Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana , Poeciliidae)

The Evolutionary Ecology of Animals Inhabiting Hydrogen Sulfide–Rich Environments

(2016) Michael Tobler et al.   Annual Review of Ecology Evolution and Systematics

Sulfide exposure results in enhanced sqr transcription through upregulating the expression and activation of HSF1 in echiuran worm Urechis unicinctus

(2016) Xiaolong Liu et al.   AQUATIC TOXICOLOGY

Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide–Rich Environments

(2016) Joanna L. Kelley et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent Substitutions in a Sodium Channel Suggest Multiple Origins of Toxin Resistance in Poison Frogs

(2016) Rebecca D. Tarvin et al.   MOLECULAR BIOLOGY AND EVOLUTION

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress

(2016) Hilary A. Uyhelji et al.   MOLECULAR ECOLOGY

Differentially expressed genes associated with adaptation to different thermal environments in three sympatric CubanAnolislizards

(2016) Hiroshi D. Akashi et al.   MOLECULAR ECOLOGY

The role of isoforms in the evolution of cryptic coloration inPeromyscusmice

(2016) Ricardo Mallarino et al.   MOLECULAR ECOLOGY

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

(2016) N. M. Reid et al.   SCIENCE

Starvation resistance and tissue-specific gene expression of stress-related genes in a naturally inbred ant population

(2016) Nick Bos et al.   Royal Society Open Science

Transcriptomic response to heat stress among ecologically divergent populations of redband trout

(2015) Shawn R Narum et al.   BMC GENOMICS

Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of TwoOryzaSpecies

(2015) Jie Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)

(2015) Markus Pfenninger et al.   MOLECULAR ECOLOGY

Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions

(2015) Ariel C. Aspiras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons

(2015) Yue Him Wong et al.   Scientific Reports

Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation

(2015) Jingqun Ao et al.   PLoS Genetics

The Molecular Basis of Phenotypic Convergence

(2014) Erica Bree Rosenblum et al.   Annual Review of Ecology Evolution and Systematics

Brain size variation in extremophile fish: local adaptation versus phenotypic plasticity

(2014) C. Eifert et al.   JOURNAL OF ZOOLOGY

Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

(2014) Matthew R. J. Morris et al.   MOLECULAR ECOLOGY

Parallel evolution of cox genes in H2S-tolerant fish as key adaptation to a toxic environment

(2014) Markus Pfenninger et al.   Nature Communications

An intracellular anion channel critical for pigmentation

(2014) Nicholas W Bellono et al.   eLife

Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension

(2014) Gang Wang et al.   Frontiers in Genetics

What is environmental stress? Insights from fish living in a variable environment

(2013) P. M. Schulte   JOURNAL OF EXPERIMENTAL BIOLOGY

Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish

(2013) Fanwei Meng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modeling Gene Expression Evolution with an Extended Ornstein–Uhlenbeck Process Accounting for Within-Species Variation

(2013) Rori V. Rohlfs et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus

(2013) Joshua B. Gross et al.   PLoS One

De Novo Sequencing of Astyanax mexicanus Surface Fish and Pachón Cavefish Transcriptomes Reveals Enrichment of Mutations in Cavefish Putative Eye Genes

(2013) Hélène Hinaux et al.   PLoS One

Circadian rhythms in Mexican blind cavefish Astyanax mexicanus in the lab and in the field

(2013) Andrew Beale et al.   Nature Communications

Tissue-Specific Transcriptomics in the Field Cricket Teleogryllus oceanicus

(2013) Nathan W. Bailey et al.   G3-Genes Genomes Genetics

Gene transcription reflects poor health status of resident European eel chronically exposed to environmental pollutants

(2012) G.E. Maes et al.   AQUATIC TOXICOLOGY

Human Sulfide:Quinone Oxidoreductase Catalyzes the First Step in Hydrogen Sulfide Metabolism and Produces a Sulfane Sulfur Metabolite

(2012) Michael R. Jackson et al.   BIOCHEMISTRY

Balancing noise and plasticity in eukaryotic gene expression

(2012) Djordje Bajić 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

Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

(2012) A. Whitehead   JOURNAL OF EXPERIMENTAL BIOLOGY

Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ

(2012) Giulia Micallef et al.   MARINE BIOTECHNOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Comparative studies of gene expression and the evolution of gene regulation

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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na,K-ATPase

(2012) S. Dobler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrogen Sulfide and Cell Signaling

(2011) Ling Li et al.   Annual Review of Pharmacology and Toxicology

A Practical Look at the Chemistry and Biology of Hydrogen Sulfide

(2011) Kenneth R. Olson   ANTIOXIDANTS & REDOX SIGNALING

Speciation in caves: experimental evidence that permanent darkness promotes reproductive isolation

(2011) R. Riesch et al.   Biology Letters

Hydrogen sulfide, bacteria, and fish: a unique, subterranean food chain

(2011) Katherine A. Roach et al.   ECOLOGY

Assessment of Chemical Mixtures and Groundwater Effects on Daphnia magna Transcriptomics

(2011) Natàlia Garcia-Reyero et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

PARALLEL AND NONPARALLEL ASPECTS OF ECOLOGICAL, PHENOTYPIC, AND GENETIC DIVERGENCE ACROSS REPLICATE POPULATION PAIRS OF LAKE AND STREAM STICKLEBACK

(2011) Renaud Kaeuffer et al.   EVOLUTION

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

An Integrated Multi-Disciplinary Approach for Studying Multiple Stressors in Freshwater Ecosystems: Daphnia as a Model Organism

(2011) Ianina Altshuler et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Transcriptomics of environmental acclimatization and survival in wild adult Pacific sockeye salmon (Oncorhynchus nerka) during spawning migration

(2011) TYLER G. EVANS et al.   MOLECULAR ECOLOGY

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

Common mechanism underlies repeated evolution of extreme pollution tolerance

(2011) A. Whitehead et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Non-additive hepatic gene expression elicited by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and 2,2′,4,4′,5,5′-hexachlorobiphenyl (PCB153) co-treatment in C57BL/6 mice

(2011) Anna K. Kopec et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

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

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

Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event

(2010) Martin Plath et al.   BMC EVOLUTIONARY BIOLOGY

INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCI

(2010) Jay F. Storz et al.   EVOLUTION

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Convergence in pigmentation at multiple levels: mutations, genes and function

(2010) M. Manceau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conflict between Noise and Plasticity in Yeast

(2010) Ben Lehner   PLoS Genetics

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Regressive Evolution inAstyanaxCavefish

(2009) William R. Jeffery   Annual Review of Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

Does a predatory insect contribute to the divergence between cave- and surface-adapted fish populations?

(2009) M. Tobler   Biology Letters

Reduced opsin gene expression in a cave-dwelling fish

(2009) M. Tobler et al.   Biology Letters

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Matrotrophy in the cave molly: an unexpected provisioning strategy in an extreme environment

(2009) Rüdiger Riesch et al.   EVOLUTIONARY ECOLOGY

Natural and sexual selection against immigrants maintains differentiation among micro-allopatric populations

(2009) M. TOBLER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Molecular and functional basis of phenotypic convergence in white lizards at White Sands

(2009) E. B. Rosenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the Origin and Spread of an Adaptive Allele in Deer Mice

(2009) C. R. Linnen et al.   SCIENCE

Interactions between effects of environmental chemicals and natural stressors: A review

(2009) Martin Holmstrup et al.   SCIENCE OF THE TOTAL ENVIRONMENT

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Coping style and immunity in animals: Making sense of individual variation

(2008) J.M. Koolhaas   BRAIN BEHAVIOR AND IMMUNITY

The Meter of Metabolism

(2008) Carla B. Green et al.   CELL

Epibiotic bacteria associated with the recently discovered Yeti crab, Kiwa hirsuta

(2008) Shana K. Goffredi et al.   ENVIRONMENTAL MICROBIOLOGY

TOXIC HYDROGEN SULFIDE AND DARK CAVES: PHENOTYPIC AND GENETIC DIVERGENCE ACROSS TWO ABIOTIC ENVIRONMENTAL GRADIENTS INPOECILIA MEXICANA

(2008) Michael Tobler et al.   EVOLUTION

Three enzymatic activities catalyze the oxidation of sulfide to thiosulfate in mammalian and invertebrate mitochondria

(2008) Tatjana M. Hildebrandt et al.   FEBS Journal

The inhibition of mitochondrial cytochrome oxidase by the gases carbon monoxide, nitric oxide, hydrogen cyanide and hydrogen sulfide: chemical mechanism and physiological significance

(2008) Chris E. Cooper et al.   JOURNAL OF BIOENERGETICS AND BIOMEMBRANES

Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient

(2008) ZACHARY A. CHEVIRON et al.   MOLECULAR ECOLOGY

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS