Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution

Search and sequence analysis tools services from EMBL-EBI in 2022

(2022) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Genomics Reveals Multiple Functions of Arylalkylamine N-Acetyltransferase in Fish

(2022) Yu Huang et al.   Frontiers in Genetics

EFR3 and phosphatidylinositol 4-kinase IIIα regulate insulin-stimulated glucose transport and GLUT4 dispersal in 3T3-L1 adipocytes

(2022) Anna M. Koester et al.   BIOSCIENCE REPORTS

Hypoxia controls plasma membrane targeting of polarity proteins by dynamic turnover of PI4P and PI(4,5)P2

(2022) Juan Lu et al.   eLife

The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes

(2021) Vid Bakovic et al.   MOLECULAR ECOLOGY

Collecting eco‐evolutionary data in the dark: Impediments to subterranean research and how to overcome them

(2021) Stefano Mammola et al.   Ecology and Evolution

Repeated evolution of circadian clock dysregulation in cavefish populations

(2021) Katya L. Mack et al.   PLoS Genetics

Phylogenetic Analysis of Core Melanin Synthesis Genes Provides Novel Insights Into the Molecular Basis of Albinism in Fish

(2021) Chao Bian et al.   Frontiers in Genetics

From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods

(2021) Hans Recknagel et al.   BIOSCIENCE

Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System

(2021) Elvira Lafuente et al.   Frontiers in Ecology and Evolution

Astyanax surface and cave fish morphs

(2020) William R. Jeffery   EvoDevo

Systemic paralogy and function of retinal determination network homologs in arachnids

(2020) Guilherme Gainett et al.   BMC GENOMICS

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus

(2019) Joshua B. Gross et al.   Genes

CRISPR mutagenesis confirms the role of oca2 in melanin pigmentation in Astyanax mexicanus

(2018) Hannah Klaassen et al.   DEVELOPMENTAL BIOLOGY

Common Genetic Basis of Eye and Pigment Loss in Two Distinct Cave Populations of the Isopod Crustacean Asellus aquaticus

(2018) Cassandra Re et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Transcriptomic Insights into the Loss of Vision in Molnár János Cave’s Crustaceans

(2018) Jorge L Pérez-Moreno et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Regulation of PI4P levels by PI4KIIIα during G-protein coupled PLC signaling inDrosophilaphotoreceptors

(2018) Sruthi S. Balakrishnan et al.   JOURNAL OF CELL SCIENCE

Pygo2 Regulates Adiposity and Glucose Homeostasis via β-Catenin–Axin2–GSK3β Signaling Pathway

(2018) Yuan-Yuan Xie et al.   DIABETES

Embryonic origin and genetic basis of cave associated phenotypes in the isopod crustacean Asellus aquaticus

(2018) Hafasa Mojaddidi et al.   Scientific Reports

Melanization in response to wounding is ancestral in arthropods and conserved in albino cave species

(2017) Helena Bilandžija et al.   Scientific Reports

Life in the Underworld: Anchialine cave biology in the era of speleogenomics

(2016) Jorge Pérez-Moreno et al.   INTERNATIONAL JOURNAL OF SPELEOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

NCBI BLAST+ integrated into Galaxy

(2015) Peter J. A. Cock et al.   GigaScience

A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus

(2015) Bethany A. Stahl et al.   PLoS One

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

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms

(2014) Daniel I Speiser et al.   BMC BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

A Potential Benefit of Albinism in Astyanax Cavefish: Downregulation of the oca2 Gene Increases Tyrosine and Catecholamine Levels as an Alternative to Melanin Synthesis

(2013) Helena Bilandžija et al.   PLoS One

EVIDENCE FOR REPEATED LOSS OF SELECTIVE CONSTRAINT IN RHODOPSIN OF AMBLYOPSID CAVEFISHES (TELEOSTEI: AMBLYOPSIDAE)

(2012) Matthew L. Niemiller et al.   EVOLUTION

Evolution of albinism in cave planthoppers by a convergent defect in the first step of melanin biosynthesis

(2012) Helena Bilandžija et al.   EVOLUTION & DEVELOPMENT

Evolution and development in cave animals: from fish to crustaceans

(2012) Meredith Protas et al.   Wiley Interdisciplinary Reviews-Developmental Biology

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Genetic basis of eye and pigment loss in the cave crustacean, Asellus aquaticus

(2011) M. E. Protas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Reduced opsin gene expression in a cave-dwelling fish

(2009) M. Tobler et al.   Biology Letters

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

DrosophilaMutants in Phospholipid Signaling Have Reduced Olfactory Responses as Adults and Larvae

(2008) Pinky Kain et al.   JOURNAL OF NEUROGENETICS