Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa

Differential transcriptomic analyses revealed genes and signaling pathways involved in iono-osmoregulation and cellular remodeling in the gills of euryhaline Mozambique tilapia, Oreochromis mossambicus

(2014) Siew Lam et al.   BMC GENOMICS

Climate change, adaptation, and phenotypic plasticity: the problem and the evidence

(2014) Juha Merilä et al.   Evolutionary Applications

Air breathing in Magadi tilapiaAlcolapia grahami, under normoxic and hyperoxic conditions, and the association with sunlight and reactive oxygen species

(2014) O. E. Johannsson et al.   JOURNAL OF FISH BIOLOGY

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

The Impacts of Read Length and Transcriptome Complexity for De Novo Assembly: A Simulation Study

(2014) Zheng Chang et al.   PLoS One

InvestigatinghspGene Expression in Liver ofChanna striatusunder Heat Stress for Understanding the Upper Thermal Acclimation

(2014) Gopal Krishna Purohit et al.   Biomed Research International

Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake

(2013) Jian Xu et al.   BMC GENOMICS

Transcriptomics of morphological color change in polychromatic Midas cichlids

(2013) Frederico Henning et al.   BMC GENOMICS

FUNCTIONAL AND POPULATION GENOMIC DIVERGENCE WITHIN AND BETWEEN TWO SPECIES OF KILLIFISH ADAPTED TO DIFFERENT OSMOTIC NICHES

(2013) Genevieve M. Kozak et al.   EVOLUTION

Evolution of the Correlation between Expression Divergence and Protein Divergence in Mammals

(2013) Maria Warnefors et al.   Genome Biology and Evolution

Pronounced genetic differentiation of small, isolated and fragmented tilapia populations inhabiting the Magadi Soda Lake in Kenya

(2013) Geraldine D. Kavembe et al.   HYDROBIOLOGIA

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation

(2013) Jian Xu et al.   PLoS One

Adaptive phenotypic plasticity and local adaptation for temperature tolerance in freshwater zooplankton

(2013) L. Y. Yampolsky et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq

(2013) BingXin Lu et al.   Science China-Life Sciences

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Augmenting transcriptome assembly by combiningde novoand genome-guided tools

(2013) Prachi Jain et al.   PeerJ

Designing a transcriptome next-generation sequencing project for a nonmodel plant species1

(2012) Susan R. Strickler et al.   AMERICAN JOURNAL OF BOTANY

Evolution in response to climate change: In pursuit of the missing evidence

(2012) Juha Merilä   BIOESSAYS

Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel

(2012) Jose Pujolar et al.   BMC GENOMICS

Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome

(2012) Joanna L Kelley et al.   BMC GENOMICS

Adaptation of teleosts to very high salinity

(2012) Gary Laverty et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

The evolution of salinity tolerance inDaphnia: a functional genomics approach

(2012) Leigh C. Latta et al.   ECOLOGY LETTERS

Adaptive responses in resurgent Lake Victoria cichlids over the past 30 years

(2012) Jacco C. van Rijssel et al.   EVOLUTIONARY ECOLOGY

Evolution at Two Levels in Fire Ants: The Relationship between Patterns of Gene Expression and Protein Sequence Evolution

(2012) B. G. Hunt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Comparative studies of gene expression and the evolution of gene regulation

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

Genetic Divergence between Freshwater and Marine Morphs of Alewife (Alosa pseudoharengus): A ‘Next-Generation’ Sequencing Analysis

(2012) Sergiusz Czesny et al.   PLoS One

New insights into the many functions of carbonic anhydrase in fish gills

(2012) Kathleen M. Gilmour   RESPIRATORY PHYSIOLOGY & NEUROBIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

(2011) Geng Chen et al.   BMC GENOMICS

Global Transcriptome Analysis of Constitutive Resistance to the White Pine Weevil in Spruce

(2011) Sébastien Verne et al.   Genome Biology and Evolution

Transepithelial potential in the Magadi tilapia, a fish living in extreme alkalinity

(2011) Chris M. Wood et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

The physiology of hyper-salinity tolerance in teleost fish: a review

(2011) R. J. Gonzalez   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Genomic approaches with natural fish populations

(2010) M. F. Oleksiak   JOURNAL OF FISH BIOLOGY

Niche Dimensions in Fishes: An Integrative View

(2010) H. O. Pörtner et al.   PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY

Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory

(2010) Luis-Miguel Chevin et al.   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation

(2009) R. LANDE   JOURNAL OF EVOLUTIONARY BIOLOGY

Carbonic anhydrase and acid-base regulation in fish

(2009) K. M. Gilmour et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

A new paradigm for ammonia excretion in aquatic animals: role of Rhesus (Rh) glycoproteins

(2009) P. A. Wright et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genomic analysis of cichlid fish ‘natural mutants’

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

A microarray-based transcriptomic time-course of hyper- and hypo-osmotic stress signaling events in the euryhaline fish Gillichthys mirabilis: osmosensors to effectors

(2008) T. G. Evans et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Transcriptional responses of the black-chinned tilapia Sarotherodon melanotheron to salinity extremes

(2008) Mbaye Tine et al.   Marine Genomics

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS