Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

A high‐quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes

(2020) Zhenqiao Song et al.   Plant Genome

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

(2019) Pavel Neumann et al.   Mobile DNA

The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

(2019) Qing Zhao et al.   Molecular Plant

Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

(2019) Pierre Baduel et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

Post-polyploid diploidization and diversification through dysploid changes

(2018) Terezie Mandáková et al.   CURRENT OPINION IN PLANT BIOLOGY

Transcriptome analysis reveals hybridization-induced genome shock in an interspecific F1 hybrid from Camellia

(2018) Min Zhang et al.   GENOME

Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids

(2018) Ulrike Göbel et al.   Genome Biology and Evolution

The causes and consequences of subgenome dominance in hybrids and recent polyploids

(2018) Kevin A. Bird et al.   NEW PHYTOLOGIST

Gene Expression Dominance in Allopolyploids: Hypotheses and Models

(2018) Samuel Bottani et al.   TRENDS IN PLANT SCIENCE

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

The transcriptional landscape of polyploid wheat

(2018) R. H. Ramírez-González et al.   SCIENCE

Desiccation tolerance evolved through gene duplication and network rewiring in Lindernia

(2018) Robert VanBuren et al.   PLANT CELL

The genome of the medicinal plant Andrographis paniculata provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide

(2018) Wei Sun et al.   PLANT JOURNAL

Homologous Recombination and the Formation of Complex Genomic Rearrangements

(2018) Aurèle Piazza et al.   TRENDS IN CELL BIOLOGY

Reconstructing the genome of the most recent common ancestor of flowering plants

(2017) Florent Murat et al.   NATURE GENETICS

The evolutionary significance of polyploidy

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

Coordinated Functional Divergence of Genes after Genome Duplication inArabidopsis thaliana

(2017) Riet De Smet et al.   PLANT CELL

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2016) Haibin Xu et al.   Molecular Plant

Genome sequence and genetic diversity of European ash trees

(2016) Elizabeth S. A. Sollars et al.   NATURE

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

(2016) Zhen Li et al.   PLANT CELL

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Polyploidy and genome evolution in plants

(2015) Pamela S Soltis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Epigenetic mechanisms of postzygotic reproductive isolation in plants

(2015) Clément Lafon-Placette et al.   CURRENT OPINION IN PLANT BIOLOGY

Persistence of Subgenomes in Paleopolyploid Cotton after 60 My of Evolution

(2015) Simon Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat

(2015) Andrea L. Harper et al.   PLANT BIOTECHNOLOGY JOURNAL

The resurrection genome ofBoea hygrometrica: A blueprint for survival of dehydration

(2015) Lihong Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)

(2015) Guanghui Zhang et al.   GigaScience

Filling annotation gaps in yeast genomes using genome-wide contact maps

(2014) Hervé Marie-Nelly et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

(2014) B. Chalhoub et al.   SCIENCE

Genome interplay in the grain transcriptome of hexaploid bread wheat

(2014) M. Pfeifer et al.   SCIENCE

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

Size Does Matter: Why Polyploid Tumor Cells are Critical Drug Targets in the War on Cancer

(2014) Jermaine Coward et al.   Frontiers in Oncology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

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

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

(2013) U. Hellsten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Domain enhanced lookup time accelerated BLAST

(2012) Grzegorz M Boratyn et al.   Biology Direct

Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model

(2012) M Eric Schranz et al.   CURRENT OPINION IN PLANT BIOLOGY

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Genomic asymmetry in allopolyploid plants: wheat as a model

(2012) M. Feldman et al.   JOURNAL OF EXPERIMENTAL BOTANY

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

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

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution

(2010) F. Murat et al.   GENOME RESEARCH

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Role of Hybridization in Plant Speciation

(2009) Pamela S. Soltis et al.   Annual Review of Plant Biology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

(2009) Eduard Kejnovsky et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS