- Haploview: analysis and visualization of LD and haplotype maps
J C Barrett
Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
Bioinformatics 21:263-5. 2005
..Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface...
- The B73 maize genome: complexity, diversity, and dynamics
Patrick S Schnable
Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA
Science 326:1112-5. 2009
..These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize...
- Initial sequencing and analysis of the human genome
E S Lander
Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
Nature 409:860-921. 2001
..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
- MapChart: software for the graphical presentation of linkage maps and QTLs
R E Voorrips
Plant Research International, P O Box 16, 6700 AA Wageningen, The Netherlands
J Hered 93:77-8. 2002
- TASSEL: software for association mapping of complex traits in diverse samples
Peter J Bradbury
United States Department of Agriculture Agricultural Research Service, Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA
Bioinformatics 23:2633-5. 2007
..Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components...
- ACT: the Artemis Comparison Tool
Tim J Carver
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Bioinformatics 21:3422-3. 2005
..ACT is part of the Artemis distribution and is similarly open source, written in Java and can run on any Java enabled platform, including UNIX, Macintosh and Windows...
- Rapid SNP discovery and genetic mapping using sequenced RAD markers
Nathan A Baird
Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
PLoS ONE 3:e3376. 2008
..Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms...
- Identifying bacterial genes and endosymbiont DNA with Glimmer
Arthur L Delcher
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
Bioinformatics 23:673-9. 2007
..This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host...
- R/qtl: QTL mapping in experimental crosses
Karl W Broman
Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
Bioinformatics 19:889-90. 2003
- The complete genome sequence of Escherichia coli K-12
F R Blattner
Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
Science 277:1453-62. 1997
..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
- Genome-wide genetic marker discovery and genotyping using next-generation sequencing
John W Davey
Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King s Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
Nat Rev Genet 12:499-510. 2011
- Circos: an information aesthetic for comparative genomics
Canada s Michael Smith Genome Sciences Center, Vancouver, British Columbia V5Z 4S6, Canada
Genome Res 19:1639-45. 2009
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
Nat Methods 5:621-8. 2008
..We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices...
- Whole-genome sequencing of multiple Arabidopsis thaliana populations
Max Planck Institute for Developmental Biology, Tubingen, Germany
Nat Genet 43:956-63. 2011
..thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations...
- Automatic annotation of organellar genomes with DOGMA
Stacia K Wyman
Department of Computer Sciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
Bioinformatics 20:3252-5. 2004
..Annotations are stored on our password-protected server to enable repeated sessions of working on the same genome. Finished annotations can be extracted for direct submission to GenBank...
- Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
Jeffrey C Barrett
Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
Nat Genet 41:703-7. 2009
..01; overall P < 5 × 10(-8)) and 4 additional regions provided nominal evidence of replication (P < 0.05). The many new candidate genes suggested by these results include IL10, IL19, IL20, GLIS3, CD69 and IL27...
- RNA-Seq: a revolutionary tool for transcriptomics
Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, Connecticut 06520, USA
Nat Rev Genet 10:57-63. 2009
..This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes...
- Efficient control of population structure in model organism association mapping
Hyun Min Kang
Department of Computer Science, University of California, Los Angeles, California 90095 1596, USA
Genetics 178:1709-23. 2008
..An R package implementation and webserver of our EMMA method are publicly available...
- MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations
E S Lander
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
Genomics 1:174-81. 1987
..MAPMAKER has been applied to the construction of linkage maps in a number of organisms, including the human and several plants, and we outline the mapping strategies that have been used...
- GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Thomas D Wu
Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
Bioinformatics 21:1859-75. 2005
- Personalized copy number and segmental duplication maps using next-generation sequencing
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
Nat Genet 41:1061-7. 2009
..2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology...
- Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits
Social, Genetics and Developmental Psychiatry Research Centre, Institute of Psychiatry, King s College London, De Crespigny Park, UK
Bioinformatics 19:149-50. 2003
..A website for performing power calculations for the design of linkage and association genetic mapping studies of complex traits...
- The genetic architecture of maize flowering time
Edward S Buckler
U S Department of Agriculture USDA Agricultural Research Service USDA ARS, USA
Science 325:714-8. 2009
..Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis...
- The structure of haplotype blocks in the human genome
Stacey B Gabriel
Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
Science 296:2225-9. 2002
..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
- Genic microsatellite markers in plants: features and applications
Rajeev K Varshney
Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
Trends Biotechnol 23:48-55. 2005
..Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed...
- Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease
Genetics Department, University Medical Center and University of Groningen, The Netherlands
Nat Genet 43:1193-201. 2011
..Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease...
- The genome of woodland strawberry (Fragaria vesca)
Department of Biological Sciences, University of North Texas, Denton, Texas, USA
Nat Genet 43:109-16. 2011
..New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted...
- A first-generation haplotype map of maize
Michael A Gore
United States Department of Agriculture Agriculture Research Service USDA ARS, USA
Science 326:1115-7. 2009
..This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through genome-wide association studies...
- Genome-wide association study of leaf architecture in the maize nested association mapping population
Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA
Nat Genet 43:159-62. 2011
..These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits...
- Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
Cell 126:1189-201. 2006
- Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne
W F Pfender
Department of Botany and Plant Pathology, USDA ARS Forage Seed and Cereal Research Unit, Oregon State University, 3450 SW Campus Way, Corvallis, OR 97331, USA
Theor Appl Genet 122:1467-80. 2011
..RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne...
- The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
G A Tuskan
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Science 313:1596-604. 2006
..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
Genome Res 18:1851-8. 2008
..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
- Next-generation DNA sequencing
Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
Nat Biotechnol 26:1135-45. 2008
- A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep
Unit of Animal Genomics, Department of Animal Production, Faculty of Veterinary Medicine and Centre for Biomedical Integrative Genoproteomics, University of Liège B43, 20 Boulevard de Colonster, 4000 Liege, Belgium
Nat Genet 38:813-8. 2006
..Analysis of SNP databases for humans and mice demonstrates that mutations creating or destroying putative miRNA target sites are abundant and might be important effectors of phenotypic variation...
- A whole-genome assembly of the domestic cow, Bos taurus
Aleksey V Zimin
Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
Genome Biol 10:R42. 2009
..The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods...
- Diversity of human copy number variation and multicopy genes
Peter H Sudmant
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
Science 330:641-6. 2010
..Our approach makes ~1000 genes accessible to genetic studies of disease association...
- Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice
National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China
Nat Genet 40:761-7. 2008
..Natural mutants with reduced function enable rice to be cultivated in temperate and cooler regions. Thus, Ghd7 has played crucial roles for increasing productivity and adaptability of rice globally...
- High-resolution mapping of expression-QTLs yields insight into human gene regulation
Jean Baptiste Veyrieras
Department of Human Genetics, The University of Chicago, Chicago, IL, USA
PLoS Genet 4:e1000214. 2008
..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation...
- A large genome center's improvements to the Illumina sequencing system
Michael A Quail
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
Nat Methods 5:1005-10. 2008
- High-resolution mapping and characterization of open chromatin across the genome
Alan P Boyle
Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
Cell 132:311-22. 2008
..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
- The genetics of Caenorhabditis elegans
Genetics 77:71-94. 1974
..Mutations in 77 of these alter the movement of the animal. Estimates of the induced mutation frequency of both the visible mutants and X chromosome lethals suggests that, just as in Drosophila, the genetic units in C. elegans are large...
- Genome sequence, comparative analysis, and population genetics of the domestic horse
C M Wade
Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
Science 326:865-7. 2009
..Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds...
- Combinatorial patterns of histone acetylations and methylations in the human genome
Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
Nat Genet 40:897-903. 2008
..Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation...
- MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
Brief Bioinform 9:299-306. 2008
..We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods...
- The protein kinase complement of the human genome
SUGEN Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
Science 298:1912-34. 2002
..We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons...
- The genome of the Western clawed frog Xenopus tropicalis
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
Science 328:633-6. 2010
..The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage...
- The genome sequence of Schizosaccharomyces pombe
The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nature 415:871-80. 2002
- Promise and pitfalls of the Immunochip
University of Queensland Diamantina Institute, Brisbane, Queensland, Australia
Arthritis Res Ther 13:101. 2011
..This chip provides a powerful tool for immunogenetics gene mapping...
- Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population
Kristen L Kump
Department of Crop Science, North Carolina State University, Raleigh, North Carolina, USA
Nat Genet 43:163-8. 2011
..Limited linkage disequilibrium was observed around some SNPs associated with SLB resistance, indicating that the maize NAM population enables high-resolution mapping of some genome regions...
- Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
Nat Genet 39:61-9. 2007
..Our results indicate that genic transcription and DNA methylation are closely interwoven processes...
- The genetics of quantitative traits: challenges and prospects
Trudy F C Mackay
Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
Nat Rev Genet 10:565-77. 2009
..This systems genetics approach enables us to understand the biology inside the 'black box' that lies between genotype and phenotype in terms of causal networks of interacting genes...
- Subspecific origin and haplotype diversity in the laboratory mouse
The Jackson Laboratory, Bar Harbor, Maine, USA
Nat Genet 43:648-55. 2011
..The subspecific origin, haplotype diversity and identity by descent maps can be visualized using the Mouse Phylogeny Viewer (see URLs)...
- Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
Nat Genet 39:457-66. 2007
..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation...
- Copy number variation: new insights in genome diversity
Jennifer L Freeman
Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
Genome Res 16:949-61. 2006
..Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases...
- High-throughput genotyping by whole-genome resequencing
National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
Genome Res 19:1068-76. 2009
- Genetic properties of the maize nested association mapping population
Michael D McMullen
United States Department of Agriculture Agriculture Research Service USDA ARS, USA
Science 325:737-40. 2009
..This implies that pericentromeric regions may contribute disproportionally to heterosis...
- Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism
Simon W Baxter
Department of Zoology, University of Cambridge, Cambridge, United Kingdom
PLoS ONE 6:e19315. 2011
..mori chromosomes shows for the first time, genetic synteny appears common beyond the Macrolepidoptera. RAD sequencing is a powerful system capable of rapidly generating chromosome specific data for non-model organisms...
- Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.)
International Crops Research Institute for the Semi Arid Tropics, Patancheru, India
Theor Appl Genet 122:1119-32. 2011
..This study suggests deployment of modern approaches like marker-assisted recurrent selection or genomic selection instead of marker-assisted backcrossing approach for breeding for drought tolerance in groundnut...
- Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature
Unit of Animal Genomics, Interdisciplinary Institute of Applied Genomics GIGA R and Faculty of Veterinary Medicine, University of Liège B34, Liege, Belgium
Nat Genet 43:405-13. 2011
..By performing expression QTL analyses, we identified a splice site variant in CHCHD7 and exploited this naturally occurring null allele to exclude CHCHD7 as single causative gene...
- Positional cloning of the wheat vernalization gene VRN1
Department of Agronomy and Range Science, University of California, Davis 95616, USA
Proc Natl Acad Sci U S A 100:6263-8. 2003
..A mutation in the promoter region of AP1 would result in the lack of recognition of the repressor and in a dominant spring growth habit...
- OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes
Max Planck Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam Golm, Germany
Curr Genet 52:267-74. 2007
..The design of the program core as a Perl module with an object-oriented interface allows easy integration into custom scripts...
- Dissection of genetically complex traits with extremely large pools of yeast segregants
Ian M Ehrenreich
Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA
Nature 464:1039-42. 2010
..Our method should have broad applications in yeast and can be extended to other organisms...
- Transposable elements and the evolution of regulatory networks
Department of Biology, Life Science Building, Box 19498, University of Texas, Arlington, Texas 76019, USA
Nat Rev Genet 9:397-405. 2008
..Here I revisit and expand earlier models and propose that genomic repeats, and in particular transposable elements, have been a rich source of material for the assembly and tinkering of eukaryotic gene regulatory systems...
- Sequencing of natural strains of Arabidopsis thaliana with short reads
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
Genome Res 18:2024-33. 2008
..Our pipeline for aligning reads and predicting SNPs and indels, SHORE, is available for download at http://1001genomes.org...
- Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
Plant Biotechnol J 7:334-46. 2009
..For a specimen region of the genome analysed in detail, segregation of alleles largely, although not entirely, followed the pattern expected for genomic markers...
- Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley
Crop and Soil Science Department, Oregon State University, Corvallis, Oregon, USA
BMC Genomics 12:4. 2011
- Prdm9 controls activation of mammalian recombination hotspots
Emil D Parvanov
The Jackson Laboratory, Bar Harbor, ME 04609, USA
Science 327:835. 2010
..The identification of Prdm9 as a protein regulating mammalian recombination hotspots initiates molecular studies of this important biological control system...
- Cytokinin oxidase regulates rice grain production
Bioscience and Biotechnology Center, Nagoya University, Nagoya 464 8601, Japan
Science 309:741-5. 2005
..QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement...
- A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping
Unit of Animal Genomics, GIGA Research and Department of Animal Production, Faculty of Veterinary Medicine, University of Liege, Belgium
Genetics 184:789-98. 2010
..We show that these cluster states can directly be used to fine map QTL. The method is computationally effective at handling large data sets based on high-density SNP panels...
- The sequence of the human genome
J C Venter
Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
Science 291:1304-51. 2001
..Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge...
- The landscape of recombination in African Americans
Anjali G Hinch
Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
Nature 476:170-5. 2011
..Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution...
- Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
Genome Res 18:1944-54. 2008
..Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes...
- Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nat Methods 6:291-5. 2009
..We illustrate this by generating and analyzing DNA sequences from extremely (G+C)-poor (Plasmodium falciparum), (G+C)-neutral (Escherichia coli) and (G+C)-rich (Bordetella pertussis) genomes...
- CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA
Bioinformatics 23:1061-7. 2007
..Unfortunately, many new genome projects lack comprehensive experimental data to derive a reliable initial set of genes...
- Global variation in copy number in the human genome
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 444:444-54. 2006
..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies...
- Revealing the architecture of gene regulation: the promise of eQTL studies
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Trends Genet 24:408-15. 2008
- Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
Aaron R Quinlan
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
Genome Res 20:623-35. 2010
..This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture...
- Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis
Yurii S Aulchenko
Department of Epidemiology and Biostatistics, Erasmus MC, 3000 CA Rotterdam, The Netherlands
Genetics 177:577-85. 2007
..However, there is little or no difference in empirical power of MG and the proposed method. In any scenario, GRAMMAR is much faster than MG and enables rapid analysis of hundreds of thousands of markers...
- Efficient mapping of mendelian traits in dogs through genome-wide association
Elinor K Karlsson
Broad Institute of Harvard and Massachusetts Institute of Technology MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Genet 39:1321-8. 2007
- Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
Rajeev K Varshney
International Crops Research Institute for the Semi Arid Tropics ICRISAT, Patancheru, India
Nat Biotechnol 30:83-9. 2012
- Mapping genes for complex traits in domestic animals and their use in breeding programmes
Michael E Goddard
Department of Agriculture and Food Systems, University of Melbourne, Royal Parade, Parkville 3010, Australia
Nat Rev Genet 10:381-91. 2009
..This approach is expected to double the rate of genetic improvement per year in many livestock systems...
- Structure of linkage disequilibrium and phenotypic associations in the maize genome
D L Remington
Department of Genetics, North Carolina State University, Raleigh, NC 27695 7614, USA
Proc Natl Acad Sci U S A 98:11479-84. 2001
..Provided the effects of population structure are effectively controlled, this research suggests that association studies show great promise for identifying the genetic basis of important traits in maize with very high resolution...
- Systems genetics of complex traits in Drosophila melanogaster
Julien F Ayroles
Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
Nat Genet 41:299-307. 2009
..Overlapping transcripts in modules associated with different traits provide insight into the molecular basis of pleiotropy between complex traits...
- Linkage and association mapping of Arabidopsis thaliana flowering time in nature
Laboratoire Génétique et Evolution des Populations Végétales, Unité Mixte de Recherche CNRS 8016, Université des Sciences et Technologies de Lille 1, Villeneuve d Ascq, France
PLoS Genet 6:e1000940. 2010
..Instead, we found a prevalence of genes involved in the regulation of the plant circadian clock. Furthermore, we identified new genomic regions lacking obvious candidate genes...
- Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars
Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
Genetics 172:1165-77. 2006
..Our results demonstrated that association mapping could complement and enhance previous QTL information for marker-assisted selection...
- Drought stress and tropical maize: QTL-by-environment interactions and stability of QTLs across environments for yield components and secondary traits
ETH Zurich, Institute of Plant Sciences, 8092 Zurich, Switzerland
Theor Appl Genet 119:913-30. 2009
..Those regions are clear targets for future marker-assisted breeding, and our results confirm that the best approach to breeding for drought tolerance includes selection under water stress...
- High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence
David L Hyten
Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
BMC Genomics 11:38. 2010
- 'Green revolution' genes encode mutant gibberellin response modulators
John Innes Centre, Norwich Research Park, UK
Nature 400:256-61. 1999
..Transgenic rice plants containing a mutant GAI allele give reduced responses to gibberellin and are dwarfed, indicating that mutant GAI orthologues could be used to increase yield in a wide range of crop species...
- A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
Martien A M Groenen
Animal Breeding and Genomics Centre, Wageningen University, 6700 AH Wageningen, The Netherlands
Genome Res 19:510-9. 2009
..4-fold higher density at recombination hot spots versus cold spots, suggesting a functional relationship between recombination frequency and cohesin binding...
- Detecting copy number variation with mated short reads
Department of Computer Science, University of Toronto, Toronto, Ontario M5R 3G4, Canada
Genome Res 20:1613-22. 2010
..Furthermore, we demonstrate that CNVer can reconstruct the absolute copy counts of segments of the donor genome and evaluate the feasibility of using CNVer with low coverage datasets...
- A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.)
Daryl J Somers
Agriculture and Agri Food Canada, Cereal Research Centre, 195 Dafoe Rd, Winnipeg, MB, Canada, R3T 2 M9
Theor Appl Genet 109:1105-14. 2004
..This enables users to predict allele sizes in new breeding populations and develop molecular breeding and genomics strategies...
- Efficiency and power in genetic association studies
Paul I W de Bakker
Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6818, Boston, Massachusetts 02114 2790, USA
Nat Genet 37:1217-23. 2005
..Power is robust to the completeness of the reference panel from which tags are selected. These findings have implications for prioritizing tag SNPs and interpreting association studies...
- A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif
A H Sinclair
Human Molecular Genetics Laboratory, Imperial Cancer Research Fund, Lincoln s Inn Fields, London, UK
Nature 346:240-4. 1990
..This gene has been termed SRY (for sex-determining region Y) and proposed to be a candidate for the elusive testis-determining gene, TDF...
- Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map
Hans van Os
Laboratory of Plant Breeding, Wageningen University, The Netherlands
Genetics 173:1075-87. 2006
- Identifying autism loci and genes by tracing recent shared ancestry
Eric M Morrow
Division of Genetics, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
Science 321:218-23. 2008
- MYH9 is associated with nondiabetic end-stage renal disease in African Americans
W H Linda Kao
Department of Epidemiology, School of Medicine and Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21287, USA
Nat Genet 40:1185-92. 2008
- Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing
Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
Nat Genet 42:400-5. 2010
..These common CNVs in Asian populations will be a useful resource for subsequent genetic studies in these populations, and the new method of calling absolute CNVs will be essential for applying CNV data to personalized medicine...
- Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
Sergei L Kosakovsky Pond
Antiviral Research Center, University of California, San Diego, CA 92103, USA
Bioinformatics 21:2531-3. 2005
..The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers...
- Mutations of the human homolog of Drosophila patched in the nevoid basal cell carcinoma syndrome
Centre for Molecular and Cell Biology, University of Queensland, St Lucia, Australia
Cell 85:841-51. 1996
..We propose that a reduction in expression of the patched gene can lead to the developmental abnormalities observed in the syndrome and that complete loss of patched function contributes to transformation of certain cell types...
- A fine-scale map of recombination rates and hotspots across the human genome
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Science 310:321-4. 2005