Research Topics
| L KruglyakSummaryAffiliation: Fred Hutchinson Cancer Research Center Country: USA Publications
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Detail Information
Publications
Prospects for whole-genome linkage disequilibrium mapping of common disease genesL Kruglyak
Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Nat Genet 22:139-44. 1999..Second, the extent of LD is similar in isolated populations unless the founding bottleneck is very narrow or the frequency of the variant is low (<5%)...- Efficient multipoint linkage analysis through reduction of inheritance spaceK Markianos
Division of Human Biology, Fred Hutchison Cancer Research Center, Seattle, WA 98109, USA
Am J Hum Genet 68:963-77. 2001..We describe and implement a set of permutation tests that allow determination of empirical significance levels in the presence of linkage disequilibrium among marker loci... - Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networksJun Zhu
Rosetta Inpharmatics, LLC, Seattle, Washington 98109, USA
Nat Genet 40:854-61. 2008..We then prospectively validate predictions, providing direct experimental evidence that predictive networks can be constructed by integrating multiple, appropriate data types... - The landscape of genetic complexity across 5,700 gene expression traits in yeastRachel B Brem
Division of Human Biology and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Proc Natl Acad Sci U S A 102:1572-7. 2005..Sixteen percent of highly heritable transcripts exhibit evidence of interacting loci. Our results will aid design of future QTL mapping studies and may shed light on the evolution of quantitative traits... - Local regulatory variation in Saccharomyces cerevisiaeJames Ronald
Department of Genome Sciences, University of Washington, Seattle, Washington, USA
PLoS Genet 1:e25. 2005..These findings point to the importance of cis-acting variation, but also suggest that there is a diverse set of mechanisms through which local variation can affect gene expression levels... - Population history and natural selection shape patterns of genetic variation in 132 genesJoshua M Akey
Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
PLoS Biol 2:e286. 2004..More generally, our results have important implications for mapping genes underlying complex human diseases... - Genetic interactions between polymorphisms that affect gene expression in yeastRachel B Brem
Program in Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, M2 B876, Seattle, Washington 98109, USA
Nature 436:701-3. 2005..Our results indicate that genetic interactions are widespread in the genetics of transcript levels, and that many QTLs will be missed by single-locus tests but can be detected by two-stage tests that allow for interactions... - Telomere length as a quantitative trait: genome-wide survey and genetic mapping of telomere length-control genes in yeastTonibelle Gatbonton
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
PLoS Genet 2:e35. 2006..Furthermore, our results laid the foundation for studying genetic determinants of telomere length-variation and their roles in human disease... - Sequence variation and linkage disequilibrium in the human T-cell receptor beta (TCRB) locusL Subrahmanyan
Department of Molecular Biotechnology, University of Washington, Seattle, WA 98195, USA
Am J Hum Genet 69:381-95. 2001..These results provide the basis for optimization of locuswide SNP typing in TCRB for studies of genotype-phenotype association... - Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arraysJames Ronald
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Genome Res 15:284-91. 2005..With this method, we discovered 70 ORFs with evidence for preferential expression of one allele in a diploid hybrid of two S. cerevisiae strains... - Polymorphisms in multiple genes contribute to the spontaneous mitochondrial genome instability of Saccharomyces cerevisiae S288C strainsLazar N Dimitrov
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Genetics 183:365-83. 2009..Moreover, the polymorphisms identified in this study open new lines of investigation into mtDNA maintenance... - Sequence-based linkage analysisItay Furman
Division of Human Biology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109-1024, USA
Am J Hum Genet 75:647-53. 2004..We validate these results experimentally by implementing the sequence-based linkage approach for chromosome 19 in CEPH pedigrees... - Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humansChristopher S Carlson
Department of Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, Washington 98195-7730, USA
Nat Genet 33:518-21. 2003.... - Genetic structure of the purebred domestic dogHeidi G Parker
Division of Human Biology, Fred Hutchinson Cancer Research Center, Post Office Box 19024, 1100 Fairview Avenue North, D4-100, Seattle, WA 98109-1024, USA
Science 304:1160-4. 2004..These results provide a genetic classification of dog breeds and will aid studies of the genetics of phenotypic breed differences... - Multiple locus linkage analysis of genomewide expression in yeastJohn D Storey
Department of Biostatistics, University of Washington, Seattle, Washington, USA
PLoS Biol 3:e267. 2005..In addition, we show that a two-dimensional scan does not truly allow one to test for simultaneous linkage, and the statistical significance measured from this existing method cannot be interpreted among many traits... - Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibriumChristopher S Carlson
Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
Am J Hum Genet 74:106-20. 2004..We demonstrate that, although common variation tends to be shared between populations, tagSNPs should be selected separately for populations with different ancestries... - A joint analysis of asthma affection status and IgE levels in multiple data sets collected for asthmaK Markianos
Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, D4100, P.O. Box 19024, Seattle, WA 98109-1024, USA
Genet Epidemiol 21:S148-53. 2001..In contrast, we observe significant linkage to IgE level on chromosome 6... - Extensive and breed-specific linkage disequilibrium in Canis familiarisNathan B Sutter
Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
Genome Res 14:2388-96. 2004..We also report low haplotype diversity within regions of high LD, with 80% of chromosomes in a breed carrying two to four haplotypes, as well as a high degree of haplotype sharing among breeds... - Genetic basis of proteome variation in yeastEric J Foss
Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Nat Genet 39:1369-75. 2007..Loci that influenced protein abundance differed from those that influenced transcript levels, emphasizing the importance of direct analysis of the proteome... - Mapping complex disease loci in whole-genome association studiesChristopher S Carlson
Department of Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, Washington 98195 7730, USA
Nature 429:446-52. 2004.... - Genetic dissection of transcriptional regulation in budding yeastRachel B Brem
Fred Hutchinson Cancer Research Center (FHCRC, 1100 Fairview Avenue North, D4-100, Seattle, WA 98109, USA and Howard Hughes Medical Institute
Science 296:752-5. 2002..We found eight such trans-acting loci, each affecting the expression of a group of 7 to 94 genes of related function... - Breeding designs for recombinant inbred advanced intercross linesMatthew V Rockman
Lewis Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
Genetics 179:1069-78. 2008..We find that the easiest crosses to perform are well suited to the task of generating populations of highly recombinant inbred lines... - Patterns of linkage disequilibrium in the human genomeKristin G Ardlie
Genomics Collaborative, 99 Erie Street, Cambridge, Massachusetts 02139, USA
Nat Rev Genet 3:299-309. 2002..In this review, we draw on empirical studies in humans and Drosophila, as well as simulation studies, to assess the current state of knowledge about patterns of LD, and consider the implications for the use of LD as a mapping tool... - Genetic basis of individual differences in the response to small-molecule drugs in yeastEthan O Perlstein
Howard Hughes Medical Institute, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Genet 39:496-502. 2007..Our results provide a step toward a systematic understanding of small-molecule drug action in genetically distinct individuals... - Identification and dissection of a complex DNA repair sensitivity phenotype in Baker's yeastAnn Demogines
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
PLoS Genet 4:e1000123. 2008..It also provides tools for understanding the effect of genetic background on sensitivity to genotoxic agents... - Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genomeMichael A Eberle
Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
PLoS Genet 2:e142. 2006..The SNP pairs exhibiting perfect LD showed a significant bias for derived, nonancestral alleles, providing evidence for positive natural selection in the human genome... - Population genomic analysis of outcrossing and recombination in yeastDouglas M Ruderfer
Lewis-Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
Nat Genet 38:1077-81. 2006..Our results provide the initial foundation for population studies of association between genotype and phenotype in S. cerevisiae... - Revealing complex traits with small molecules and naturally recombinant yeast strainsEthan O Perlstein
Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
Chem Biol 13:319-27. 2006..The systematic combination of natural variants of yeast and small molecules that modulate evolutionarily conserved cellular processes can enable a better understanding of the general features of complex traits... - Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarrayDavid Gresham
Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
Science 311:1932-6. 2006..We applied this approach to elucidate the genetic basis of phenotypic variants and to identify the small number of single-base pair changes accumulated during experimental evolution of yeast... - Comment on 'Discrepancies in dbSNP confirmations rates and allele frequency distributions from varying genotyping error rates and patterns'Christopher S Carlson
Bioinformatics 21:141-3. 2005 - Gene-environment interaction in yeast gene expressionErin N Smith
Lewis Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
PLoS Biol 6:e83. 2008..These observations will guide the design of studies aimed at understanding the genetic basis of complex traits... - Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegansMichael F Palopoli
Department of Biology, Bowdoin College, 6500 College Station, Brunswick, Maine 04011, USA
Nature 454:1019-22. 2008..The reduced selection on male?male competition associated with the origin of hermaphroditism may have permitted the global spread of a loss-of-function mutation with restricted pleiotropy... - Rise of the machinesDavid Gresham
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
PLoS Genet 4:e1000134. 2008 - Genetics. It's the sequence, stupid!Hilary A Coller
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Science 322:380-1. 2008 - The road to genome-wide association studiesLeonid Kruglyak
Lewis Sigler Institute for Integrative Genomics, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
Nat Rev Genet 9:314-8. 2008..Here, I look back at how the necessary pieces fell into place, focusing on the less well-chronicled days before the launch of the HapMap project, and speculate about future developments... - Widespread genetic incompatibility in C. elegans maintained by balancing selectionHannah S Seidel
Lewis Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
Science 319:589-94. 2008..Our data suggest that long-term maintenance of a balanced polymorphism has permitted the incompatibility to persist despite gene flow across the rest of the genome... - A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening setTara C Matise
Department of Genetics, Rutgers University, Piscataway, NJ, 08840, USA
Am J Hum Genet 73:271-84. 2003..Evaluations indicate that this SNP screening set is more informative than the Marshfield Clinic's commonly used microsatellite-based screening set... - Evolution. An embarrassment of switchesLeonid Kruglyak
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
Science 317:758-9. 2007 - Genetics of global gene expressionMatthew V Rockman
Lewis-Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
Nat Rev Genet 7:862-72. 2006.... - Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populationsDana C Crawford
Department of Genome Sciences, University of Washington, Seattle 98195 7730, USA
Am J Hum Genet 74:610-22. 2004.... - Molecular genetics: DNA analysis of a putative dog cloneHeidi G Parker
Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Nature 440:E1-2. 2006..In light of recent concerns regarding the creation of cloned human cell lines from the same institution, we have undertaken an independent test to determine the validity of the claims made by Lee et al.... - Power tools for human geneticsLeonid Kruglyak
Nat Genet 37:1299-300. 2005 - No bias in linkage analysisGoncalo Abecasis
Am J Hum Genet 75:722-3; author reply 723-7. 2004