Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

(2021) Magdalena Bohutínská et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seq-ing Higher Ground: Functional Investigation of Adaptive Variation Associated With High-Altitude Adaptation

(2020) James E. Hall et al.   Frontiers in Genetics

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

(2019) Ticao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata

(2019) Tuomas Hämälä et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

The genomes of two Eutrema species provide insight into plant adaptation to high altitudes

(2018) Xinyi Guo et al.   DNA RESEARCH

The rate and potential relevance of new mutations in a colonizing plant lineage

(2018) Moises Exposito-Alonso et al.   PLoS Genetics

Molecular tools enabling pennycress (Thlaspi arvense ) as a model plant and oilseed cash cover crop

(2018) Michaela McGinn et al.   PLANT BIOTECHNOLOGY JOURNAL

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Competing species leave many potential niches unfilled

(2017) Ben Ashby et al.   Nature Ecology & Evolution

SweepFinder2: increased sensitivity, robustness and flexibility

(2016) Michael DeGiorgio et al.   BIOINFORMATICS

Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars

(2016) José Antonio Campoy et al.   BMC PLANT BIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

Population Genomics for Understanding Adaptation in Wild Plant Species

(2015) Detlef Weigel et al.   Annual Review of Genetics

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop

(2015) K. M. Dorn et al.   DNA RESEARCH

Altitude Adaptation: A Glimpse Through Various Lenses

(2015) Tatum S. Simonson   HIGH ALTITUDE MEDICINE & BIOLOGY

Phylogeography of Thlaspi arvense (Brassicaceae) in China Inferred from Chloroplast and Nuclear DNA Sequences and Ecological Niche Modeling

(2015) Miao An et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

(2015) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History

(2015) Nora Hohmann et al.   PLANT CELL

Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance

(2015) Mallikarjuna Rao Kovi et al.   Frontiers in Plant Science

ANGSD: Analysis of Next Generation Sequencing Data

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Genetic Convergence in the Adaptation of Dogs and Humans to the High-Altitude Environment of the Tibetan Plateau

(2014) Guo-Dong Wang et al.   Genome Biology and Evolution

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

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

New approaches to facilitate rapid domestication of a wild plant to an oilseed crop: Example pennycress (Thlaspi arvense L.)

(2014) John C. Sedbrook et al.   PLANT SCIENCE

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

(2014) Shengyi Liu et al.   Nature Communications

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

De novoassembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock

(2013) Kevin M. Dorn et al.   PLANT JOURNAL

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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Soybean Seed Yield and Quality as a Response to Field Pennycress Residue

(2012) Winthrop B. Phippen et al.   CROP SCIENCE

Independent FLC Mutations as Causes of Flowering-Time Variation in Arabidopsis thaliana and Capsella rubella

(2012) Y.-L. Guo et al.   GENETICS

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo et al.   NATURE GENETICS

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

(2012) Matthew W Horton et al.   NATURE GENETICS

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

Insights into salt tolerance from the genome ofThellungiella salsuginea

(2012) Hua-Jun Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

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Statistical methods for detecting natural selection from genomic data

(2011) Yoshiyuki Suzuki   GENES & GENETIC SYSTEMS

DOG1 expression is predicted by the seed-maturation environment and contributes to geographical variation in germination in Arabidopsis thaliana

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The genome of the extremophile crucifer Thellungiella parvula

(2011) Maheshi Dassanayake et al.   NATURE GENETICS

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

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Genetic diversity and population structure of Sicilian sheep breeds using microsatellite markers

(2011) M. Tolone et al.   SMALL RUMINANT RESEARCH

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Why is adaptation prevented at ecological margins? New insights from individual-based simulations

(2010) Jon R. Bridle et al.   ECOLOGY LETTERS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Flowering and fruiting phenology of 24 plant species on the north slope of Mt. Qomolangma (Mt. Everest)

(2010) Liyun Zhang et al.   Journal of Mountain Science

Arabidopsis thaliana populations show clinal variation in a climatic gradient associated with altitude

(2010) Alicia Montesinos-Navarro et al.   NEW PHYTOLOGIST

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

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

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

The evolutionary significance of ancient genome duplications

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

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

China: The third pole

(2008) Jane Qiu   NATURE

Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks

(2008) A. Motegi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA