Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Developing a community-based genetic nomenclature for anole lizards

(2011) Kenro Kusumi et al.   BMC GENOMICS

Somitogenesis in the anole lizard and alligator reveals evolutionary convergence and divergence in the amniote segmentation clock

(2011) Walter L. Eckalbar et al.   DEVELOPMENTAL BIOLOGY

CONVERGENT EVOLUTION OF PHENOTYPIC INTEGRATION AND ITS ALIGNMENT WITH MORPHOLOGICAL DIVERSIFICATION IN CARIBBEAN ANOLIS ECOMORPHS

(2011) Jason J. Kolbe et al.   EVOLUTION

The Anolis Lizard Genome: An Amniote Genome without Isochores

(2011) Matthew K. Fujita et al.   Genome Biology and Evolution

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Relationships among reproductive morphology, behavior, and testosterone in a natural population of green anole lizards

(2011) Michele A. Johnson et al.   PHYSIOLOGY & BEHAVIOR

Evolutionary Genomics Implies a Specific Function of Ant4 in Mammalian and Anole Lizard Male Germ Cells

(2011) Chae Ho Lim et al.   PLoS One

Repeated modification of early limb morphogenesis programmes underlies the convergence of relative limb length in Anolis lizards

(2011) T. J. Sanger et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Creating a Buzz About Insect Genomes

(2011) G. E. Robinson et al.   SCIENCE

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

The Evolution and Diversity of DNA Transposons in the Genome of the Lizard Anolis carolinensis

(2010) Peter A. Novick et al.   Genome Biology and Evolution

Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor

(2010) D.E. Janes et al.   Genome Biology and Evolution

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Behavioural display systems across nine Anolis lizard species: sexual dimorphisms in structure and function

(2010) M. A. Johnson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

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

Reptilian heart development and the molecular basis of cardiac chamber evolution

(2009) Kazuko Koshiba-Takeuchi et al.   NATURE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

(2008) Yingjia Shen et al.   NUCLEIC ACIDS RESEARCH

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Brian J Haas et al.   GENOME BIOLOGY