tarashansky et al.   eLife

A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC

(2021) Vishaka Gopalan et al.   CANCER RESEARCH

Whole-body integration of gene expression and single-cell morphology

(2021) Hernando M. Vergara et al.   CELL

The Evolutionary Assembly of Neuronal Machinery

(2020) Detlev Arendt   CURRENT BIOLOGY

The architecture of cell differentiation in choanoflagellates and sponge choanocytes

(2019) Davis Laundon et al.   PLOS BIOLOGY

Evolution of neuronal types and families

(2019) Detlev Arendt et al.   CURRENT OPINION IN NEUROBIOLOGY

Reconstructing complex lineage trees from scRNA-seq data using MERLoT

(2019) R Gonzalo Parra et al.   NUCLEIC ACIDS RESEARCH

Visualization of protein crystals by high-energy phase-contrast X-ray imaging

(2019) Maxim Polikarpov et al.   Acta Crystallographica Section D-Structural Biology

Evidence of Signaling and Adhesion Roles for β-Catenin in the Sponge Ephydatia muelleri

(2018) Klaske J Schippers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Early metazoan cell type diversity and the evolution of multicellular gene regulation

(2018) Arnau Sebé-Pedrós et al.   Nature Ecology & Evolution

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multicut brings automated neurite segmentation closer to human performance

(2017) Thorsten Beier et al.   NATURE METHODS

Conserved gene regulatory module specifies lateral neural borders across bilaterians

(2017) Yongbin Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzymatic production of single-molecule FISH and RNA capture probes

(2017) Imre Gaspar et al.   RNA

Gut-like ectodermal tissue in a sea anemone challenges germ layer homology

(2017) Patrick R. H. Steinmetz et al.   Nature Ecology & Evolution

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges

(2016) Jesús F. Peña et al.   EvoDevo

Functions of Rab Proteins at Presynaptic Sites

(2016) Beyenech Binotti et al.   Cells

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Hydrogen sulfide in signaling pathways

(2015) Beata Olas   CLINICA CHIMICA ACTA

Dynamic Transport and Cementation of Skeletal Elements Build Up the Pole-and-Beam Structured Skeleton of Sponges

(2015) Sohei Nakayama et al.   CURRENT BIOLOGY

Unbiased View of Synaptic and Neuronal Gene Complement in Ctenophores: Are There Pan-neuronal and Pan-synaptic Genes across Metazoa?

(2015) Leonid L. Moroz et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Gastric pouches and the mucociliary sole: setting the stage for nervous system evolution

(2015) D. Arendt et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Independent origins of neurons and synapses: insights from ctenophores

(2015) Leonid L. Moroz et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The ancestral gene repertoire of animal stem cells

(2015) Alexandre Alié et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

(2015) Cong Liang et al.   Nature Communications

mvmorph: anrpackage for fitting multivariate evolutionary models to morphometric data

(2015) Julien Clavel et al.   Methods in Ecology and Evolution

Ultra-large alignments using phylogeny-aware profiles

(2015) Nam-phuong D. Nguyen et al.   GENOME BIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

(2014) Ana Riesgo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

(2014) Sofia A. V. Fortunato et al.   NATURE

Evolution of the Pax-Six-Eya-Dach network: the calcisponge case study

(2014) Sofia AV Fortunato et al.   EvoDevo

TomoPy: a framework for the analysis of synchrotron tomographic data

(2014) Dogˇa Gürsoy et al.   JOURNAL OF SYNCHROTRON RADIATION

The evolution and function of the Pax/Six regulatory network in sponges

(2013) A. Rivera et al.   EVOLUTION & DEVELOPMENT

SLC18: Vesicular neurotransmitter transporters for monoamines and acetylcholine

(2013) Hakeem O. Lawal et al.   MOLECULAR ASPECTS OF MEDICINE

Kruppel-like factor 5 controls villus formation and initiation of cytodifferentiation in the embryonic intestinal epithelium

(2012) Sheila M. Bell et al.   DEVELOPMENTAL BIOLOGY

High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy

(2012) Juan Carlos Tapia et al.   Nature Protocols

The Presynaptic Active Zone

(2012) Thomas C. Südhof   NEURON

Synaptic Cell Adhesion

(2012) M. Missler et al.   Cold Spring Harbor Perspectives in Biology

Synaptic Vesicle Endocytosis

(2012) Y. Saheki et al.   Cold Spring Harbor Perspectives in Biology

Synaptic Vesicle Pools and Dynamics

(2012) A. A. Alabi et al.   Cold Spring Harbor Perspectives in Biology

The contractile sponge epithelium sensu lato - body contraction of the demosponge Tethya wilhelma is mediated by the pinacoderm

(2011) M. Nickel et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Postsynaptic Organization of Synapses

(2011) M. Sheng et al.   Cold Spring Harbor Perspectives in Biology

Synaptic Vesicle Exocytosis

(2011) T. C. Sudhof et al.   Cold Spring Harbor Perspectives in Biology

Evidence for glutamate, GABA and NO in coordinating behaviour in the sponge, Ephydatia muelleri (Demospongiae, Spongillidae)

(2010) G. R. D. Elliott et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

The SNX-PX-BAR Family in Macropinocytosis: The Regulation of Macropinosome Formation by SNX-PX-BAR Proteins

(2010) Jack T. H. Wang et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

WNT/β-Catenin Signalling and Epithelial Patterning in the Homoscleromorph Sponge Oscarella

(2009) Pascal Lapébie et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Mind bomb 2, a founder myoblast-specific protein, regulates myoblast fusion and muscle stability

(2008) M. Carrasco-Rando et al.   DEVELOPMENT