Hagfish and lamprey Hox genes reveal conservation of temporal colinearity in vertebrates

Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

(2017) Jacqueline Deschamps et al.   GENES & DEVELOPMENT

Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

(2017) Sabrina M. Schiemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scallop genome provides insights into evolution of bilaterian karyotype and development

(2017) Shi Wang et al.   Nature Ecology & Evolution

Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain

(2016) Fumiaki Sugahara et al.   NATURE

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

(2015) Yuichiro Hara et al.   BMC GENOMICS

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

(2015) Jeramiah J. Smith et al.   GENOME RESEARCH

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Enigmatic Orthology Relationships between Hox Clusters of the African Butterfly Fish and Other Teleosts Following Ancient Whole-Genome Duplication

(2014) Kyle J. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates

(2014) Hugo J. Parker et al.   NATURE

On the optimal trimming of high-throughput mRNA sequence data

(2014) Matthew D. MacManes   Frontiers in Genetics

Evolution of Hox gene clusters in deuterostomes

(2013) Juan Pascual-Anaya et al.   BMC DEVELOPMENTAL BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum)

(2013) T. K. Mehta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of asymmetric gene repertoire between cyclostomes and gnathostomes

(2013) Shigehiro Kuraku   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods

(2012) Marc Sultan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Genetic Consequences of Programmed Genome Rearrangement

(2012) Jeramiah J. Smith et al.   CURRENT BIOLOGY

Craniofacial development of hagfishes and the evolution of vertebrates

(2012) Yasuhiro Oisi et al.   NATURE

Broken colinearity of the amphioxus Hox cluster

(2012) Juan Pascual-Anaya et al.   EvoDevo

Evolution of repeated structures along the body axis of jawed vertebrates, insights from the Scyliorhinus canicula Hox code

(2011) Silvan Oulion et al.   EVOLUTION & DEVELOPMENT

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

2R or not 2R is not the question anymore

(2010) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Unexpectedly large number of conserved noncoding regions within the ancestral chordate Hox cluster

(2008) Juan Pascual-Anaya et al.   DEVELOPMENT GENES AND EVOLUTION

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

(2008) L. Z. Holland et al.   GENOME RESEARCH

The amphioxusHox cluster: characterization, comparative genomics, and evolution

(2008) Chris T. Amemiya et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Timing of Genome Duplications Relative to the Origin of the Vertebrates: Did Cyclostomes Diverge before or after?

(2008) S. Kuraku et al.   MOLECULAR BIOLOGY AND EVOLUTION

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

Noncanonical role of Hox14 revealed by its expression patterns in lamprey and shark

(2008) S. Kuraku et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA