Bloom, Joshua S, Khan, Zia, Kruglyak, Leonid, Singh, Mona, Caudy, Amy A
Abstract Background High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring...
Khan, Zia, Bloom, Joshua S., Kruglyak, Leonid, Singh, Mona
Motivation: High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences...
Gene–Environment Interaction in Yeast Gene Expression (2008)
Erin N. Smith, Leonid Kruglyak
The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but such gene–environment interactions are poorly understood. Recently developed...
Leonid Kruglyak, Mark J. Daly, Eric S. Lander, Eric S. L
this paper allows very rapid multipoint likelihood calculation in nuclear families (with or without parental consanguinity), and the accompanying software package makes multipoint mapping feasible in...
Michael A. Eberle, Mark J. Rieder, Leonid Kruglyak, Deborah A. Nickerson
Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the extent of association, i.e., linkage...
Frequency-Matching SNPs Reveals Extended Linkage Disequilibrium in Genic Regions (2006)
Michael A Eberle, Mark J Rieder, Leonid Kruglyak, Deborah A. Nickerson
Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the extent of association, i.e. linkage...
Tonibelle Gatbonton, Maria Imbesi, Melisa Nelson, Joshua M. Akey, Douglas M. Ruderfer, Leonid Kruglyak, ...
Tonibelle Gatbonton, Maria Imbesi, Melisa Nelson, Joshua M. Akey, Douglas M. Ruderfer, Leonid Kruglyak, ...
Telomere length-variation in deletion strains of Saccharomyces cerevisiae was used to identify genes and pathways that regulate telomere length. We found 72 genes that when deleted confer short...
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast (2005)
John D. Storey, Joshua M. Akey, Leonid Kruglyak
Complex traits are frequently under control of multiple loci. This new method simultaneously maps multiple gene expression quantitative trait loci and assesses their significance within Saccharomyces...
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast (2005)
John D. Storey, Joshua M. Akey, Leonid Kruglyak
With the ability to measure thousands of related phenotypes from a single biological sample, it is now feasible to genetically dissect systems-level biological phenomena. The genetics of...
Local Regulatory Variation in Saccharomyces cerevisiae (2005)
James Ronald, Rachel B. Brem, Jacqueline Whittle, Leonid Kruglyak
Naturally occurring sequence variation that affects gene expression is an important source of phenotypic differences among individuals within a species. We and others have previously shown that such...
Carlson, Christopher S., Reider, Mark J., Nickerson, Deborah A., Eberle, Michael A., Kruglyak, Leonid
Ronald, James, Akey, Joshua M., Whittle, Jacqueline, Smith, Erin N., Yvert, Gael, Kruglyak, Leonid
Oligonucleotide microarrays provide a high-throughput method for exploring genomes. In addition to their utility for gene-expression analysis, oligonucleotide-expression arrays have also been used to...
Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes (2004)
Joshua M. Akey, Michael A. Eberle, Mark J. Rieder, Christopher S. Carlson, Mark D. Shriver, Deborah A. Nickerson, ...
An analysis of 132 human genes suggests that the migration of modern humans out of Africa into new environments was accompanied by genetic adaptations to emergent selective forces.
Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes (2004)
Joshua M. Akey, Michael A. Eberle, Mark J. Rieder, Christopher S. Carlson, Mark D. Shriver, Deborah A. Nickerson, ...
Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex...
Carlson, Christopher S., Eberle, Michael A., Reider, Mark J., Kruglyak, Leonid, Nickerson, Deborah A.
Extensive and breed-specific linkage disequilibrium in Canis familiaris (2004)
Sutter, Nathan B., Eberle, Michael A., Parker, Heidi G., Pullar, Barbara J., Kirkness, Ewen F., Kruglyak, Leonid, ...
The 156 breeds of registered dogs in the United States offer a unique opportunity to map genes important in disease susceptibility, morphology, and behavior. Linkage disequilibrium (LD) is of current...
Extensive and breed-specific linkage disequilibrium in Canis familiaris (2004)
Sutter, Nathan B., Eberle, Michael A., Parker, Heidi G., Pullar, Barbara J., Kirkness, Ewen F., Kruglyak, Leonid, ...
The 156 breeds of registered dogs in the United States offer a unique opportunity to map genes important in disease susceptibility, morphology, and behavior. Linkage disequilibrium (LD) is of current...
Carlson, Christopher S., Eberle, Michael A., Reider, Mark J., Kruglyak, Leonid, Nickerson, Deborah A.
Precise gene localization by phenotypic assay of radiation hybrid cells
Rasko, John E. J., Battini, Jean-Luc, Kruglyak, Leonid, Cox, David R., Miller, A. Dusty
A high resolution map of the human genome previously has been constructed by using the G3 panel of human/hamster radiation hybrid cell lines and >15,000 unique human genetic markers. By determining...
Linkage of a neurophysiological deficit in schizophrenia to a chromosome 15 locus
Freedman, Robert, Coon, Hilary, Myles-Worsley, Marina, Orr-Urtreger, Avi, Olincy, Ann, Davis, Ashley, ...
Inheritance of a defect in a neuronal mechanism that regulates response to auditory stimuli was studied in nine families with multiple cases of schizophrenia. The defect, a decrease in the normal...
Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes
Akey, Joshua M, Eberle, Michael A, Rieder, Mark J, Carlson, Christopher S, Shriver, Mark D, Nickerson, Deborah A, ...
Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex...
Extensive and breed-specific linkage disequilibrium in Canis familiaris
Sutter, Nathan B., Eberle, Michael A., Parker, Heidi G., Pullar, Barbara J., Kirkness, Ewen F., Kruglyak, Leonid, ...
The 156 breeds of registered dogs in the United States offer a unique opportunity to map genes important in disease susceptibility, morphology, and behavior. Linkage disequilibrium (LD) is of current...
Ronald, James, Akey, Joshua M., Whittle, Jacqueline, Smith, Erin N., Yvert, Gael, Kruglyak, Leonid
Oligonucleotide microarrays provide a high-throughput method for exploring genomes. In addition to their utility for gene-expression analysis, oligonucleotide-expression arrays have also been used to...
The landscape of genetic complexity across 5,700 gene expression traits in yeast
Brem, Rachel B., Kruglyak, Leonid
Many studies have identified quantitative trait loci (QTLs) that contribute to continuous variation in heritable traits of interest. However, general principles regarding the distribution of QTL...
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast
Storey, John D, Akey, Joshua M, Kruglyak, Leonid
With the ability to measure thousands of related phenotypes from a single biological sample, it is now feasible to genetically dissect systems-level biological phenomena. The genetics of...
Local Regulatory Variation in Saccharomyces cerevisiae
Ronald, James, Brem, Rachel B, Whittle, Jacqueline, Kruglyak, Leonid
Naturally occurring sequence variation that affects gene expression is an important source of phenotypic differences among individuals within a species. We and others have previously shown that such...
Sequence Variation and Linkage Disequilibrium in the Human T-Cell Receptor β (TCRB) Locus
Subrahmanyan, Lakshman, Eberle, Michael A., Clark, Andrew G., Kruglyak, Leonid, Nickerson, Deborah A.
The T-cell receptor (TCR) plays a central role in the immune system, and >90% of human T cells present a receptor that consists of the α TCR subunit (TCRA) and the β subunit (TCRB). Here we report...
Ardlie, Kristin, Liu-Cordero, Shau Neen, Eberle, Michael A., Daly, Mark, Barrett, Jeff, Winchester, Ellen, ...
Understanding the pattern of linkage disequilibrium (LD) in the human genome is important both for successful implementation of disease-gene mapping approaches and for inferences about human...
Efficient Multipoint Linkage Analysis through Reduction of Inheritance Space
Markianos, Kyriacos, Daly, Mark J., Kruglyak, Leonid
Computational constraints currently limit exact multipoint linkage analysis to pedigrees of moderate size. We introduce new algorithms that allow analysis of larger pedigrees by reducing the time and...
Exact Multipoint Quantitative-Trait Linkage Analysis in Pedigrees by Variance Components
Pratt, Stephen C., Daly, Mark J., Kruglyak, Leonid
Methods based on variance components are powerful tools for linkage analysis of quantitative traits, because they allow simultaneous consideration of all pedigree members. The central idea is to...
Full-Genome Scan for Linkage in 50 Families Segregating the Bipolar Affective Disease Phenotype
Friddle, Carl, Koskela, Rebecca, Ranade, Koustubh, Hebert, Joan, Cargill, Michele, Clark, Chris D., ...
A genome scan of ∼12-cM initial resolution was done on 50 of a set of 51 carefully ascertained unilineal multiplex families segregating the bipolar affective disorder phenotype. In addition to...
Genetic interactions between polymorphisms that affect gene expression in yeast
Brem, Rachel B., Storey, John D., Whittle, Jacqueline, Kruglyak, Leonid
Interactions between polymorphisms at different quantitative trait loci (QTLs) are thought to contribute to the genetics of many traits, and can dramatically impact the power of genetic studies to...
Gatbonton, Tonibelle, Imbesi, Maria, Nelson, Melisa, Akey, Joshua M, Ruderfer, Douglas M, Kruglyak, Leonid, ...
Telomere length-variation in deletion strains of Saccharomyces cerevisiae was used to identify genes and pathways that regulate telomere length. We found 72 genes that when deleted confer short...
Gatbonton, Tonibelle, Imbesi, Maria, Nelson, Melisa, Akey, Joshua M, Ruderfer, Douglas M, Kruglyak, Leonid, ...
Eberle, Michael A, Rieder, Mark J, Kruglyak, Leonid, Nickerson, Deborah A
Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the extent of association, i.e., linkage...
Precise gene localization by phenotypic assay of radiation hybrid cells
Rasko, John E. J., Battini, Jean-Luc, Kruglyak, Leonid, Cox, David R., Miller, A. Dusty
A high resolution map of the human genome previously has been constructed by using the G3 panel of human/hamster radiation hybrid cell lines and >15,000 unique human genetic markers. By determining...
Linkage of a neurophysiological deficit in schizophrenia to a chromosome 15 locus
Freedman, Robert, Coon, Hilary, Myles-Worsley, Marina, Orr-Urtreger, Avi, Olincy, Ann, Davis, Ashley, ...
Inheritance of a defect in a neuronal mechanism that regulates response to auditory stimuli was studied in nine families with multiple cases of schizophrenia. The defect, a decrease in the normal...
A New Susceptibility Locus for Autosomal Dominant Pancreatic Cancer Maps to Chromosome 4q32-34
Eberle, Michael A., Pfützer, Roland, Pogue-Geile, Kay L., Bronner, Mary P., Crispin, David, Kimmey, Michael B., ...
Pancreatic cancer is the fifth leading cause of cancer death in the United States. Nearly every person diagnosed with pancreatic cancer will die from it, usually in
Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes
Akey, Joshua M, Eberle, Michael A, Rieder, Mark J, Carlson, Christopher S, Shriver, Mark D, Nickerson, Deborah A, ...
Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex...
Extensive and breed-specific linkage disequilibrium in Canis familiaris
Sutter, Nathan B., Eberle, Michael A., Parker, Heidi G., Pullar, Barbara J., Kirkness, Ewen F., Kruglyak, Leonid, ...
The 156 breeds of registered dogs in the United States offer a unique opportunity to map genes important in disease susceptibility, morphology, and behavior. Linkage disequilibrium (LD) is of current...
Ronald, James, Akey, Joshua M., Whittle, Jacqueline, Smith, Erin N., Yvert, Gael, Kruglyak, Leonid
Oligonucleotide microarrays provide a high-throughput method for exploring genomes. In addition to their utility for gene-expression analysis, oligonucleotide-expression arrays have also been used to...
The landscape of genetic complexity across 5,700 gene expression traits in yeast
Brem, Rachel B., Kruglyak, Leonid
Many studies have identified quantitative trait loci (QTLs) that contribute to continuous variation in heritable traits of interest. However, general principles regarding the distribution of QTL...
A 3.9-Centimorgan-Resolution Human Single-Nucleotide Polymorphism Linkage Map and Screening Set
Matise, Tara C., Sachidanandam, Ravi, Clark, Andrew G., Kruglyak, Leonid, Wijsman, Ellen, Kakol, Jerzy, ...
Recent advances in technologies for high-throughout single-nucleotide polymorphism (SNP)–based genotyping have improved efficiency and cost so that it is now becoming reasonable to consider the use...
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast
Storey, John D, Akey, Joshua M, Kruglyak, Leonid
With the ability to measure thousands of related phenotypes from a single biological sample, it is now feasible to genetically dissect systems-level biological phenomena. The genetics of...
Carlson, Christopher S., Eberle, Michael A., Rieder, Mark J., Yi, Qian, Kruglyak, Leonid, Nickerson, Deborah A.
Common genetic polymorphisms may explain a portion of the heritable risk for common diseases. Within candidate genes, the number of common polymorphisms is finite, but direct assay of all existing...
Crawford, Dana C., Carlson, Christopher S., Rieder, Mark J., Carrington, Dana P., Yi, Qian, Smith, Joshua D., ...
Recent studies have suggested that a significant fraction of the human genome is contained in blocks of strong linkage disequilibrium, ranging from ∼5 to >100 kb in length, and that within these...
Sequence-Based Linkage Analysis
Furman, Itay, Rieder, Mark J., Da Ponte, Suzanne, Carrington, Dana P., Nickerson, Deborah A., Kruglyak, Leonid, ...
The rapid decrease in the cost of DNA sequencing will enable its use for novel applications. Here, we investigate the use of DNA sequencing for simultaneous discovery and genotyping of polymorphisms...
Abecasis, Goncalo, Cox, Nancy, Daly, Mark J., Kruglyak, Leonid, Laird, Nan, Markianos, Kyriacos, ...
Local Regulatory Variation in Saccharomyces cerevisiae
Ronald, James, Brem, Rachel B, Whittle, Jacqueline, Kruglyak, Leonid
Naturally occurring sequence variation that affects gene expression is an important source of phenotypic differences among individuals within a species. We and others have previously shown that such...
Sequence Variation and Linkage Disequilibrium in the Human T-Cell Receptor β (TCRB) Locus
Subrahmanyan, Lakshman, Eberle, Michael A., Clark, Andrew G., Kruglyak, Leonid, Nickerson, Deborah A.
The T-cell receptor (TCR) plays a central role in the immune system, and >90% of human T cells present a receptor that consists of the α TCR subunit (TCRA) and the β subunit (TCRB). Here we report...
Ardlie, Kristin, Liu-Cordero, Shau Neen, Eberle, Michael A., Daly, Mark, Barrett, Jeff, Winchester, Ellen, ...
Understanding the pattern of linkage disequilibrium (LD) in the human genome is important both for successful implementation of disease-gene mapping approaches and for inferences about human...
Efficient Multipoint Linkage Analysis through Reduction of Inheritance Space
Markianos, Kyriacos, Daly, Mark J., Kruglyak, Leonid
Computational constraints currently limit exact multipoint linkage analysis to pedigrees of moderate size. We introduce new algorithms that allow analysis of larger pedigrees by reducing the time and...
Exact Multipoint Quantitative-Trait Linkage Analysis in Pedigrees by Variance Components
Pratt, Stephen C., Daly, Mark J., Kruglyak, Leonid
Methods based on variance components are powerful tools for linkage analysis of quantitative traits, because they allow simultaneous consideration of all pedigree members. The central idea is to...
Full-Genome Scan for Linkage in 50 Families Segregating the Bipolar Affective Disease Phenotype
Friddle, Carl, Koskela, Rebecca, Ranade, Koustubh, Hebert, Joan, Cargill, Michele, Clark, Chris D., ...
A genome scan of ∼12-cM initial resolution was done on 50 of a set of 51 carefully ascertained unilineal multiplex families segregating the bipolar affective disorder phenotype. In addition to...
Gatbonton, Tonibelle, Imbesi, Maria, Nelson, Melisa, Akey, Joshua M, Ruderfer, Douglas M, Kruglyak, Leonid, ...
Telomere length-variation in deletion strains of Saccharomyces cerevisiae was used to identify genes and pathways that regulate telomere length. We found 72 genes that when deleted confer short...
Gatbonton, Tonibelle, Imbesi, Maria, Nelson, Melisa, Akey, Joshua M, Ruderfer, Douglas M, Kruglyak, Leonid, ...
Eberle, Michael A, Rieder, Mark J, Kruglyak, Leonid, Nickerson, Deborah A
Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the extent of association, i.e., linkage...
Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains
Schacherer, Joseph, Ruderfer, Douglas M., Gresham, David, Dolinski, Kara, Botstein, David, Kruglyak, Leonid
Ten years have passed since the genome of Saccharomyces cerevisiae–more precisely, the S288c strain–was completely sequenced. However, experimental work in yeast is commonly performed using...
Identification and Dissection of a Complex DNA Repair Sensitivity Phenotype in Baker's Yeast
Demogines, Ann, Smith, Erin, Kruglyak, Leonid, Alani, Eric
Complex traits typically involve the contribution of multiple gene variants. In this study, we took advantage of a high-density genotyping analysis of the BY (S288c) and RM strains of Saccharomyces...
Breeding Designs for Recombinant Inbred Advanced Intercross Lines
Rockman, Matthew V., Kruglyak, Leonid
Recombinant inbred lines derived from an advanced intercross, in which multiple generations of mating have increased the density of recombination breakpoints, are powerful tools for mapping the loci...
Comparative Developmental Expression Profiling of Two C. elegans Isolates
Capra, Emily J., Skrovanek, Sonja M., Kruglyak, Leonid
Gene expression is known to change during development and to vary among genetically diverse strains. Previous studies of temporal patterns of gene expression during C. elegans development were...
Recombinational Landscape and Population Genomics of Caenorhabditis elegans
Rockman, Matthew V., Kruglyak, Leonid
Recombination rate and linkage disequilibrium, the latter a function of population genomic processes, are the critical parameters for mapping by linkage and association, and their patterns in...
Gene–Environment Interaction in Yeast Gene Expression
Smith, Erin N, Kruglyak, Leonid
The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but such gene–environment interactions are poorly understood. Recently developed...
Using Expression and Genotype to Predict Drug Response in Yeast
Ruderfer, Douglas M., Roberts, David C., Schreiber, Stuart L., Perlstein, Ethan O., Kruglyak, Leonid
Personalized, or genomic, medicine entails tailoring pharmacological therapies according to individual genetic variation at genomic loci encoding proteins in drug-response pathways. It has been...
Protein quantification across hundreds of experimental conditions
Khan, Zia, Bloom, Joshua S., Garcia, Benjamin A., Singh, Mona, Kruglyak, Leonid
Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds...