Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Evolutionary origin of gastrulation: insights from sponge development

(2014) Nagayasu Nakanishi et al.   BMC BIOLOGY

BLIND ordering of large-scale transcriptomic developmental timecourses

(2014) L. Anavy et al.   DEVELOPMENT

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

(2014) D. A. Bitton et al.   GENOME RESEARCH

The ctenophore genome and the evolutionary origins of neural systems

(2014) Leonid L. Moroz et al.   NATURE

The Characterization of Sponge NLRs Provides Insight into the Origin and Evolution of This Innate Immune Gene Family in Animals

(2013) Benedict Yuen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Early evolution of the T-box transcription factor family

(2013) A. Sebe-Pedros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans

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

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

(2013) J. F. Ryan et al.   SCIENCE

The Capsaspora genome reveals a complex unicellular prehistory of animals

(2013) Hiroshi Suga et al.   Nature Communications

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

(2013) Stephen R Fairclough et al.   GENOME BIOLOGY

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Functionalization of a protosynaptic gene expression network

(2012) C. Conaco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A complex ‘mRNA degradation code’ controls gene expression during animal development

(2012) Claudio R. Alonso   TRENDS IN GENETICS

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

(2012) Tamar Hashimshony et al.   Cell Reports

The molecular biology of memory: cAMP, PKA, CRE, CREB-1, CREB-2, and CPEB

(2012) Eric R Kandel   Molecular Brain

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Signals for pre-mRNA cleavage and polyadenylation

(2011) Bin Tian et al.   Wiley Interdisciplinary Reviews-RNA

Perspectives on the RNA polymerase II core promoter

(2011) James T. Kadonaga   Wiley Interdisciplinary Reviews-Developmental Biology

Structure and expression of conserved Wnt pathway components in the demosponge Amphimedon queenslandica

(2010) Maja Adamska et al.   EVOLUTION & DEVELOPMENT

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 Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Early evolution of metazoan transcription factors

(2009) Bernard M Degnan et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa

(2009) E. A. Sperling et al.   MOLECULAR BIOLOGY AND EVOLUTION

Early origin of the bilaterian developmental toolkit

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

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

(2009) Bernd Schierwater et al.   PLOS BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genesis and Expansion of Metazoan Transcription Factor Gene Classes

(2008) Claire Larroux et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

(2008) Nicole King et al.   NATURE

The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo

(2008) J. E. Bestman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY