An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

The genomic context of retrocopies increases their chance of functional relevancy in mammals

(2020) João Paulo Machado et al.   GENOMICS

The Evolution of Human Cancer Gene Duplications across Mammals

(2020) Marc Tollis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement

(2019) Kun Lu et al.   Nature Communications

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

(2019) Arda Soylev et al.   BIOINFORMATICS

Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals

(2019) Nashaiman Pervaiz et al.   BMC EVOLUTIONARY BIOLOGY

The evolution of gene duplicates in angiosperms and the impact of protein-protein interactions and the mechanism of duplication

(2019) Jonas Defoort et al.   Genome Biology and Evolution

Inferring synteny between genome assemblies: a systematic evaluation

(2018) Dang Liu et al.   BMC BIOINFORMATICS

The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation

(2018) Jonathan F Wendel et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

SWIMM 2.0: Enhanced Smith–Waterman on Intel’s Multicore and Manycore Architectures Based on AVX-512 Vector Extensions

(2018) Enzo Rucci et al.   INTERNATIONAL JOURNAL OF PARALLEL PROGRAMMING

Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time

(2018) Thomas J. Y. Kono et al.   G3-Genes Genomes Genetics

Dot2dot: Accurate Whole-Genome Tandem Repeats Discovery

(2018) Loredana M Genovese et al.   BIOINFORMATICS

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Structure and Origin of theWhite CapLocus and Its Role in Evolution of Grain Color in Maize

(2017) Bao-Cai Tan et al.   GENETICS

The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

(2017) Claudio Casola et al.   Genome Biology and Evolution

Gene duplication and neo-functionalization in the evolutionary and functional divergence of the metazoan copper transporters Ctr1 and Ctr2

(2017) Brandon L. Logeman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

(2017) Michiel Van Bel et al.   NUCLEIC ACIDS RESEARCH

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces

(2017) Adrian M Altenhoff et al.   NUCLEIC ACIDS RESEARCH

The high-quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi-winter morphotype

(2017) Fengming Sun et al.   PLANT JOURNAL

Structure and Origin of theWhite CapLocus and Its Role in Evolution of Grain Color in Maize

(2017) Bao-Cai Tan et al.   GENETICS

Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution

(2016) Debarun Acharya et al.   BMC GENOMICS

MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species

(2016) Jeong-Ho Baek et al.   Evolutionary Bioinformatics

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

(2016) Jinghua Yang et al.   NATURE GENETICS

Synteny Portal: a web-based application portal for synteny block analysis

(2016) Jongin Lee et al.   NUCLEIC ACIDS RESEARCH

Evolution of gene duplication in plants

(2016) Nicholas Panchy et al.   PLANT PHYSIOLOGY

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences

(2015) Michael Freeling et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus

(2015) Mario Vallejo-Marín et al.   EVOLUTION

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

(2015) Jean-Francois Gout et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis thaliana

(2015) Andrej A Arsovski et al.   PLANT PHYSIOLOGY

Mechanisms of Gene Duplication and Amplification

(2015) Andrew B. Reams et al.   Cold Spring Harbor Perspectives in Biology

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes

(2015) Param Priya Singh et al.   PLoS Computational Biology

PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees

(2014) Joseph MEX Lucas et al.   BMC BIOINFORMATICS

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

(2014) Thomas E. Hughes et al.   GENOME RESEARCH

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

(2014) Evgenia V. Kriventseva et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

(2014) Guénola Drillon et al.   PLoS One

Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches

(2014) Ning Yang et al.   PLoS One

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

(2014) B. Shapiro et al.   SCIENCE

Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

(2013) Daniel A. Dalquen et al.   Genome Biology and Evolution

Locally Duplicated Ohnologs Evolve Faster Than Nonlocally Duplicated Ohnologs in Arabidopsis and Rice

(2013) Yupeng Wang   Genome Biology and Evolution

Hieranoid: Hierarchical Orthology Inference

(2013) Fabian Schreiber et al.   JOURNAL OF MOLECULAR BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

(2013) W.-k. Jiang et al.   PLANT PHYSIOLOGY

Neofunctionalization of young duplicate genes in Drosophila

(2013) R. Assis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting long tandem duplications in genomic sequences

(2012) Eric Audemard et al.   BMC BIOINFORMATICS

Genome Evolution Due to Allopolyploidization in Wheat

(2012) M. Feldman et al.   GENETICS

Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant

(2012) T. Makino et al.   GENOME RESEARCH

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

(2011) Jan Fostier et al.   BIOINFORMATICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

OrthoInspector: comprehensive orthology analysis and visual exploration

(2011) Benjamin Linard et al.   BMC BIOINFORMATICS

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus

(2011) E. Rodgers-Melnick et al.   GENOME RESEARCH

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

On the Origins of Mendelian Disease Genes in Man: The Impact of Gene Duplication

(2011) J. E. Dickerson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

(2011) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

(2011) Yupeng Wang et al.   PLoS One

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

DRIMM-Synteny: decomposing genomes into evolutionary conserved segments

(2010) Son K. Pham et al.   BIOINFORMATICS

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

(2010) M. Muffato et al.   BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Genome-wide computational prediction of tandem gene arrays: application in yeasts

(2010) Laurence Despons et al.   BMC GENOMICS

Retrogenes Reveal the Direction of Sex-Chromosome Evolution in Mosquitoes

(2010) M. A. Toups et al.   GENETICS

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

A new repeat-masking method enables specific detection of homologous sequences

(2010) Martin C. Frith   NUCLEIC ACIDS RESEARCH

CYNTENATOR: Progressive Gene Order Alignment of 17 Vertebrate Genomes

(2010) Christian Rödelsperger et al.   PLoS One

Ohnologs in the human genome are dosage balanced and frequently associated with disease

(2010) T. Makino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maintenance of duplicate genes and their functional redundancy by reduced expression

(2010) Wenfeng Qian et al.   TRENDS IN GENETICS

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

Accurate identification of orthologous segments among multiple genomes

(2009) Tsuyoshi Hachiya et al.   BIOINFORMATICS

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

OrthoClusterDB: an online platform for synteny blocks

(2009) Man-Ping Ng et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

(2009) M. W. Hahn   JOURNAL OF HEREDITY

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice

(2009) C. Zou et al.   PLANT PHYSIOLOGY

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

(2009) O. Akerborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

The origins and impact of primate segmental duplications

(2009) Tomas Marques-Bonet et al.   TRENDS IN GENETICS

Tandemly Arrayed Genes in Vertebrate Genomes

(2008) Deng Pan et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

Recurrent Tandem Gene Duplication Gave Rise to Functionally Divergent Genes in Drosophila

(2008) C. Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mouse segmental duplication and copy number variation

(2008) Xinwei She et al.   NATURE GENETICS

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

(2008) K. Hanada et al.   PLANT PHYSIOLOGY

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS

Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution

(2008) Tanya Vavouri et al.   TRENDS IN GENETICS

Pervasive and Persistent Redundancy among Duplicated Genes in Yeast

(2008) E. Jedediah Dean et al.   PLoS Genetics