The octopus genome and the evolution of cephalopod neural and morphological novelties

Deep Vertebrate Roots for Mammalian Zinc Finger Transcription Factor Subfamilies

(2014) Hui Liu et al.   Genome Biology and Evolution

Mobile DNA elements in the generation of diversity and complexity in the brain

(2014) Jennifer A. Erwin et al.   NATURE REVIEWS NEUROSCIENCE

Clustered protocadherins

(2013) W. V. Chen et al.   DEVELOPMENT

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Synaptic scaffold evolution generated components of vertebrate cognitive complexity

(2012) Jess Nithianantharajah et al.   NATURE NEUROSCIENCE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

A-to-I RNA Editing: Effects on Proteins Key to Neural Excitability

(2012) Joshua J.C. Rosenthal et al.   NEURON

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules

(2011) Björn Kröger et al.   BIOESSAYS

Alternative Sites of Synaptic Plasticity in Two Homologous “Fan-out Fan-in” Learning and Memory Networks

(2011) Tal Shomrat et al.   CURRENT BIOLOGY

Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation

(2011) Masa-aki Yoshida et al.   GENE

Comparative Analysis of Chromosome Counts Infers Three Paleopolyploidies in the Mollusca

(2011) Nathaniel M. Hallinan et al.   Genome Biology and Evolution

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

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

(2011) Jarrod A. Chapman et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Chemoaffinity Revisited: Dscams, Protocadherins, and Neural Circuit Assembly

(2010) S. Lawrence Zipursky et al.   CELL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction

(2010) Vincent Croset et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Candidate chemoreceptor subfamilies differentially expressed in the chemosensory organs of the mollusc Aplysia

(2009) Scott F Cummins et al.   BMC BIOLOGY

The Evolution of Flexible Behavioral Repertoires in Cephalopod Molluscs

(2009) Frank W. Grasso et al.   BRAIN BEHAVIOR AND EVOLUTION

An extra double-stranded RNA binding domain confers high activity to a squid RNA editing enzyme

(2009) J. P. Palavicini et al.   RNA

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE