Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata

Synonymous mutation of miR396a target sites in Growth Regulating Factor 15 (GRF15) enhances photosynthetic efficiency and heat tolerance in poplar

(2021) Yiyang Zhao et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide role of codon usage on transcription and identification of potential regulators

(2021) Fangzhou Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

(2021) Ammar Zaghlool et al.   Scientific Reports

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

USP15: a review of its implication in immune and inflammatory processes and tumor progression

(2021) Anna Georges et al.   GENES AND IMMUNITY

Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid abalone

(2021) Qizhen Xiao et al.   BMC GENOMICS

Microhabitat temperature variation combines with physiological variation to enhance thermal resilience of the intertidal mussel Mytilisepta virgata

(2021) Xiao‐xu Li et al.   FUNCTIONAL ECOLOGY

An integrated, multi‐level analysis of thermal effects on intertidal molluscs for understanding species distribution patterns

(2021) Yun‐wei Dong et al.   BIOLOGICAL REVIEWS

Thermal adaptation of mRNA secondary structure: stability versus lability

(2021) Ming-ling Liao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitophagy: Molecular Mechanisms, New Concepts on Parkin Activation and the Emerging Role of AMPK/ULK1 Axis

(2021) Roberto Iorio et al.   Cells

Expression level is a major modifier of the fitness landscape of a protein coding gene

(2021) Zhuoxing Wu et al.   Nature Ecology & Evolution

Distinguishing between active plasticity due to thermal acclimation and passive plasticity due to Q 10 effects: Why methodology matters

(2020) Justin C. Havird et al.   FUNCTIONAL ECOLOGY

The effects of cold stress on Mytilus species in the natural environment

(2020) Andrey Victorovich Boroda et al.   CELL STRESS & CHAPERONES

Effects of balancing selection and microhabitat temperature variations on heat tolerance of the intertidal black mussel Septifer virgatus

(2020) Guodong Han et al.   Integrative Zoology

Genotype-environment interactions rule the response of a widespread butterfly to temperature variation

(2020) Franziska Günter et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Living on the upper intertidal mudflat: Different behavioral and physiological responses to high temperature between two sympatric cerithidea snails with divergent habitat-use strategies

(2020) Xiao-xu Li et al.   MARINE ENVIRONMENTAL RESEARCH

Correlation between intermediary metabolism, Hsp gene expression, and oxidative stress-related proteins in long-term thermal-stressed Mytilus galloprovincialis

(2020) Konstantinos Feidantsis et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

SMART: recent updates, new developments and status in 2020

(2020) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Nonsynonymous, synonymous and nonsense mutations in human cancer-related genes undergo stronger purifying selections than expectation

(2019) Duan Chu et al.   BMC CANCER

QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

(2019) David B. Lowry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The distribution of fitness effects among synonymous mutations in a gene under directional selection

(2019) Eleonore Lebeuf-Taylor et al.   eLife

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

Natural selection on the Arabidopsis thaliana genome in present and future climates

(2019) Moises Exposito-Alonso et al.   NATURE

OUP accepted manuscript

(2018)   BIOINFORMATICS

Life in the intertidal: Cellular responses, methylation and epigenetics

(2018) Melody S. Clark et al.   FUNCTIONAL ECOLOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Synthesizing the role of epigenetics in the response and adaptation of species to climate change in freshwater ecosystems

(2018) Guilherme Jeremias et al.   MOLECULAR ECOLOGY

The optimization of mRNA expression level by its intrinsic properties—Insights from codon usage pattern and structural stability of mRNA

(2018) Manish P. Victor et al.   GENOMICS

Biologists ignore ocean weather at their peril

(2018) Amanda E. Bates et al.   NATURE

Divergence and plasticity shape adaptive potential of the Pacific oyster

(2018) Li Li et al.   Nature Ecology & Evolution

Genetic adaptation as a biological buffer against climate change: potential and limitations

(2017) Luc De Meester et al.   Integrative Zoology

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Codon-Resolution Analysis Reveals a Direct and Context-Dependent Impact of Individual Synonymous Mutations on mRNA Level

(2017) Siyu Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Untangling the roles of microclimate, behaviour and physiological polymorphism in governing vulnerability of intertidal snails to heat stress

(2017) Yun-wei Dong et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium

(2016) Deepa Agashe et al.   MOLECULAR BIOLOGY AND EVOLUTION

Role of mRNA structure in the control of protein folding

(2016) Guilhem Faure et al.   NUCLEIC ACIDS RESEARCH

Codon usage is an important determinant of gene expression levels largely through its effects on transcription

(2016) Zhipeng Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11

(2015) Caitlyn Vlasschaert et al.   BMC EVOLUTIONARY BIOLOGY

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Analysis of synonymous codon usage patterns in sixty-four different bivalve species

(2015) Marco Gerdol et al.   PeerJ

Heat stress induced apoptosis is triggered by transcription-independent p53, Ca2+ dyshomeostasis and the subsequent Bax mitochondrial translocation

(2015) Z. T. Gu et al.   Scientific Reports

The deubiquitinase USP15 antagonizes Parkin-mediated mitochondrial ubiquitination and mitophagy

(2014) Tom Cornelissen et al.   HUMAN MOLECULAR GENETICS

Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo

(2014) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Heat Stress Induces Apoptosis through a Ca2+-Mediated Mitochondrial Apoptotic Pathway in Human Umbilical Vein Endothelial Cells

(2014) Li Li et al.   PLoS One

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

(2014) Susan F. Bailey et al.   Nature Communications

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

(2013) Mian Zhou et al.   NATURE

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

(2013) S. A. Shabalina et al.   NUCLEIC ACIDS RESEARCH

Silent Substitutions Predictably Alter Translation Elongation Rates and Protein Folding Efficiencies

(2012) Paige S. Spencer et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

The Physiology of Global Change: Linking Patterns to Mechanisms

(2011) George N. Somero   Annual Review of Marine Science

Side matters: Microhabitat influence on intertidal heat stress over a large geographical scale

(2011) Rui Seabra et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Robolimpets: measuring intertidal body temperatures using biomimetic loggers

(2011) Fernando P. Lima et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Variations in cardiac performance and heat shock protein expression to thermal stress in two differently zoned limpets on a tropical rocky shore

(2011) Yun-wei Dong et al.   MARINE BIOLOGY

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

(2009) S. A. Bustin et al.   CLINICAL CHEMISTRY

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION