Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

Regionalized nervous system in Hydra and the mechanism of its development

(2019) Yukihiko Noro et al.   GENE EXPRESSION PATTERNS

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

(2018) Arnau Sebé-Pedrós et al.   CELL

Microfluidics for electrophysiology, imaging, and behavioral analysis of Hydra

(2018) Krishna N. Badhiwala et al.   LAB ON A CHIP

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

A new view of embryo development and regeneration

(2018) Richard M. Harland   SCIENCE

Cell type transcriptome atlas for the planarianSchmidtea mediterranea

(2018) Christopher T. Fincher et al.   SCIENCE

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Hydra Mesoglea Proteome Identifies Thrombospondin as a Conserved Component Active in Head Organizer Restriction

(2018) Mark Lommel et al.   Scientific Reports

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

A secreted antibacterial neuropeptide shapes the microbiome of Hydra

(2017) René Augustin et al.   Nature Communications

PaxA, but not PaxC, is required for cnidocyte development in the sea anemone Nematostella vectensis

(2017) Leslie S. Babonis et al.   EvoDevo

Sequential development of apical-basal and planar polarities in aggregating epitheliomuscular cells of Hydra

(2016) Anna Seybold et al.   DEVELOPMENTAL BIOLOGY

Evaluation of TagSeq, a reliable low-cost alternative for RNAseq

(2016) Brian K. Lohman et al.   Molecular Ecology Resources

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Animal Phylogeny and Its Evolutionary Implications

(2014) Casey W. Dunn et al.   Annual Review of Ecology Evolution and Systematics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Nodal signalling determines biradial asymmetry in Hydra

(2014) Hiroshi Watanabe et al.   NATURE

Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps

(2014) Yasuharu Takaku et al.   Scientific Reports

Generation of Transgenic Hydra by Embryo Microinjection

(2014) Celina E. Juliano et al.   Jove-Journal of Visualized Experiments

Agalma: an automated phylogenomics workflow

(2013) Casey W Dunn et al.   BMC BIOINFORMATICS

A small molecule screen identifies a novel compound that induces a homeotic transformation in Hydra

(2013) K. M. Glauber et al.   DEVELOPMENT

Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway

(2013) Robyn S.M. Lim et al.   DEVELOPMENTAL BIOLOGY

PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells

(2013) C. E. Juliano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

(2013) A. de Mendoza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interstitial stem cells in Hydra: multipotency and decision-making

(2012) Charles N. David   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Stemness in Hydra - a current perspective

(2012) Bert Hobmayer et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Germline stem cells and sex determination in Hydra

(2012) Chiemi Nishimiya-Fujisawa et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Molecular Signatures of the Three Stem Cell Lineages in Hydra and the Emergence of Stem Cell Function at the Base of Multicellularity

(2012) Georg Hemmrich et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Microglia Sculpt Postnatal Neural Circuits in an Activity and Complement-Dependent Manner

(2012) Dorothy P. Schafer et al.   NEURON

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

(2012) J. Fraune et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Phagocytic activity of neuronal progenitors regulates adult neurogenesis

(2011) Zhenjie Lu et al.   NATURE CELL BIOLOGY

The Hydra polyp: Nothing but an active stem cell community

(2010) Thomas C. G. Bosch et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Nematogalectin, a nematocyst protein with GlyXY and galectin domains, demonstrates nematocyte-specific alternative splicing in Hydra

(2010) J. S. Hwang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal antimicrobial peptides

(2010) S. Fraune et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cnidarian nematocyst: a miniature extracellular matrix within a secretory vesicle

(2010) Suat Özbek   PROTOPLASMA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Origins of neurogenesis, a cnidarian view

(2009) Brigitte Galliot et al.   DEVELOPMENTAL BIOLOGY

Multiple Wnts are involved in Hydra organizer formation and regeneration

(2009) Tobias Lengfeld et al.   DEVELOPMENTAL BIOLOGY

Early origin of the bilaterian developmental toolkit

(2009) D. H. Erwin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Wnt/ -Catenin and noncanonical Wnt signaling interact in tissue evagination in the simple eumetazoan Hydra

(2009) I. Philipp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata

(2008) Oliver Voigt et al.   BMC GENOMICS

Uncovering the evolutionary history of innate immunity: The simple metazoan Hydra uses epithelial cells for host defence

(2008) Thomas C.G. Bosch et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Cilium Evolution: Identification of a Novel Protein, Nematocilin, in the Mechanosensory Cilium of Hydra Nematocytes

(2008) J. S. Hwang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Cell type complexity in the basal metazoan Hydra is maintained by both stem cell based mechanisms and transdifferentiation

(2007) Stefan Siebert et al.   DEVELOPMENTAL BIOLOGY