The mid-developmental transition and the evolution of animal body plans

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

(2015) Thomas C. Boothby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) S. Anders et al.   BIOINFORMATICS

BLIND ordering of large-scale transcriptomic developmental timecourses

(2014) L. Anavy et al.   DEVELOPMENT

Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer

(2014) Tamar Hashimshony et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

(2013) J. F. Ryan et al.   SCIENCE

von Baer's law for the ages: lost and found principles of developmental evolution

(2013) Arhat Abzhanov   TRENDS IN GENETICS

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Developmental diversity in free-living flatworms

(2012) José Martín-Durán et al.   EvoDevo

The normal development of Platynereis dumerilii (Nereididae, Annelida)

(2011) Antje HL Fischer et al.   Frontiers in Zoology

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

Germ layer specification and axial patterning in the embryonic development of the freshwater planarian Schmidtea polychroa

(2010) José María Martín-Durán et al.   DEVELOPMENTAL BIOLOGY

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

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

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

(2010) Joseph F Ryan et al.   EvoDevo

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New method to deliver exogenous material into developing planarian embryos

(2008) José María Martín-Durán et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE