Gene regulatory effects of a large chromosomal inversion in highland maize

Fast and flexible linear mixed models for genome-wide genetics

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Efficient induction of heritable inversions in plant genomes using the CRISPR /Cas system

(2019) Carla Schmidt et al.   PLANT JOURNAL

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE CELL BIOLOGY

The genomic pool of standing structural variation outnumbers single nucleotide polymorphism by three-fold in the marine teleost Chrysophrys auratus

(2019) Andrew Catanach et al.   MOLECULAR ECOLOGY

Evolutionary and functional impact of common polymorphic inversions in the human genome

(2019) Carla Giner-Delgado et al.   Nature Communications

Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude

(2019) Margaux-Alison Fustier et al.   PLoS Genetics

Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex

(2018) J.M. Coughlan et al.   MOLECULAR ECOLOGY

Linked genetic variation and not genome structure causes widespread differential expression associated with chromosomal inversions

(2018) Iskander Said et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eco-Evolutionary Genomics of Chromosomal Inversions

(2018) Maren Wellenreuther et al.   TRENDS IN ECOLOGY & EVOLUTION

Gene Regulatory Divergence Between Locally Adapted Ecotypes in Their Native Habitats

(2018) Billie A. Gould et al.   MOLECULAR ECOLOGY

Association mapping desiccation resistance within chromosomal inversions in the African malaria vector Anopheles gambiae

(2018) Diego Ayala et al.   MOLECULAR ECOLOGY

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

Structure of local adaptation across the landscape: flowering time and fitness in Mexican maize (Zea mays L. subsp. mays) landraces

(2018) Kristin L. Mercer et al.   GENETIC RESOURCES AND CROP EVOLUTION

MaizeGDB 2018: the maize multi-genome genetics and genomics database

(2018) John L Portwood et al.   NUCLEIC ACIDS RESEARCH

Effects of Chilling on the Structure, Function and Development of Chloroplasts

(2018) Xiaomin Liu et al.   Frontiers in Plant Science

A study of allelic diversity underlying flowering-time adaptation in maize landraces

(2017) J Alberto Romero Navarro et al.   NATURE GENETICS

The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster

(2017) Erik Lavington et al.   G3-Genes Genomes Genetics

Young inversion with multiple linked QTLs under selection in a hybrid zone

(2017) Cheng-Ruei Lee et al.   Nature Ecology & Evolution

Genomic Evidence for Adaptive Inversion Clines inDrosophila melanogaster

(2016) Martin Kapun et al.   MOLECULAR BIOLOGY AND EVOLUTION

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Human inversions and their functional consequences

(2015) Marta Puig et al.   Briefings in Functional Genomics

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

(2015) Brad T. Townsley et al.   Frontiers in Plant Science

A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models - TheRPackagepbkrtest

(2015) Ulrich Halekoh et al.   Journal of Statistical Software

New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis

(2014) Brent M. Horton et al.   ANIMAL BEHAVIOUR

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

doublesex is a mimicry supergene

(2014) K. Kunte et al.   NATURE

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

(2014) Jeffrey C. Glaubitz et al.   PLoS One

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Complex Patterns of Local Adaptation in Teosinte

(2013) Tanja Pyhäjärvi et al.   Genome Biology and Evolution

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

The Genomic Signature of Crop-Wild Introgression in Maize

(2013) Matthew B. Hufford et al.   PLoS Genetics

Sequence-Based Detection and Breakpoint Assembly of Polymorphic Inversions

(2012) R. B. Corbett-Detig et al.   GENETICS

Where's the Money? Inversions, Genes, and the Hunt for Genomic Targets of Selection

(2012) M. Kirkpatrick et al.   GENETICS

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

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

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

A Gene Regulatory Network Model for Floral Transition of the Shoot Apex in Maize and Its Dynamic Modeling

(2012) Zhanshan Dong et al.   PLoS One

Inferences from the Historical Distribution of Wild and Domesticated Maize Provide Ecological and Evolutionary Insight

(2012) Matthew B. Hufford et al.   PLoS One

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

(2011) Mathieu Joron et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Coalescent patterns for chromosomal inversions in divergent populations

(2011) R. F. Guerrero et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide atlas of transcription during maize development

(2011) Rajandeep S. Sekhon et al.   PLANT JOURNAL

B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize

(2011) S. R. Eichten et al.   PLANT PHYSIOLOGY

Evolution of a mimicry supergene from a multilocus architecture

(2011) R. T. Jones et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Distribution and Most Recent Common Ancestor of the 17q21 Inversion in Humans

(2010) Michael P. Donnelly et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Is local adaptation in Mimulus guttatus caused by trade-offs at individual loci?

(2010) M. C. HALL et al.   MOLECULAR ECOLOGY

Genetic signals of origin, spread, and introgression in a large sample of maize landraces

(2010) J. van Heerwaarden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The Population Genomics of Trans-Specific Inversion Polymorphisms in Anopheles gambiae

(2009) B. J. White et al.   GENETICS

The Genetic Architecture of Maize Flowering Time

(2009) E. S. Buckler et al.   SCIENCE

Semantic Similarity in Biomedical Ontologies

(2009) Catia Pesquita et al.   PLoS Computational Biology

Revisiting the Impact of Inversions in Evolution: From Population Genetic Markers to Drivers of Adaptive Shifts and Speciation?

(2008) Ary A. Hoffmann et al.   Annual Review of Ecology Evolution and Systematics

Cold tolerance of maize seedlings as determined by root morphology and photosynthetic traits

(2007) Andreas Hund et al.   EUROPEAN JOURNAL OF AGRONOMY