Published in BMC Genomics on June 05, 2013
Temperature-induced variation in gene expression burst size in metazoan cells. BMC Mol Biol (2015) 1.38
Using genomics to characterize evolutionary potential for conservation of wild populations. Evol Appl (2014) 1.07
RNA-Seq technology and its application in fish transcriptomics. OMICS (2013) 1.02
Biological invasions, climate change and genomics. Evol Appl (2014) 0.95
Genomics: moving behavioural ecology beyond the phenotypic gambit. Anim Behav (2014) 0.85
Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line. Cell Stress Chaperones (2015) 0.85
Transcriptome and Molecular Pathway Analysis of the Hepatopancreas in the Pacific White Shrimp Litopenaeus vannamei under Chronic Low-Salinity Stress. PLoS One (2015) 0.83
The environmental genomics of metazoan thermal adaptation. Heredity (Edinb) (2015) 0.82
De novo transcriptome sequencing of the snail Echinolittorina malaccana: identification of genes responsive to thermal stress and development of genetic markers for population studies. Mar Biotechnol (NY) (2014) 0.82
Transcriptome Analysis of the Hepatopancreas in the Pacific White Shrimp (Litopenaeus vannamei) under Acute Ammonia Stress. PLoS One (2016) 0.81
Comparative Transcriptome Analysis in the Hepatopancreas Tissue of Pacific White Shrimp Litopenaeus vannamei Fed Different Lipid Sources at Low Salinity. PLoS One (2015) 0.81
De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PLoS One (2016) 0.81
RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout. PLoS One (2014) 0.80
Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake. BMC Genomics (2013) 0.79
RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation. BMC Genomics (2016) 0.78
The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes. Evol Appl (2016) 0.78
Transciptomic and histological analysis of hepatopancreas, muscle and gill tissues of oriental river prawn (Macrobrachium nipponense) in response to chronic hypoxia. BMC Genomics (2015) 0.77
In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata). BMC Genomics (2014) 0.76
Gene Expression Reaction Norms Unravel the Molecular and Cellular Processes Underpinning the Plastic Phenotypes of Alternanthera Philoxeroides in Contrasting Hydrological Conditions. Front Plant Sci (2015) 0.75
Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus). Int J Mol Sci (2016) 0.75
Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection. Genes (Basel) (2017) 0.75
Transcriptomic analyses on muscle tissues of Litopenaeus vannamei provide the first profile insight into the response to low temperature stress. PLoS One (2017) 0.75
Transcriptional mechanisms underlying life-history responses to climate change in the three-spined stickleback. Evol Appl (2017) 0.75
Transcriptional response to heat shock in liver of snow trout (Schizothorax richardsonii)-a vulnerable Himalayan Cyprinid fish. Funct Integr Genomics (2016) 0.75
Protein analysis and gene expression indicate differential vulnerability of Iberian fish species under a climate change scenario. PLoS One (2017) 0.75
Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species. Sci Rep (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics (2005) 46.40
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
The heat-shock proteins. Annu Rev Genet (1988) 22.28
A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform (2010) 18.05
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (2012) 9.68
Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res (2010) 4.18
Molecular and evolutionary basis of the cellular stress response. Annu Rev Physiol (2005) 3.85
Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) (2010) 3.22
A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data. Am J Bot (2012) 2.44
Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing. BMC Genomics (2012) 2.19
Liver damage in heatstroke. Am J Med (1970) 1.81
Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Mol Ecol (2012) 1.69
Transcriptome sequencing and de novo analysis for Ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform. PLoS One (2012) 1.51
Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient. Mol Ecol (2008) 1.50
Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus. Proc Natl Acad Sci U S A (1989) 1.44
Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. BMC Genomics (2012) 1.38
Aging reduces adaptive capacity and stress protein expression in the liver after heat stress. J Appl Physiol (1985) (2000) 1.27
The consequences of phenotypic plasticity for ecological speciation. J Evol Biol (2010) 1.23
Ecological genomics: understanding gene and genome function in the natural environment. Heredity (Edinb) (2007) 1.19
Regulation of heat shock genes in isolated hepatocytes from an Antarctic fish, Trematomus bernacchii. J Exp Biol (2004) 1.18
The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein-level analysis. J Exp Biol (2006) 1.15
The transcriptomics of life-history trade-offs in whitefish species pairs (Coregonus sp.). Mol Ecol (2008) 1.13
Heat- and cold-inducible regulation of HSP70 expression in zebrafish ZF4 cells. Comp Biochem Physiol B Biochem Mol Biol (2003) 1.07
Tissue-specific HSP70 response in animals undergoing heat stress. Am J Physiol (1995) 1.07
From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis. BMC Genomics (2007) 1.04
Transcriptomic characterization of temperature stress responses in larval zebrafish. PLoS One (2012) 1.00
The genetic consequences of spatially varying selection in the panmictic American eel (Anguilla rostrata). Genetics (2011) 1.00
Landscape genetic analyses reveal cryptic population structure and putative selection gradients in a large-scale estuarine environment. Mol Ecol (2008) 1.00
Heat shock genes and the heat shock response in zebrafish embryos. Biochem Cell Biol (1997) 0.99
De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing. PLoS One (2012) 0.99
Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish. Mol Ecol (2007) 0.97
De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus). BMC Genomics (2012) 0.96
RNA-Seq reveals complex genetic response to Deepwater Horizon oil release in Fundulus grandis. BMC Genomics (2012) 0.93
Effects of thermal acclimation on transcriptional responses to acute heat stress in the eurythermal fish Gillichthys mirabilis (Cooper). Am J Physiol Regul Integr Comp Physiol (2011) 0.93
Transcriptome responses to heat stress in the nucleated red blood cells of the rainbow trout (Oncorhynchus mykiss). Physiol Genomics (2010) 0.93
Identification of genes associated with heat tolerance in Arctic charr exposed to acute thermal stress. Physiol Genomics (2011) 0.92
Thermal acclimation changes DNA-binding activity of heat shock factor 1 (HSF1) in the goby Gillichthys mirabilis: implications for plasticity in the heat-shock response in natural populations. J Exp Biol (2002) 0.91
Characterization of the heat shock response in mature zebrafish (Danio rerio). Exp Gerontol (2003) 0.91
Natural selection in the water: freshwater invasion and adaptation by water colour in the Amazonian pufferfish. J Evol Biol (2012) 0.90
Transcriptional responses to thermal acclimation in the eurythermal fish Gillichthys mirabilis (Cooper 1864). Am J Physiol Regul Integr Comp Physiol (2010) 0.89
Influence of temperature on Drosophila alcohol dehydrogenase polymorphism. J Hered (1974) 0.88
Tissue-specific expression of zebrafish (Danio rerio) heat shock factor 1 mRNAs in response to heat stress. J Exp Biol (2000) 0.87
Heat stress-induced heat shock protein 70 expression is dependent on ERK activation in zebrafish (Danio rerio) cells. Comp Biochem Physiol A Mol Integr Physiol (2008) 0.87
What is needed for next-generation ecological and evolutionary genomics? Trends Ecol Evol (2012) 0.85
Retracted Characterization of the spotted seal Phoca largha transcriptome using Illumina paired-end sequencing and development of SSR markers. Comp Biochem Physiol Part D Genomics Proteomics (2012) 0.83
Ribosomal genes and heat shock proteins as putative markers for chronic, sublethal heat stress in Arctic charr: applications for aquaculture and wild fish. Physiol Genomics (2011) 0.82
Multigeneration assessment of nonylphenol and endosulfan using a model Australian freshwater fish, Melanotaenia fluviatilis. Environ Toxicol (2008) 0.80
The efficacy of the aquatic anaesthetic AQUI-S for anaesthesia of a small freshwater fish, Melanotaenia australis. J Fish Biol (2009) 0.76
Oceanic spawning migration of the European eel (Anguilla anguilla). Science (2009) 2.55
Identifying Canadian freshwater fishes through DNA barcodes. PLoS One (2008) 2.49
Generic scan using AFLP markers as a means to assess the role of directional selection in the divergence of sympatric whitefish ecotypes. Mol Biol Evol (2004) 2.15
All roads lead to home: panmixia of European eel in the Sargasso Sea. Mol Ecol (2011) 2.03
AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites. Mol Ecol (2003) 1.91
Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Mol Ecol (2010) 1.71
Natural hybrids in Atlantic eels (Anguilla anguilla, A. rostrata): evidence for successful reproduction and fluctuating abundance in space and time. Mol Ecol (2006) 1.66
Population genetics of the American eel (Anguilla rostrata): FST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species. Mol Ecol (2012) 1.59
Differential reproductive success and heritability of alternative reproductive tactics in wild Atlantic salmon (Salmo salar L.). Evolution (2003) 1.54
SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar). Mol Ecol (2012) 1.51
Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multilocus analysis surpasses genome scan. Mol Ecol (2014) 1.44
Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems. Mol Ecol (2007) 1.43
Genetic calibration of species diversity among North America's freshwater fishes. Proc Natl Acad Sci U S A (2011) 1.41
Evolutionary change in human-altered environments. Mol Ecol (2008) 1.40
Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics (2010) 1.39
Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon. Mol Ecol (2006) 1.38
Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise. Proc Natl Acad Sci U S A (2008) 1.36
Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation. Mol Ecol (2008) 1.34
Clinal variation in MHC diversity with temperature: evidence for the role of host-pathogen interaction on local adaptation in Atlantic salmon. Evolution (2007) 1.34
Genetic consequences of interbreeding between farmed and wild Atlantic salmon: insights from the transcriptome. Mol Ecol (2008) 1.32
Oceanic variability and coastal topography shape genetic structure in a long-dispersing sea urchin. Ecology (2007) 1.25
Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling. PLoS One (2012) 1.21
Consequences of unequal population size, asymmetric gene flow and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis). Mol Ecol (2004) 1.21
Decline of North Atlantic eels: a fatal synergy? Proc Biol Sci (2003) 1.20
Phylogeographic history and gene flow among giant Galápagos tortoises on southern Isabela Island. Genetics (2005) 1.18
Adaptive divergence between freshwater and marine sticklebacks: insights into the role of phenotypic plasticity from an integrated analysis of candidate gene expression. Evolution (2009) 1.17
The rise and fall of isolation by distance in the anadromous brook charr (Salvelinus fontinalis Mitchill). Genetics (2003) 1.15
Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change? Mol Ecol (2012) 1.15
The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing. Evolution (2013) 1.15
Lonesome George is not alone among Galápagos tortoises. Curr Biol (2007) 1.13
High genetic diversity and no inbreeding in the endangered copper redhorse, Moxostoma hubbsi (Catostomidae, Pisces): the positive sides of a long generation time. Mol Ecol (2006) 1.12
Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia's arid zone, the golden perch (Macquaria ambigua). Mol Ecol (2010) 1.11
MHC standing genetic variation and pathogen resistance in wild Atlantic salmon. Philos Trans R Soc Lond B Biol Sci (2009) 1.11
Adaptive migratory divergence among sympatric brook charr populations. Evolution (2005) 1.10
MHC adaptive divergence between closely related and sympatric African cichlids. PLoS One (2007) 1.10
The transcriptional landscape of cross-specific hybrids and its possible link with growth in brook charr (Salvelinus fontinalis Mitchill). Genetics (2010) 1.09
Microsatellite markers for the praying mantid Ciulfina rentzi (Liturgusidae). Mol Ecol Resour (2009) 1.09
Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation. BMC Evol Biol (2009) 1.08
The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Mol Ecol (2010) 1.08
Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Mol Ecol (2012) 1.08
Strong and consistent natural selection associated with armour reduction in sticklebacks. Mol Ecol (2011) 1.08
Divergent selection maintains adaptive differentiation despite high gene flow between sympatric rainbow smelt ecotypes (Osmerus mordax Mitchill). Mol Ecol (2003) 1.07
Genetically based phenotype-environment association for swimming behavior in lake whitefish ecotypes (Coregonus clupeaformis Mitchill). Evolution (2002) 1.06
A comparative mitogenomic analysis of the potential adaptive value of Arctic charr mtDNA introgression in brook charr populations (Salvelinus fontinalis Mitchill). Mol Biol Evol (2002) 1.06
Differences in transcription levels among wild, domesticated, and hybrid Atlantic salmon (Salmo salar) from two environments. Mol Ecol (2012) 1.05
Glacial cycles as an allopatric speciation pump in north-eastern American freshwater fishes. Mol Ecol (2012) 1.03
Reduced fitness of Atlantic salmon released in the wild after one generation of captive breeding. Evol Appl (2012) 1.03
DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts. Mol Ecol Resour (2009) 1.02
The phenomics and expression quantitative trait locus mapping of brain transcriptomes regulating adaptive divergence in lake whitefish species pairs (Coregonus sp.). Genetics (2008) 1.01
Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population. Mol Ecol (2010) 1.01
The genetic consequences of spatially varying selection in the panmictic American eel (Anguilla rostrata). Genetics (2011) 1.00
The seabird paradox: dispersal, genetic structure and population dynamics in a highly mobile, but philopatric albatross species. Mol Ecol (2008) 1.00
Landscape genetic analyses reveal cryptic population structure and putative selection gradients in a large-scale estuarine environment. Mol Ecol (2008) 1.00
Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.). Mol Ecol (2012) 0.99
Isolation and characterization of microsatellite markers for Passiflora contracta. Int J Mol Sci (2012) 0.99
Genetic evidence for sex-biased dispersal in resident bottlenose dolphins (Tursiops aduncus). Mol Ecol (2004) 0.98
Genetic evidence for kin aggregation in the intertidal acorn barnacle (Semibalanus balanoides). Mol Ecol (2006) 0.97
Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis). Mol Ecol (2012) 0.97
Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats. Biol Lett (2009) 0.96
Population genomics of wild and laboratory zebrafish (Danio rerio). Mol Ecol (2011) 0.96
A road map for molecular ecology. Mol Ecol (2013) 0.95
Integrative use of spatial, genetic, and demographic analyses for investigating genetic connectivity between migratory, montane, and sedentary caribou herds. Mol Ecol (2007) 0.95
The landscape genetics of yellow perch (Perca flavescens) in a large fluvial ecosystem. Mol Ecol (2008) 0.95
Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish. Mol Biol Evol (2013) 0.94
Genome-wide survey of the gene expression response to saprolegniasis in Atlantic salmon. Mol Immunol (2006) 0.94
Comparative genomics reveals adaptive protein evolution and a possible cytonuclear incompatibility between European and American Eels. Mol Biol Evol (2012) 0.94
Antagonistic effect of indigenous skin bacteria of brook charr (Salvelinus fontinalis) against Flavobacterium columnare and F. psychrophilum. Vet Microbiol (2011) 0.94
Combining next-generation sequencing and online databases for microsatellite development in non-model organisms. Sci Rep (2013) 0.93
A recent shark radiation: molecular phylogeny, biogeography and speciation of wobbegong sharks (family: Orectolobidae). Mol Phylogenet Evol (2009) 0.92
Major disruption of gene expression in hybrids between young sympatric anadromous and resident populations of brook charr (Salvelinus fontinalis Mitchill). J Evol Biol (2009) 0.92
Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Mol Ecol (2012) 0.92
Life history and demographic determinants of effective/census size ratios as exemplified by brown trout (Salmo trutta). Evol Appl (2012) 0.92
Candidate genes and adaptive radiation: insights from transcriptional adaptation to the limnetic niche among coregonine fishes (Coregonus spp., Salmonidae). Mol Biol Evol (2008) 0.91
Fast transcriptional responses to domestication in the brook charr Salvelinus fontinalis. Genetics (2010) 0.91
Geographic variation of multiple paternity in the American lobster, Homarus americanus. Mol Ecol (2005) 0.91
Migratory charr schools exhibit population and kin associations beyond juvenile stages. Mol Ecol (2005) 0.90
Surviving with low genetic diversity: the case of albatrosses. Proc Biol Sci (2007) 0.90
Genetic structure of a recent climate change-driven range extension. Mol Ecol (2010) 0.90
Shifting patterns in genetic control at the embryo-alevin boundary in brook charr. Evolution (2004) 0.89
"Nested" cryptic diversity in a widespread marine ecosystem engineer: a challenge for detecting biological invasions. BMC Evol Biol (2011) 0.89
Coding Gene Single Nucleotide Polymorphism Mapping and Quantitative Trait Loci Detection for Physiological Reproductive Traits in Brook Charr, Salvelinus fontinalis. G3 (Bethesda) (2012) 0.89
Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci. Mol Ecol (2014) 0.88
Parallelism in the oxygen transport system of the lake whitefish: the role of physiological divergence in ecological speciation. Mol Ecol (2012) 0.88
Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon. Mol Ecol (2013) 0.88
RNA-seq reveals transcriptomic shock involving transposable elements reactivation in hybrids of young lake whitefish species. Mol Biol Evol (2014) 0.88
Mate choice for major histocompatibility complex genetic divergence as a bet-hedging strategy in the Atlantic salmon (Salmo salar). Proc Biol Sci (2011) 0.88
Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia). Mol Phylogenet Evol (2012) 0.88
The complete mitochondrial genome of two recently derived species of the fish genus Nannoperca (Perciformes, Percichthyidae). Mol Biol Rep (2011) 0.88
Permanent genetic resources added to Molecular Ecology Resources Database 1 February 2013-31 March 2013. Mol Ecol Resour (2013) 0.88
The influence of gene-environment interactions on GHR and IGF-1 expression and their association with growth in brook charr, Salvelinus fontinalis (Mitchill). BMC Genet (2007) 0.87
Stocking impacts the expression of candidate genes and physiological condition in introgressed brook charr (Salvelinus fontinalis) populations. Evol Appl (2012) 0.87
Landscape genomics in Atlantic salmon (Salmo salar): searching for gene-environment interactions driving local adaptation. Evolution (2013) 0.86
Evolutionary ecotoxicology of wild yellow perch (Perca flavescens) populations chronically exposed to a polymetallic gradient. Aquat Toxicol (2007) 0.86
Tug of war between continental gene flow and rearing site philopatry in a migratory bird: the sex-biased dispersal paradigm reconsidered. Mol Ecol (2009) 0.86
Isolation, characterization, and cross-amplification of microsatellite markers for the Petunia integrifolia (Solanaceae) complex. Am J Bot (2011) 0.85
What is needed for next-generation ecological and evolutionary genomics? Trends Ecol Evol (2012) 0.85
Five cryptic species in the amazonian catfish Centromochlus existimatus identified based on biogeographic predictions and genetic data. PLoS One (2012) 0.85
Does catch and release affect the mating system and individual reproductive success of wild Atlantic salmon (Salmo salar L.)? Mol Ecol (2012) 0.84
Effects of chronic metal exposure on wild fish populations revealed by high-throughput cDNA sequencing. Ecotoxicology (2011) 0.84