GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity

Local adaptation along an environmental cline in a species with an inversion polymorphism

(2017) M. Wellenreuther et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genome evolution, structural rearrangements and speciation

(2017) P. G. D. Feulner et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

A combination of sexual and ecological divergence contributes to rearrangement spread during initial stages of speciation

(2017) Genevieve M. Kozak et al.   MOLECULAR ECOLOGY

Hidden genetic variation shapes the structure of functional elements in Drosophila

(2017) Mahul Chakraborty et al.   NATURE GENETICS

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

(2016) Elaina M. Tuttle et al.   CURRENT BIOLOGY

Prezygotic isolation, mating preferences, and the evolution of chromosomal inversions

(2016) Andrius J. Dagilis et al.   EVOLUTION

A Segregating Inversion Generates Fitness Variation in Yellow Monkeyflower (Mimulus guttatus)

(2016) Y. W. Lee et al.   GENETICS

Tracking changes in chromosomal arrangements and their genetic content during adaptation

(2016) J. Santos et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering

(2016) Samina Naseeb et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inversions and the origin of behavioral differences in cod

(2016) Kieran Samuk   MOLECULAR ECOLOGY

Chromosomal inversions and ecotypic differentiation inAnopheles gambiae: the perspective from whole-genome sequencing

(2016) R. Rebecca Love et al.   MOLECULAR ECOLOGY

Population structure and local selection yield high genomic variation inMimulus guttatus

(2016) Joshua R. Puzey et al.   MOLECULAR ECOLOGY

Genetic loci with parent-of-origin effects cause hybrid seed lethality in crosses between Mimulus species

(2016) Austin G. Garner et al.   NEW PHYTOLOGIST

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

(2016) Helena Staňková et al.   PLANT BIOTECHNOLOGY JOURNAL

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

(2016) Candice N. Hirsch et al.   PLANT CELL

Molecular, genetic and evolutionary analysis of a paracentric inversion inArabidopsis thaliana

(2016) Paul Fransz et al.   PLANT JOURNAL

Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster

(2016) Jennifer L. Hackett et al.   PLoS One

A genomic selection component analysis characterizes migration-selection balance

(2015) Patrick J. Monnahan et al.   EVOLUTION

Centromere-associated meiotic drive and female fitness variation inMimulus

(2015) Lila Fishman et al.   EVOLUTION

A Nonhomogeneous Hidden Markov Model for Gene Mapping Based on Next-Generation Sequencing Data

(2015) Fatemeh Zamanzad Ghavidel et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

(2015) Anthony Long et al.   NATURE REVIEWS GENETICS

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

(2014) T. M. Beissinger et al.   GENETICS

Chromosomal Evolution and Patterns of Introgression in Helianthus

(2014) J. G. Barb et al.   GENETICS

Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae)

(2014) L Fishman et al.   HEREDITY

Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations

(2014) Matthew W. Hahn et al.   G3-Genes Genomes Genetics

High-Resolution Linkage Map and Chromosome-Scale Genome Assembly for Cassava ( Manihot esculenta Crantz) from 10 Populations

(2014)   G3-Genes Genomes Genetics

A High-Resolution Genetic Map of Yellow Monkeyflower Identifies Chemical Defense QTLs and Recombination Rate Variation

(2014) Liza M. Holeski et al.   G3-Genes Genomes Genetics

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

(2014) Carlos W Nossa et al.   GigaScience

Promises and limitations of hitchhiking mapping

(2013) Sergey V Nuzhdin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Genomic Signal of Partial Sweeps in Mimulus guttatus

(2013) John K. Kelly et al.   Genome Biology and Evolution

The Standing Pool of Genomic Structural Variation in a Natural Population of Mimulus guttatus

(2013) Lex E. Flagel et al.   Genome Biology and Evolution

Complex Patterns of Local Adaptation in Teosinte

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

Gene flow and gene flux shape evolutionary patterns of variation in Drosophila subobscura

(2013) C Pegueroles et al.   HEREDITY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

Sequence-Based Detection and Breakpoint Assembly of Polymorphic Inversions

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

Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize

(2012) Zhou Fang et al.   GENETICS

Properties and Power of the Drosophila Synthetic Population Resource for the Routine Dissection of Complex Traits

(2012) Elizabeth G. King et al.   GENETICS

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks

(2012) PHILINE G. D. FEULNER et al.   MOLECULAR ECOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

Population Genomics of Inversion Polymorphisms in Drosophila melanogaster

(2012) Russell B. Corbett-Detig et al.   PLoS Genetics

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

GENETIC ARCHITECTURE AND ADAPTIVE SIGNIFICANCE OF THE SELFING SYNDROME INCAPSELLA

(2011) Tanja Slotte et al.   EVOLUTION

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

R/qtl: high-throughput multiple QTL mapping: Fig. 1.

(2010) Danny Arends et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

(2010) David B. Lowry et al.   PLOS BIOLOGY

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Centromere-Associated Female Meiotic Drive Entails Male Fitness Costs in Monkeyflowers

(2008) L. Fishman et al.   SCIENCE