The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation

Comparative transcriptomics of anal fin pigmentation patterns in cichlid fishes

(2016) M. Emília Santos et al.   BMC GENOMICS

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

(2016) Elaina M. Tuttle et al.   CURRENT BIOLOGY

Signalling pathways in trophic skeletal development and morphogenesis: Insights from studies on teleost fish

(2016) Ehsan Pashay Ahi   DEVELOPMENTAL BIOLOGY

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes

(2016) Kevin J. Parsons et al.   MOLECULAR ECOLOGY

Accumulation of transposable elements inHoxgene clusters during adaptive radiation ofAnolislizards

(2016) Nathalie Feiner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A beak size locus in Darwins finches facilitated character displacement during a drought

(2016) S. Lamichhaney et al.   SCIENCE

Adaptive radiation of Darwin's finches revisited using whole genome sequencing

(2015) Markus Sällman Almén et al.   BIOESSAYS

Intron retention in mRNA: No longer nonsense

(2015) Justin J.-L. Wong et al.   BIOESSAYS

A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history

(2015) Bhart-Anjan S. Bhullar et al.   EVOLUTION

An alternative splicing event amplifies evolutionary differences between vertebrates

(2015) S. Gueroussov et al.   SCIENCE

The genomics of organismal diversification illuminated by adaptive radiations

(2015) Daniel Berner et al.   TRENDS IN GENETICS

Form, function and phylogeny: comparative morphometrics of Lake Tanganyika's cichlid tribe Tropheini

(2015) Katrin A. Wanek et al.   ZOOLOGICA SCRIPTA

Constraint and diversification of developmental trajectories in cichlid facial morphologies

(2015) Kara E. Powder et al.   EvoDevo

Nested Levels of Adaptive Divergence: The Genetic Basis of Craniofacial Divergence and Ecological Sexual Dimorphism

(2015) Kevin J. Parsons et al.   G3-Genes Genomes Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Fast adaptive responses in the oral jaw of Lake Victoria cichlids

(2014) Jacco C. van Rijssel et al.   EVOLUTION

Comparative Transcriptomics in East African Cichlids Reveals Sex- and Species-Specific Expression and New Candidates for Sex Differentiation in Fishes

(2014) Astrid Böhne et al.   Genome Biology and Evolution

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Molecular investigation of mechanical strain-induced phenotypic plasticity in the ecologically important pharyngeal jaws of cichlid fish

(2014) H. M. Gunter et al.   JOURNAL OF APPLIED ICHTHYOLOGY

Comparative Transcriptomics of Convergent Evolution: Different Genes but Conserved Pathways Underlie Caste Phenotypes across Lineages of Eusocial Insects

(2014) Ali J. Berens et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Nonsynonymous Mutation in the Transcriptional Regulator lbh Is Associated with Cichlid Craniofacial Adaptation and Neural Crest Cell Development

(2014) Kara E. Powder et al.   MOLECULAR BIOLOGY AND EVOLUTION

Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish

(2014) Ralf F. Schneider et al.   MOLECULAR ECOLOGY

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Cryptic genetic variation: evolution's hidden substrate

(2014) Annalise B. Paaby et al.   NATURE REVIEWS GENETICS

Hedgehog signaling mediates adaptive variation in a dynamic functional system in the cichlid feeding apparatus

(2014) Y. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

The evolution of cichlid fish egg-spots is linked with a cis-regulatory change

(2014) M. Emília Santos et al.   Nature Communications

The cavefish genome reveals candidate genes for eye loss

(2014) Suzanne E. McGaugh et al.   Nature Communications

Transcriptomics of morphological color change in polychromatic Midas cichlids

(2013) Frederico Henning et al.   BMC GENOMICS

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

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Drift and conservation of differential exon usage across tissues in primate species

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation

(2011) Moritz Muschick et al.   BMC EVOLUTIONARY BIOLOGY

Functional and Genetic Integration in the Skulls of Lake Malawi Cichlids

(2011) W. James Cooper et al.   Evolutionary Biology

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

(2011) Jessica Alföldi et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Craniofacial divergence and ongoing adaptation via the hedgehog pathway

(2011) Reade B. Roberts et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two developmental modules establish 3D beak-shape variation in Darwin's finches

(2011) R. Mallarino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Gene expression patterns in bone following mechanical loading

(2010) Sara M Mantila Roosa et al.   JOURNAL OF BONE AND MINERAL RESEARCH

MorphoJ: an integrated software package for geometric morphometrics

(2010) CHRISTIAN PETER KLINGENBERG   Molecular Ecology Resources

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Bentho-Pelagic Divergence of Cichlid Feeding Architecture Was Prodigious and Consistent during Multiple Adaptive Radiations within African Rift-Lakes

(2010) W. James Cooper et al.   PLoS One

Phenotypic plasticity's impacts on diversification and speciation

(2010) David W. Pfennig et al.   TRENDS IN ECOLOGY & EVOLUTION

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Roles for Bmp4 and CaM1 in Shaping the Jaw: Evo-Devo and Beyond

(2009) Kevin J. Parsons et al.   Annual Review of Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini

(2009) Stephan Koblmüller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Genomic screening identifies novel linkages and provides further evidence for a role of MYH9 in nonsyndromic cleft lip and palate

(2008) Brett T Chiquet et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS