Published in Genome Res on January 13, 2011
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Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One (2012) 4.52
TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One (2014) 3.45
Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet (2013) 2.83
Crop genomics: advances and applications. Nat Rev Genet (2011) 2.72
Molecular spandrels: tests of adaptation at the genetic level. Nat Rev Genet (2011) 2.07
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J (2013) 2.02
Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol (2011) 1.93
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NGS technologies for analyzing germplasm diversity in genebanks. Brief Funct Genomics (2012) 1.76
Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics (2011) 1.76
Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philos Trans R Soc Lond B Biol Sci (2012) 1.71
Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics (2012) 1.68
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Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics (2012) 1.55
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The genetic basis of parental care evolution in monogamous mice. Nature (2017) 1.40
Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One (2013) 1.30
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Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing. Proc Natl Acad Sci U S A (2013) 1.16
Detecting selective sweeps from pooled next-generation sequencing samples. Mol Biol Evol (2012) 1.13
Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. Mol Ecol (2011) 1.11
Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet (2016) 1.10
Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. BMC Genomics (2012) 1.05
959 Nematode Genomes: a semantic wiki for coordinating sequencing projects. Nucleic Acids Res (2011) 1.04
A whole-genome DNA marker map for cotton based on the D-genome sequence of Gossypium raimondii L. G3 (Bethesda) (2013) 1.02
Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. Gigascience (2014) 1.01
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Targeted capture in evolutionary and ecological genomics. Mol Ecol (2015) 1.01
Genotyping by genome reducing and sequencing for outbred animals. PLoS One (2013) 1.00
De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach. BMC Genomics (2013) 0.99
The use of museum specimens with high-throughput DNA sequencers. J Hum Evol (2014) 0.99
Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC Genomics (2014) 0.98
Genetic interactions involving five or more genes contribute to a complex trait in yeast. PLoS Genet (2014) 0.98
Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship. PLoS One (2012) 0.97
Complex trait divergence contributes to environmental niche differentiation in ecological speciation of Boechera stricta. Mol Ecol (2013) 0.96
Genetic architecture and adaptive significance of the selfing syndrome in Capsella. Evolution (2012) 0.96
Next-generation mapping of complex traits with phenotype-based selection and introgression. Genetics (2011) 0.96
Genetic anchoring of whole-genome shotgun assemblies. Front Genet (2014) 0.96
Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol. PLoS One (2014) 0.95
Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus. BMC Genomics (2013) 0.94
Construction of high-density genetic linkage maps for orange-spotted grouper Epinephelus coioides using multiplexed shotgun genotyping. BMC Genet (2013) 0.94
Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing. G3 (Bethesda) (2015) 0.91
Genotyping 1000 yeast strains by next-generation sequencing. BMC Genomics (2013) 0.90
Genetic analysis of an elite super-hybrid rice parent using high-density SNP markers. Rice (N Y) (2013) 0.89
DNA fingerprinting in botany: past, present, future. Investig Genet (2014) 0.89
A Major Locus Controls a Genital Shape Difference Involved in Reproductive Isolation Between Drosophila yakuba and Drosophila santomea. G3 (Bethesda) (2015) 0.88
Identification of major quantitative trait loci underlying floral pollination syndrome divergence in Penstemon. Philos Trans R Soc Lond B Biol Sci (2014) 0.88
A new genotype imputation method with tolerance to high missing rate and rare variants. PLoS One (2014) 0.87
Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). DNA Res (2015) 0.87
Rapid and inexpensive whole-genome genotyping-by-sequencing for crossover localization and fine-scale genetic mapping. G3 (Bethesda) (2015) 0.87
RESTseq--efficient benchtop population genomics with RESTriction Fragment SEQuencing. PLoS One (2013) 0.86
The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci Rep (2016) 0.86
High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species. Elife (2014) 0.86
Natural courtship song variation caused by an intronic retroelement in an ion channel gene. Nature (2016) 0.86
Identification of SNPs in closely related Temperate Japonica rice cultivars using restriction enzyme-phased sequencing. PLoS One (2013) 0.85
Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana. Genetics (2015) 0.85
Towards the identification of the loci of adaptive evolution. Methods Ecol Evol (2015) 0.85
A perspective on micro-evo-devo: progress and potential. Genetics (2013) 0.85
Genotyping by sequencing approaches to characterise crop genomes: choosing the right tool for the right application. Plant Biotechnol J (2016) 0.85
A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms. BMC Genomics (2014) 0.84
Reconstruction of Genome Ancestry Blocks in Multiparental Populations. Genetics (2015) 0.84
A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation. G3 (Bethesda) (2014) 0.84
Using Mendelian inheritance to improve high-throughput SNP discovery. Genetics (2014) 0.84
Western white pine SNP discovery and high-throughput genotyping for breeding and conservation applications. BMC Plant Biol (2014) 0.83
Next generation sequencing technologies for next generation plant breeding. Front Plant Sci (2014) 0.83
Genetic assimilation: a review of its potential proximate causes and evolutionary consequences. Ann Bot (2015) 0.83
The expanding genetic toolbox of the wasp Nasonia vitripennis and its relatives. Genetics (2015) 0.82
Balancing selection shapes density-dependent foraging behaviour. Nature (2016) 0.81
Genomics in eels--towards aquaculture and biology. Mar Biotechnol (NY) (2012) 0.81
Loci and candidate gene identification for resistance to Phytophthora sojae via association analysis in soybean [Glycine max (L.) Merr]. Mol Genet Genomics (2016) 0.81
An Efficient Genotyping Method in Chicken Based on Genome Reducing and Sequencing. PLoS One (2015) 0.79
The Genetics of Resistance to Morinda Fruit Toxin During the Postembryonic Stages in Drosophila sechellia. G3 (Bethesda) (2015) 0.79
Dissection of the complex genetic basis of craniofacial anomalies using haploid genetics and interspecies hybrids in Nasonia wasps. Dev Biol (2015) 0.78
Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes. Heredity (Edinb) (2015) 0.78
Genomic resources for multiple species in the Drosophila ananassae species group. Fly (Austin) (2013) 0.77
Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life. Genome Biol Evol (2015) 0.77
A genomic selection component analysis characterizes migration-selection balance. Evolution (2015) 0.77
Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. Front Plant Sci (2014) 0.77
A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3 (Bethesda) (2016) 0.77
Quantitative trait loci from identification to exploitation for crop improvement. Plant Cell Rep (2017) 0.77
Genetics of Intraspecies Variation in Avoidance Behavior Induced by a Thermal Stimulus in Caenorhabditis elegans. Genetics (2015) 0.76
Genetic Mapping by Bulk Segregant Analysis in Drosophila: Experimental Design and Simulation-Based Inference. Genetics (2016) 0.76
MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Sci Rep (2015) 0.76
High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L. BMC Genomics (2016) 0.75
Fast and accurate construction of ultra-dense consensus genetic maps using evolution strategy optimization. PLoS One (2015) 0.75
Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster. PLoS One (2016) 0.75
A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations. Theor Appl Genet (2016) 0.75
Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq). Int J Mol Sci (2016) 0.75
High throughput preparation of fly genomic DNA in 96-well format using a paint-shaker. Fly (Austin) (2015) 0.75
Fine Mapping of a Resistance Gene RpsHN that Controls Phytophthora sojae Using Recombinant Inbred Lines and Secondary Populations. Front Plant Sci (2017) 0.75
QTL underlying some agronomic traits in barley detected by SNP markers. BMC Genet (2016) 0.75
Genetic dissection of intraspecific variation in a male-specific sexual trait in Drosophila melanogaster. Heredity (Edinb) (2016) 0.75
Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. PLoS One (2016) 0.75
Linkage illuminates a complex genome. Nat Biotechnol (2011) 0.75
Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing. G3 (Bethesda) (2017) 0.75
CRCDA--Comprehensive resources for cancer NGS data analysis. Database (Oxford) (2015) 0.75
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics (2003) 53.11
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One (2008) 13.64
High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature (2008) 6.10
High-throughput genotyping by whole-genome resequencing. Genome Res (2009) 5.74
Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34
High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science (2008) 5.02
Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature (2010) 4.32
The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics (2000) 3.78
A versatile vector set for animal transgenesis. Dev Genes Evol (2000) 3.26
Quantitative trait loci in Drosophila. Nat Rev Genet (2001) 3.17
Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci U S A (2010) 2.63
Speed-mapping quantitative trait loci using microarrays. Nat Methods (2007) 2.26
Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. PLoS Genet (2010) 1.94
Genome-tagged mice (GTM): two sets of genome-wide congenic strains. Genomics (2001) 1.79
Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet (2009) 1.78
Mapping of Drosophila mutations using site-specific male recombination. Genetics (1998) 1.67
Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res (2010) 1.26
High-throughput methods for SNP genotyping. Methods Mol Biol (2009) 1.22
A rapid method to map mutations in Drosophila. Genome Biol (2001) 1.20
Laboratory methods for high-throughput genotyping. Cold Spring Harb Protoc (2009) 1.04
Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat Genet (2007) 12.62
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature (2010) 10.66
The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol (2005) 10.13
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (2007) 9.85
Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet (2007) 5.69
Morphological evolution through multiple cis-regulatory mutations at a single gene. Nature (2007) 4.14
Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature (2010) 3.72
Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism. Nature (2003) 3.39
A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome. PLoS Biol (2006) 2.98
Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet (2010) 2.61
A comparison of parthenogenetic and sexual embryogenesis of the pea aphid Acyrthosiphon pisum (Hemiptera: Aphidoidea). J Exp Zool B Mol Dev Evol (2003) 2.35
Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature (2010) 2.34
Worldwide population differentiation at disease-associated SNPs. BMC Med Genomics (2008) 2.32
Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2007) 2.29
Developmental origin and evolution of bacteriocytes in the aphid-Buchnera symbiosis. PLoS Biol (2003) 2.12
Asymmetric cardiac hypertrophy at autopsy in patients who received FK506 (tacrolimus) or cyclosporine A after liver transplant. Transplantation (2002) 2.12
The temporal requirements for insulin signaling during development in Drosophila. PLoS Biol (2005) 2.02
Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature (2011) 1.83
Multi-channel acoustic recording and automated analysis of Drosophila courtship songs. BMC Biol (2013) 1.81
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
The evolution of selfing in Arabidopsis thaliana. Science (2007) 1.62
People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population. Eur J Hum Genet (2011) 1.58
The pea aphid, Acyrthosiphon pisum: an emerging genomic model system for ecological, developmental and evolutionary studies. Bioessays (2006) 1.49
A dual-genome microarray for the pea aphid, Acyrthosiphon pisum, and its obligate bacterial symbiont, Buchnera aphidicola. BMC Genomics (2006) 1.48
Natural selection and developmental constraints in the evolution of allometries. Science (2005) 1.41
Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera). Genome Biol (2006) 1.38
Genetic variation for an aphid wing polyphenism is genetically linked to a naturally occurring wing polymorphism. Proc Biol Sci (2005) 1.21
High-resolution quantitative trait locus mapping reveals sign epistasis controlling ovariole number between two Drosophila species. Genetics (2006) 1.12
Molecular phylogenetic evidence for multiple gains or losses of ant mutualism within the aphid genus Chaitophorus. Mol Phylogenet Evol (2003) 1.11
Common genome-wide patterns of transcript accumulation underlying the wing polyphenism and polymorphism in the pea aphid (Acyrthosiphon pisum). Evol Dev (2007) 1.07
TALE-mediated modulation of transcriptional enhancers in vivo. Nat Methods (2013) 1.06
Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship. PLoS One (2012) 0.97
Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution. Proc Natl Acad Sci U S A (2012) 0.94
Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al. Cell (2009) 0.94
Aphids evolved novel secreted proteins for symbiosis with bacterial endosymbiont. Proc Biol Sci (2013) 0.93
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Motor control of Drosophila courtship song. Cell Rep (2013) 0.92
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Internal and external constraints in the evolution of morphological allometries in a butterfly. Evolution (2007) 0.89
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Fast left ventricular mass and volume assessment in mice with three-dimensional guide-point modeling. J Magn Reson Imaging (2009) 0.88
Natural courtship song variation caused by an intronic retroelement in an ion channel gene. Nature (2016) 0.86
Sex and death in the male pea aphid, Acyrthosiphon pisum: The life-history effects of a wing dimorphism. J Insect Sci (2007) 0.83
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How different are recently diverged species?: more than 150 phenotypic differences have been reported for the D. melanogaster species subgroup. Fly (Austin) (2009) 0.81
Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum. BMC Genet (2009) 0.81
Tinker where the tinkering's good. Trends Genet (2008) 0.80
Variation in fiber number of a male-specific muscle between Drosophila species: a genetic and developmental analysis. Evol Dev (2007) 0.79
Pupariation site preference within and between Drosophila sibling species. Evolution (2013) 0.77
The pea aphid uses a version of the terminal system during oviparous, but not viviparous, development. Evodevo (2013) 0.77
Preparation and mounting of adult Drosophila structures in Canada balsam. Cold Spring Harb Protoc (2012) 0.76
Rapid mounting of adult Drosophila structures in Hoyer's medium. Cold Spring Harb Protoc (2012) 0.76
Preparation of cuticles from unhatched first-instar Drosophila larvae. Cold Spring Harb Protoc (2011) 0.76
Preparation of cuticles from feeding Drosophila larvae. Cold Spring Harb Protoc (2011) 0.75
An unsupervised method for quantifying the behavior of paired animals. Phys Biol (2017) 0.75
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Editorial overview: Making evolutionary sense of everything. Curr Opin Genet Dev (2017) 0.75