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2025
Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle
RNA Biology
2025
Predicting the translation efficiency of messenger RNA in mammalian cells
Nature Biotechnology
2025
Acute neuroendocrine challenge elicits enhanced cortisol response and parallel transcriptomic changes in patients with migraine
PAIN Reports
2025
Macroevolutionary divergence of gene expression driven by selection on protein abundance
Science
2025
Perspective: Are Grapes Worthy of the Moniker Superfood?
Journal of Agricultural and Food Chemistry
2025
Body-Wide Expression Profiles of Commonly Assessed Cardiac Biomarkers in a Large Cohort of Human Tissue Donors
Cardiology
2025
Transcription Kinetics in the Coronavirus Life Cycle
WIREs RNA
2025
Gene Signatures and Oncology Treatment Implications
Hematology/Oncology Clinics of North America
2025
Role of resistin in the porcine uterus: effects on endometrial steroidogenesis
Reproduction, Fertility and Development
2025
Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait
Molecular Biology and Evolution
2024
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Genome Biology
2024
Resource allocation in mammalian systems
Biotechnology Advances
2024
Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
Proceedings of the National Academy of Sciences
2024
Replication Study of the Association of GAS6 and PROS1 Polymorphisms with Behçet’s Disease in a Japanese Population
Ocular Immunology and Inflammation
2024
Thiostrepton induces oxidative stress, mitochondrial dysfunction and ferroptosis in HaCaT cells
Cellular Signalling
2023
SPECK: an unsupervised learning approach for cell surface receptor abundance estimation for single-cell RNA-sequencing data
Bioinformatics Advances
2023
Gene expression flux analysis reveals specific regulatory modalities of gene expression
iScience
2023
Uncovering biology by single-cell proteomics
Communications Biology
2023
Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq
Advanced Genetics
2023
Micro and macroevolution of sea anemone venom phenotype
Nature Communications
2023
Environmental Enrichment Increased Bdnf Transcripts in the Prefrontal Cortex: Implications for an Epigenetically Controlled Mechanism
Neuroscience
2023
Molecular responses to acute exercise and their relevance for adaptations in skeletal muscle to exercise training
Physiological Reviews
2023
An integrated proteome and transcriptome of B cell maturation defines poised activation states of transitional and mature B cells
Nature Communications
2023
Discordant skeletal muscle gene and protein responses to exercise
Trends in Biochemical Sciences
2023
MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge
BMC Bioinformatics
2023
Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease
Patterns
2022
The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation
RNA
2022
The Involvement of RAGE and Its Ligands during Progression of ALS in SOD1 G93A Transgenic Mice
International Journal of Molecular Sciences
2022
A critical period of translational control during brain development at codon resolution
Nature Structural & Molecular Biology
2022
False-positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5′ UTR annotations
Proceedings of the National Academy of Sciences
2022
Combinatorial peptides: A library that continuously probes low‐abundance proteins
ELECTROPHORESIS
2022
Vitamin D boosts immune response of macrophages through a regulatory network of microRNAs and mRNAs
The Journal of Nutritional Biochemistry
2022
Consequences of Chromosome Loss: Why Do Cells Need Each Chromosome Twice?
Cells
2022
Experimental reproducibility limits the correlation between mRNA and protein abundances in tumor proteomic profiles
Cell Reports Methods
2022
Regulation of gene expression via translational buffering
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research
2022
Quantification of Intracellular Proteins in Single Cells Based on Engineered Picoliter Droplets
Langmuir
2022
Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles
Nucleic Acids Research
2022
How thermal challenges change gene regulation in the songbird brain and gonad: Implications for sexual selection in our changing world
Molecular Ecology
2022
Sex differences in immune gene expression in the brain of a small shorebird
Immunogenetics
2022
Neuromethods
2022
Day and night isotope labelling reveal metabolic pathway specific regulation of protein synthesis rates in Arabidopsis
The Plant Journal
2022
Interpretation of exercise-induced changes in human skeletal muscle mRNA expression depends on the timing of the post-exercise biopsies
PeerJ
2021
Feasibility of Developing Radiotracers for MDM2: Synthesis and Preliminary Evaluation of an 18F-Labeled Analogue of the MDM2 Inhibitor SP-141
Pharmaceuticals
2021
Proteomic/transcriptomic analysis of erythropoiesis
Current Opinion in Hematology
2021
Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma
PLOS Computational Biology
2021
ALKBH4 promotes tumourigenesis with a poor prognosis in non-small-cell lung cancer
Scientific Reports
2021
Resistance Exercise, Aging, Disuse, and Muscle Protein Metabolism
Comprehensive Physiology
2021
Application of Domain- and Genotype-Specific Models to Infer Post-Transcriptional Regulation of Segmentation Gene Expression in Drosophila
Life
2021
Regulation of mRNA translation in stem cells; links to brain disorders
Cellular Signalling
2021
Transcription factors: Bridge between cell signaling and gene regulation
PROTEOMICS
2021
Comprehensive Physiology
2021
Gene and protein expression in human megakaryocytes derived from induced pluripotent stem cells
Journal of Thrombosis and Haemostasis
2021
Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2021
Multi-omics approaches in cancer research with applications in tumor subtyping, prognosis, and diagnosis
Computational and Structural Biotechnology Journal
2021
Measuring expression heterogeneity of single-cell cytoskeletal protein complexes
Nature Communications
2021
A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them
Cells
2021
Multiplexed Single-Cell Plasmonic Immunoassay of Intracellular Signaling Proteins Enables Non-Destructive Monitoring of Cell Fate
Analytical Chemistry
2020
Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity
Nature Structural & Molecular Biology
2020
Cancer Treatment and Research
2020
The translational landscape of ground state pluripotency
Nature Communications
2020
Timing effciency in small-RNA-regulated post-transcriptional processes
Physical Review E
2020
Insight on Transcriptional Regulation of the Energy Sensing AMPK and Biosynthetic mTOR Pathway Genes
Frontiers in Cell and Developmental Biology
2020
Metabolic labeling of RNA uncovers the contribution of transcription and decay rates on hypoxia-induced changes in RNA levels
RNA
2020
Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes
Nature Communications
2020
The Membrane Protein Sortilin Can Be Targeted to Inhibit Pancreatic Cancer Cell Invasion
The American Journal of Pathology
2020
How Do the Different Proteomic Strategies Cope with the Complexity of Biological Regulations in a Multi-Omic World? Critical Appraisal and Suggestions for Improvements
Proteomes
2020
Deep Proteomic Deconvolution of Interferons and HBV Transfection Effects on a Hepatoblastoma Cell Line
ACS Omega
2020
Recent advances in understanding resistance exercise training-induced skeletal muscle hypertrophy in humans
F1000Research
2020
Midkine: The Who, What, Where, and When of a Promising Neurotrophic Therapy for Perinatal Brain Injury
Frontiers in Neurology
2020
Molecular mechanisms behind mRNA localization in axons
Open Biology
2020
Perspectives on transcriptomics in animal physiology studies
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology
2020
Expression of chemerin and its receptors in the ovaries of prepubertal and mature gilts
Molecular Reproduction and Development
2020
Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks
Cell Reports
2020
Transcription Analysis of the Chemerin Impact on Gene Expression Profile in the Luteal Cells of Gilts
Genes
2020
What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?
Proteomes
2020
NLRP3 inflammasome is involved in nerve recovery after sciatic nerve injury
International Immunopharmacology
2020
Large-scale informatic analysis to algorithmically identify blood biomarkers of neurological damage
Proceedings of the National Academy of Sciences
2020
New Oxford Textbook of Psychiatry
2019
GPCRomics: An Approach to Discover GPCR Drug Targets
Trends in Pharmacological Sciences
2019
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes
Genome Biology
2019
The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis
PLOS ONE
2019
Molecular stressors underlying exercise training‐induced improvements in K+ regulation during exercise and Na+,K+‐ATPase adaptation in human skeletal muscle
Acta Physiologica
2019
GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner
PLOS Genetics
2019
Oncogenic kinases and perturbations in protein synthesis machinery and energetics in neoplasia
Journal of Molecular Endocrinology
2019
Phosphorylation and Signal Transduction Pathways in Translational Control
Cold Spring Harbor Perspectives in Biology
2019
Multi-Omics Strategies Uncover Host–Pathogen Interactions
ACS Infectious Diseases
2019
Modelling and measuring intracellular competition for finite resources during gene expression
Journal of The Royal Society Interface
2019
Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth
PLOS ONE
2019
Variable protein homeostasis in housekeeping and non-housekeeping pathways under mycotoxins stress
Scientific Reports
2019
Proteomic Atlas of the Human Brain in Alzheimer’s Disease
Journal of Proteome Research
2019
Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues
Molecular Systems Biology
2019
Quantitative analysis reveals genotype- and domain- specific differences between mRNA and protein expression of segmentation genes in Drosophila
Developmental Biology
2019
Translational offsetting as a mode of estrogen receptor α‐dependent regulation of gene expression
The EMBO Journal
2019
Is it useful to use several “omics” for obtaining valuable results?
Molecular Biology Reports
2019
Exploiting Interdata Relationships in Next-generation Proteomics Analysis
Molecular & Cellular Proteomics
2019
Big data in yeast systems biology
FEMS Yeast Research
2019
Central dogma rates and the trade-off between precision and economy in gene expression
Nature Communications
2019
Exploring the Diversity and Novelty of Toxin Genes in Naja sumatrana, the Equatorial Spitting Cobra from Malaysia through De Novo Venom-Gland Transcriptomics
Toxins
2019
Analyzing the stability of gene expression using a simple reaction-diffusion model in an early Drosophila embryo
Mathematical Biosciences
2019
Translational Control in Stem Cells
Frontiers in Genetics
2019
Generally applicable transcriptome-wide analysis of translation using anota2seq
Nucleic Acids Research
2019
GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors
PLOS Biology
2019
Poor transcript‐protein correlation in the brain: negatively correlating gene products reveal neuronal polarity as a potential cause
Journal of Neurochemistry
2018
Cold-water immersion after training sessions: effects on fiber type-specific adaptations in muscle K+transport proteins to sprint-interval training in men
Journal of Applied Physiology
2018
Imaging mRNA In Vivo, from Birth to Death
Annual Review of Biophysics
2018
Microparticle Delivery of Protein Markers for Single‐Cell Western Blotting from Microwells
Small
2018
The exon–intron gene structure upstream of the initiation codon predicts translation efficiency
Nucleic Acids Research
2018
Negative Evidence for a Functional Role of Neuronal DNMT3a in Persistent Pain
Frontiers in Molecular Neuroscience
2018
Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells
Cell Systems
2018
A genetics‐based approach confirms immune associations with life history across multiple populations of an aquatic vertebrate (Gasterosteus aculeatus)
Molecular Ecology
2018
Glutathione S-Transferase Protein Expression in Different Life Stages of Zebrafish (Danio rerio)
Toxicological Sciences
2018
Physical Cues Controlling Seasonal Immune Allocation in a Natural Piscine Model
Frontiers in Immunology
2018
Layers of regulation of cell-cycle gene expression in the budding yeastSaccharomyces cerevisiae
Molecular Biology of the Cell
2018
Correlation Analyses Reveal a Limited Role of Transcription in Genome-Wide Differential MicroRNA Expression in Mammals
Frontiers in Genetics
2018
High-throughput sequencing provides an insight into the hepatotoxicity mechanism of MC-LR in HepG2 cells
Toxin Reviews
2018
A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms
Scientific Reports
2018
Shifts in the relationship between mRNA and protein abundance of gill ion-transporters during smolt development and seawater acclimation in Atlantic salmon (Salmo salar)
Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology
2018
Integrative transcriptome and proteome analyses define marked differences between Neospora caninum isolates throughout the tachyzoite lytic cycle
Journal of Proteomics
2018
The iron regulatory proteins are defective in repressing translationviaexogenous 5′ iron responsive elements despite their relative abundance in leukemic cellular models
Metallomics
2018
Post-translational buffering leads to convergent protein expression levels between primates
Genome Biology
2018
Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism
Bioinformatics
2018
Comparative Transcriptomic Response of Primary and Immortalized Macrophages to Murine Norovirus Infection
The Journal of Immunology
2018
Integrated omics dissection of proteome dynamics during cardiac remodeling
Nature Communications
2017
A comparative review of computational methods for pathway perturbation analysis: dynamical and topological perspectives
Molecular BioSystems
2017
Transcription factor proteomics—Tools, applications, and challenges
PROTEOMICS
2017
Ribosome profiling and dynamic regulation of translation in mammals
Current Opinion in Genetics & Development
2017
Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics
Cell Systems
2017
Differential subnetwork of chemokines/cytokines in human, mouse, and rat brain cells after oxygen–glucose deprivation
Journal of Cerebral Blood Flow & Metabolism
2017
Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction
Molecular & Cellular Proteomics
2017
Global analysis of gene expression reveals mRNA superinduction is required for the inducible immune response to a bacterial pathogen
eLife
2017
Neural Stem Cell Activation and the Role of Protein Synthesis
Brain Plasticity
2017
Reconstructing the regulatory circuit of cell fate determination in yeast mating response
PLOS Computational Biology
2017
Dynamics of chromatin accessibility during TGF-β-induced EMT of Ras-transformed mammary gland epithelial cells
Scientific Reports
2017
Transcriptome analysis of a wild bird reveals physiological responses to the urban environment
Scientific Reports
2017
Discovering relationships between nuclear receptor signaling pathways, genes, and tissues in Transcriptomine
Science Signaling
2017
High-selectivity cytology via lab-on-a-disc western blotting of individual cells
Lab on a Chip
2017
A proteomic atlas of insulin signalling reveals tissue‐specific mechanisms of longevity assurance
Molecular Systems Biology
2017
Associating transcription factors and conserved RNA structures with gene regulation in the human brain
Scientific Reports
2017
Characterization of Odorant Receptors from a Non-ditrysian Moth, Eriocrania semipurpurella Sheds Light on the Origin of Sex Pheromone Receptors in Lepidoptera
Molecular Biology and Evolution
2017
Joule Heating-Induced Dispersion in Open Microfluidic Electrophoretic Cytometry
Analytical Chemistry
2017
Ribosome profiling the cell cycle: lessons and challenges
Current Genetics
2017
Subcellular western blotting of single cells
Microsystems & Nanoengineering
2017
In vitro and in vivo inhibition of proangiogenic retinal phenotype by an antisense oligonucleotide downregulating uPAR expression
Biochemical and Biophysical Research Communications
2017
Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line
PLOS ONE
2017
Protective effect of Rumenic acid rich cow's milk against colitis is associated with the activation of Nrf2 pathway in a murine model
Prostaglandins, Leukotrienes and Essential Fatty Acids
2017
Coordinated Pulses of mRNA and of Protein Translation or Degradation Produce EGF-Induced Protein Bursts
Cell Reports
2017
Impact of Alternative Splicing on the Human Proteome
Cell Reports
2017
Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them
Nucleic Acids Research
2017
Can we predict protein from mRNA levels?
Nature
2017
Post-transcriptional regulation across human tissues
PLOS Computational Biology
2017
Comparative venom gland transcriptomics ofNaja kaouthia(monocled cobra) from Malaysia and Thailand: elucidating geographical venom variation and insights into sequence novelty
PeerJ
2017
Hill function‐based models of transcriptional switches: impact of specific, nonspecific, functional and nonfunctional binding
Biological Reviews
2016
Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress
Molecular Systems Biology
2016
Hydrogel Pore‐Size Modulation for Enhanced Single‐Cell Western Blotting
Advanced Materials
2016
Engagement of the B-cell receptor of chronic lymphocytic leukemia cells drives global and MYC-specific mRNA translation
Blood
2016
On the Dependency of Cellular Protein Levels on mRNA Abundance
Cell
2016
Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish
Nature Communications
2016
Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs
PROTEOMICS
2016
A transcriptome-based model of central memory CD4 T cell death in HIV infection
BMC Genomics
2016
Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla
PLOS ONE
2016
Effects of Controlled Cortical Impact on the Mouse Brain Vasculome
Journal of Neurotrauma
2016
Evolving insights into RNA modifications and their functional diversity in the brain
Nature Neuroscience
2016
Pervasive isoform‐specific translational regulation via alternative transcription start sites in mammals
Molecular Systems Biology
2016
Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites
PLOS Computational Biology
2016
The interdependence of transcript and protein abundance: new data–new complexities
Molecular Systems Biology
2016
Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans
Nature Communications
2016
The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
Nature
2016
Reconciling proteomics with next generation sequencing
Current Opinion in Chemical Biology
2016
Co-option and evolution of non-olfactory proteinaceous pheromones in a terrestrial lungless salamander
Journal of Proteomics
2016
nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs
Genome Research
2016
Revealing the vectors of cellular identity with single-cell genomics
Nature Biotechnology
2016
Mechanisms of fate decision and lineage commitment during haematopoiesis
Immunology & Cell Biology
2016
In the Driver’s Seat
Journal of Biological Rhythms
2016
The Werner syndrome RECQ helicase targets G4 DNA in human cells to modulate transcription
Human Molecular Genetics
2016
Proteomic Analysis Reveals GLUT1 to be a Novel Discriminating Marker of Human Arterial Endothelium In vivo and loss of Venous Identity in Cell Culture
Open Journal of Proteomics and Genomics
2016
Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring
Molecular & Cellular Proteomics
2016
Detection of Isoforms Differing by a Single Charge Unit in Individual Cells
Angewandte Chemie
2016
Single cell–resolution western blotting
Nature Protocols
2016
Detection of Isoforms Differing by a Single Charge Unit in Individual Cells
Angewandte Chemie International Edition
2016
Mafb lineage tracing to distinguish macrophages from other immune lineages reveals dual identity of Langerhans cells
Journal of Experimental Medicine
2016
Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches
Cell Systems
2015
Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation
Molecular BioSystems
2015
Effect of Polymer Hydration State on In-Gel Immunoassays
Analytical Chemistry
2015
Alternative mRNA transcription, processing, and translation: insights from RNA sequencing
Trends in Genetics
2015
Mammalian target of rapamycin complex 1 (mTORC1) Is required for mouse spermatogonial differentiation in vivo
Developmental Biology
2015
Translational regulation shapes the molecular landscape of complex disease phenotypes
Nature Communications
2015
Combinatorial Peptide Ligand Libraries as a “Trojan Horse” in Deep Discovery Proteomics
Analytical Chemistry
2015
Microfluidics: reframing biological enquiry
Nature Reviews Molecular Cell Biology
2015
Statistics requantitates the central dogma
Science
2015
Sortilin is associated with breast cancer aggressiveness and contributes to tumor cell adhesion and invasion
Oncotarget
2015
Uncovering Hidden Layers of Cell Cycle Regulation through Integrative Multi-omic Analysis
PLOS Genetics
2015
Assessing the translational landscape of myogenic differentiation by ribosome profiling
Nucleic Acids Research
2015
Cellular and molecular insights into Hox protein action
Development
2015
Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms
G3 Genes|Genomes|Genetics
2015
Global sensitivity analysis of a dynamic model for gene expression inDrosophilaembryos
PeerJ
2015
Estimating binding properties of transcription factors from genome-wide binding profiles
Nucleic Acids Research
2015
Multilevel Regulation and Translational Switches in Synthetic Biology
IEEE Transactions on Biomedical Circuits and Systems
2015
Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast
PLOS Genetics
2015
The role of regulatory variation in complex traits and disease
Nature Reviews Genetics
2015
Comparative computational analysis of pluripotency in human and mouse stem cells
Scientific Reports
2015
Dynamic profiling of the protein life cycle in response to pathogens
Science
2015
Estimating a Structured Covariance Matrix From Multilab Measurements in High-Throughput Biology
Journal of the American Statistical Association
2015
Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium
Nucleic Acids Research
2015
Comprehensive comparison of large-scale tissue expression datasets
PeerJ
2015
Predictive analytics of environmental adaptability in multi-omic network models
Scientific Reports
2014
Single-molecule analysis of transcription factor binding at transcription sites in live cells
Nature Communications
2014
Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells
PeerJ
2014
Decoding neuroproteomics: integrating the genome, translatome and functional anatomy
Nature Neuroscience
2014
Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain
RNA Biology
2014
Genetic Influences on Translation in Yeast
PLoS Genetics
2014
RNA Polymerase III Accurately Initiates Transcription from RNA Polymerase II Promoters in Vitro
Journal of Biological Chemistry
2014
Decoding neural transcriptomes and epigenomes via high-throughput sequencing
Nature Neuroscience
2014
Dynamics of miRNA driven feed-forward loop depends upon miRNA action mechanisms
BMC Genomics
2014
Nonadditive Gene Expression in Polyploids
Annual Review of Genetics
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