Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes

The Evolutionary Genomics of Cichlid Fishes: Explosive Speciation and Adaptation in the Postgenomic Era

(2014) Frederico Henning et al.   Annual Review of Genomics and Human Genetics

Geographic Mode of Speciation and Genomic Divergence

(2013) Jeffrey L. Feder et al.   Annual Review of Ecology Evolution and Systematics

Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish

(2013) Helen M. Gunter et al.   MOLECULAR ECOLOGY

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

(2013) M. Friedman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MULTOVL: fast multiple overlaps of genomic regions

(2012) A. Aszodi   BIOINFORMATICS

REPRODUCTIVE ISOLATION AND LOCAL ADAPTATION QUANTIFIED FOR A CHROMOSOME INVERSION IN A MALARIA MOSQUITO

(2012) Diego Ayala et al.   EVOLUTION

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

(2012) T. Zichner et al.   GENOME RESEARCH

Origins of Shared Genetic Variation in African Cichlids

(2012) Yong-Hwee E. Loh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks

(2012) PHILINE G. D. FEULNER et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

(2011) Bujie Zhan et al.   BMC GENOMICS

Repeated colonization and hybridization in Lake Malawi cichlids

(2011) Domino A. Joyce et al.   CURRENT BIOLOGY

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

(2011) Felicity C. Jones et al.   CURRENT BIOLOGY

Comparative Transcriptomics of Eastern African Cichlid Fishes Shows Signs of Positive Selection and a Large Contribution of Untranslated Regions to Genetic Diversity

(2011) Laura Baldo et al.   Genome Biology and Evolution

Natural genetic variation caused by small insertions and deletions in the human genome

(2011) R. E. Mills et al.   GENOME RESEARCH

Positive Darwinian Selection Drives the Evolution of the Morphology-Related Gene, EPCAM, in Particularly Species-Rich Lineages of African Cichlid Fishes

(2011) Shaohua Fan et al.   JOURNAL OF MOLECULAR EVOLUTION

Identification and Characterization of Gene Expression Involved in the Coloration of Cichlid Fish Using Microarray and qRT-PCR Approaches

(2011) Helen M. Gunter et al.   JOURNAL OF MOLECULAR EVOLUTION

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages

(2011) S. Fan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags

(2010) Bo-Young Lee et al.   BMC GENOMICS

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Sympatric and Allopatric Divergence of MHC Genes in Threespine Stickleback

(2010) Blake Matthews et al.   PLoS One

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

(2010) David B. Lowry et al.   PLOS BIOLOGY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

CHROMOSOMAL INVERSIONS AND SPECIES DIFFERENCES: WHEN ARE GENES AFFECTING ADAPTIVE DIVERGENCE AND REPRODUCTIVE ISOLATION EXPECTED TO RESIDE WITHIN INVERSIONS?

(2009) Jeffrey L. Feder et al.   EVOLUTION

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Pleistocene desiccation in East Africa bottlenecked but did not extirpate the adaptive radiation of Lake Victoria haplochromine cichlid fishes

(2009) K. R. Elmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Relaxed selection in the wild

(2009) David C. Lahti et al.   TRENDS IN ECOLOGY & EVOLUTION

The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity

(2009) Christopher M. Hofmann et al.   PLOS BIOLOGY

Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs

(2008) Walter Salzburger et al.   BMC GENOMICS

Genomic analysis of cichlid fish ‘natural mutants’

(2008) Shigehiro Kuraku et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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