Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed

An analytic approach for interpretable predictive models in high-dimensional data in the presence of interactions with exposures

(2018) Sahir Rai Bhatnagar et al.   GENETIC EPIDEMIOLOGY

Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data

(2018) Timothy P. Bilton et al.   GENETICS

The relative contribution of natural landscapes and human-mediated factors on the connectivity of a noxious invasive weed

(2018) Diego F. Alvarado-Serrano et al.   HEREDITY

Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa

(2018) Pierre Baduel et al.   PLoS Genetics

Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data

(2018) Timothy P. Bilton et al.   GENETICS

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

(2017) Jessica Stapley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Nucleotide Diversity at Site 106 of EPSPS in Lolium perenne L. ssp. multiflorum from California Indicates Multiple Evolutionary Origins of Herbicide Resistance

(2017) Elizabeth Karn et al.   Frontiers in Plant Science

The remarkable repeated evolution of herbicide resistance

(2016) R. S. Baucom   AMERICAN JOURNAL OF BOTANY

Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory

(2016) Adam Kuester et al.   ECOLOGY LETTERS

Fitness costs of herbicide resistance across natural populations of the common morning glory,Ipomoea purpurea

(2016) Megan L. Van Etten et al.   EVOLUTION

A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weedIpomoea purpurea

(2016) Adam Kuester et al.   MOLECULAR ECOLOGY

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Climate change increases the risk of herbicide-resistant weeds due to enhanced detoxification

(2016) Maor Matzrafi et al.   PLANTA

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

(2016) Atsushi Hoshino et al.   Nature Communications

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Winter wheat (Triticum aestivum L.) response to herbicides as affected by application timing and temperature

(2015) Melody A. Robinson et al.   CANADIAN JOURNAL OF PLANT SCIENCE

Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don

(2015) H. Hirakawa et al.   DNA RESEARCH

The geographic mosaic of herbicide resistance evolution in the common morning glory,Ipomoea purpurea: Evidence for resistance hotspots and low genetic differentiation across the landscape

(2015) Adam Kuester et al.   Evolutionary Applications

A Multistate Study of the Association Between Glyphosate Resistance and EPSPS Gene Amplification in Waterhemp (Amaranthus tuberculatus)

(2015) Laura A. Chatham et al.   WEED SCIENCE

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Detecting Recent Positive Selection with High Accuracy and Reliability by Conditional Coalescent Tree

(2014) Minxian Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

EPSPSamplification in glyphosate-resistant spiny amaranth (Amaranthus spinosus): a case of gene transfer via interspecific hybridization from glyphosate-resistant Palmer amaranth (Amaranthus palmeri)

(2014) Vijay K Nandula et al.   PEST MANAGEMENT SCIENCE

Tandem Amplification of a Chromosomal Segment Harboring 5-Enolpyruvylshikimate-3-Phosphate Synthase Locus Confers Glyphosate Resistance in Kochia scoparia

(2014) M. Jugulam et al.   PLANT PHYSIOLOGY

Underpinning Sustainable Vector Control through Informed Insecticide Resistance Management

(2014) Edward K. Thomsen et al.   PLoS One

Occurrence and Characterization of Kochia (Kochia scoparia) Accessions with Resistance to Glyphosate in Montana

(2014) Vipan Kumar et al.   WEED TECHNOLOGY

4P: fast computing of population genetics statistics from large DNA polymorphism panels

(2014) Andrea Benazzo et al.   Ecology and Evolution

De Novo Assembly and Annotation of the Transcriptome of the Agricultural Weed Ipomoea purpurea Uncovers Gene Expression Changes Associated with Herbicide Resistance

(2014) Trent Leslie et al.   G3-Genes Genomes Genetics

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

Quantifying single nucleotide variant detection sensitivity in exome sequencing

(2013) Alison M Meynert et al.   BMC BIOINFORMATICS

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Key role for a glutathione transferase in multiple-herbicide resistance in grass weeds

(2013) I. Cummins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Deciphering the evolution of herbicide resistance in weeds

(2013) Christophe Délye et al.   TRENDS IN GENETICS

Unravelling the genetic bases of non-target-site-based resistance (NTSR) to herbicides: a major challenge for weed science in the forthcoming decade

(2012) Christophe Délye   PEST MANAGEMENT SCIENCE

Shikimate leaf disc assay for early detection of glyphosate resistance in Conyza canadensis and relative transcript levels of EPSPS and ABC transporter genes

(2012) N NOL et al.   WEED RESEARCH

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Evolution in Action: Plants Resistant to Herbicides

(2010) Stephen B. Powles et al.   Annual Review of Plant Biology

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Geographical variation in resistance to acetyl-coenzyme A carboxylase-inhibiting herbicides across the range of the arable weed Alopecurus myosuroides (black-grass)

(2010) Christophe Délye et al.   NEW PHYTOLOGIST

Characterization of the horseweed (Conyza canadensis) transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide resistance genes

(2010) Yanhui Peng et al.   PEST MANAGEMENT SCIENCE

Causes and evolutionary significance of genetic convergence

(2010) Pascal-Antoine Christin et al.   TRENDS IN GENETICS

Functional Genomics Analysis of Horseweed (Conyza canadensis) with Special Reference to the Evolution of Non–Target-Site Glyphosate Resistance

(2010) Joshua S. Yuan et al.   WEED SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Safener responsiveness and multiple herbicide resistance in the weed black-grass (Alopecurus myosuroides)

(2009) Ian Cummins et al.   PLANT BIOTECHNOLOGY JOURNAL

Gene amplification confers glyphosate resistance in Amaranthus palmeri

(2009) T. A. Gaines et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CONSTRAINTS ON THE EVOLUTION OF TOLERANCE TO HERBICIDE IN THE COMMON MORNING GLORY: RESISTANCE AND TOLERANCE ARE MUTUALLY EXCLUSIVE

(2008) Regina S. Baucom et al.   EVOLUTION