High expression of new genes in trochophore enlightening the ontogeny and evolution of trochozoans

Animal Evolution: Are Phyla Real?

(2016) Andreas Hejnol et al.   CURRENT BIOLOGY

Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution

(2016) Bryan A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Michal Levin et al.   NATURE

Molluscan Larvae: Pelagic Juveniles or Slowly Metamorphosing Larvae?

(2016) Louise R. Page   BIOLOGICAL BULLETIN

Reinforcing the Egg-Timer: Recruitment of Novel Lophotrochozoa Homeobox Genes to Early and Late Development in the Pacific Oyster

(2015) Jordi Paps et al.   Genome Biology and Evolution

Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis

(2015) Hajk-Georg Drost et al.   MOLECULAR BIOLOGY AND EVOLUTION

A “Developmental Hourglass” in Fungi

(2015) Xuanjin Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Animal Phylogeny and Its Evolutionary Implications

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

New genes important for development

(2014) C. Kemkemer et al.   EMBO REPORTS

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

(2014) B. A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Identification of Conserved and Novel MicroRNAs in the Pacific Oyster Crassostrea gigas by Deep Sequencing

(2014) Fei Xu et al.   PLoS One

Life cycle evolution: was the eumetazoan ancestor a holopelagic, planktotrophic gastraea?

(2013) Claus Nielsen   BMC EVOLUTIONARY BIOLOGY

Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR

(2013) Yishuai Du et al.   FISH & SHELLFISH IMMUNOLOGY

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

A transcriptomic hourglass in plant embryogenesis

(2012) Marcel Quint et al.   NATURE

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

The normal development of Platynereis dumerilii (Nereididae, Annelida)

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

Plasticity of Hatching and the Duration of Planktonic Development in Marine Invertebrates

(2011) F. X. Oyarzun et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Optimally weighted Z-test is a powerful method for combining probabilities in meta-analysis

(2011) D. V. ZAYKIN   JOURNAL OF EVOLUTIONARY BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa

(2010) Tomislav Domazet-Lošo et al.   BMC 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

Indirect development, transdifferentiation and the macroregulatory evolution of metazoans

(2010) C. Arenas-Mena   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Origins of the other metazoan body plans: the evolution of larval forms

(2008) R. A Raff   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES