Comparative transcriptomic analysis of fireflies (Coleoptera: Lampyridae) to explore the molecular adaptations to fresh water

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation

(2018) Zach G. Gayk et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptomic analysis of adaptive mechanisms in response to sudden salinity drop in the mud crab, Scylla paramamosain

(2018) Huan Wang et al.   BMC GENOMICS

Molecular Footprints of Aquatic Adaptation Including Bone Mass Changes in Cetaceans

(2018) Xuming Zhou et al.   Genome Biology and Evolution

Mitochondrial phylogeny, divergence history and high-altitude adaptation of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora ) inhabiting the Tibetan Plateau

(2018) Ming-Long Yuan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene sequence variations and expression patterns of mitochondrial genes are associated with the adaptive evolution of two Gynaephora species (Lepidoptera: Lymantriinae) living in different high-elevation environments

(2017) Qi-Lin Zhang et al.   GENE

Miro1-mediated mitochondrial positioning shapes intracellular energy gradients required for cell migration

(2017) Max-Hinderk Schuler et al.   MOLECULAR BIOLOGY OF THE CELL

Comparative transcriptomic analysis of Tibetan Gynaephora to explore the genetic basis of insect adaptation to divergent altitude environments

(2017) Qi-Lin Zhang et al.   Scientific Reports

Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome

(2017) Xinhua Fu et al.   GigaScience

ATP5B regulates mitochondrial fission and fusion in mammalian cells

(2016) Hyemin Seo et al.   Animal Cells and Systems

Odonata (dragonflies and damselflies) as a bridge between ecology and evolutionary genomics

(2016) Seth Bybee et al.   Frontiers in Zoology

Rates and patterns of molecular evolution in freshwater versus terrestrial insects

(2016) T. Fatima Mitterboeck et al.   GENOME

Genomewide analysis of ABCBs with a focus on ABCB1 and ABCB19 in Malus domestica

(2016) JUAN JUAN MA et al.   JOURNAL OF GENETICS

Transcriptome analysis reveals candidate genes involved in luciferin metabolism inLuciola aquatilis(Coleoptera: Lampyridae)

(2016) Wanwipa Vongsangnak et al.   PeerJ

Habitat-dependent diversification and parallel molecular evolution: Water scavenger beetles as a case study

(2016) Ke-Qing Song et al.   Current Zoology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes

(2015) Vikas Kumar et al.   BMC GENOMICS

Transcriptomic analysis provides insight into high-altitude acclimation in domestic goats

(2015) Qianzi Tang et al.   GENE

Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes

(2015) Ying Wang et al.   Genome Biology and Evolution

The Drosophila Chitinase-Like Protein IDGF3 Is Involved in Protection against Nematodes and in Wound Healing

(2015) Lucie Kucerova et al.   Journal of Innate Immunity

Genetic adaptations of the plateau zokor in high-elevation burrows

(2015) Yong Shao et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Functional characterization of chitinase-3 reveals involvement of chitinases in early embryo immunity in zebrafish

(2014) Zinan Teng et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus

(2014) Liandong Yang et al.   Genome Biology and Evolution

A proteomic screen with Drosophila Opa1-like identifies Hsc70-5/Mortalin as a regulator of mitochondrial morphology and cellular homeostasis

(2014) Shamik Banerjee et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

ATP synthase subunit alpha and LV mass in ischaemic human hearts

(2014) Esther Roselló-Lletí et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

An investigation into environment dependent nanomechanical properties of shallow water shrimp (Pandalus platyceros) exoskeleton

(2014) Devendra Verma et al.   Materials Science & Engineering C-Materials for Biological Applications

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Mitochondrial proteomic analysis reveals the molecular mechanisms underlying reproductive toxicity of zearalenone in MLTC-1 cells

(2014) Yuzhe Li et al.   TOXICOLOGY

Freshwater Biodiversity and Aquatic Insect Diversification

(2013) Klaas-Douwe B. Dijkstra et al.   Annual Review of Entomology

Efficient utilization of aerobic metabolism helps Tibetan locusts conquer hypoxia

(2013) Dejian Zhao et al.   BMC GENOMICS

Minke whale genome and aquatic adaptation in cetaceans

(2013) Hyung-Soon Yim et al.   NATURE GENETICS

Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations

(2013) Xuming Zhou et al.   Nature Communications

HypoxiaDB: a database of hypoxia-regulated proteins

(2013) Pankaj Khurana et al.   Database-The Journal of Biological Databases and Curation

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: A comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris

(2012) Weizhao Yang et al.   BMC GENOMICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Adaptive evolution of energy metabolism genes and the origin of flight in bats

(2010) Y.-Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting signatures of balancing selection to identify targets of anti-parasite immunity

(2010) Gareth D. Weedall et al.   TRENDS IN PARASITOLOGY

Nitric Oxide, Cytochrome C Oxidase, and the Cellular Response to Hypoxia

(2009) Cormac T. Taylor et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Mitochondria of cold hardy insects: Responses to cold and hypoxia assessed at enzymatic, mRNA and DNA levels

(2008) D MCMULLEN et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Domain organization and phylogenetic analysis of proteins from the chitin deacetylase gene family of Tribolium castaneum and three other species of insects

(2008) Radhika Dixit et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

An RNA Interference Screen Identifies a Novel Regulator of Target of Rapamycin That Mediates Hypoxia Suppression of Translation in Drosophila S2 Cells

(2008) Soo-Jung Lee et al.   MOLECULAR BIOLOGY OF THE CELL

Mechanisms Underlying Hypoxia Tolerance in Drosophila melanogaster: hairy as a Metabolic Switch

(2008) Dan Zhou et al.   PLoS Genetics

Flash Signal Evolution, Mate Choice, and Predation in Fireflies

(2007) Sara M. Lewis et al.   Annual Review of Entomology