Enrichment of sequencing targets from the human genome by solution hybridization (2009)
Tewhey, Ryan, Nakano, Masakazu, Wang, Xiaoyun, Pabón-Peña, Carlos, Novak, Barbara, Giuffre, Angelica, ...
Abstract To exploit fully the potential of current sequencing technologies for population-based studies, one must enrich for loci from the human genome. Here we evaluate the hybridization-based...
Evaluation of next generation sequencing platforms for population targeted sequencing studies (2009)
Harismendy, Olivier, Ng, Pauline C, Strausberg, Robert L, Wang, Xiaoyun, Stockwell, Timothy B, Beeson, Karen Y, ...
Abstract Background Next generation sequencing (NGS) platforms are currently being utilized for targeted sequencing of candidate genes or genomic intervals to perform sequence-based association...
Genetic determinants of phenotypic diversity in humans (2008)
Rahim, Nazli G, Harismendy, Olivier, Topol, Eric J, Frazer, Kelly A
Abstract New technologies for rapidly assaying DNA sequences have revealed that the degree and nature of human genetic variation is far more complex then previously realized. These same technologies...
Resource PipMaker—A Web Server for Aligning Two Genomic DNA Sequences (2007)
Scott Schwartz, Zheng Zhang, Kelly A. Frazer, Arian Smit, Cathy Riemer, John Bouck, ...
PipMaker
A second generation human haplotype map of over 3.1 million SNPs (2007)
Frazer, Kelly A., Ballinger, Dennis G., Cox, David R., Hinds, David A., Stuve, Laura L., Gibbs, Richard A., ...
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and...
Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana (2007)
Clark, Richard M., Schweikert, Gabriele, Toomajian, Christopher, Ossowski, Stephan, Zeller, Georg, Shinn, Paul, ...
Allele-Specific KRT1 Expression Is a Complex Trait (2006)
Heng Tao, David R. Cox, Kelly A. Frazer
The differential expression of alleles occurs commonly in humans and is likely an important genetic factor underlying heritable differences in phenotypic traits. Understanding the molecular basis of...
Analysis of allelic differential expression in human white blood cells (2006)
Pant, P.V. Krishna, Tao, Heng, Beilharz, Erica J., Ballinger, Dennis G., Cox, David R., Frazer, Kelly A.
Allelic variation of gene expression is common in humans, and is of interest because of its potential contribution to variation in heritable traits. To identify human genes with allelic expression...
Analysis of allelic differential expression in human white blood cells (2006)
Pant, P.V. Krishna, Tao, Heng, Beilharz, Erica J., Ballinger, Dennis G., Cox, David R., Frazer, Kelly A.
Allelic variation of gene expression is common in humans, and is of interest because of its potential contribution to variation in heritable traits. To identify human genes with allelic expression...
Donfack, Joseph, Schneider, Daniel H, Tan, Zheng, Kurz, Thorsten, Dubchak, Inna, Frazer, Kelly A, ...
Abstract Background Evolutionarily conserved sequences likely have biological function. Methods To determine whether variation in conserved sequences in non-coding DNA contributes to risk for human...
Donfack, Joseph, Schneider, Daniel H., Tan, Zheng, Kurz, Thorsten, Dubchak, Inna, Frazer, Kelly A., ...
Background: Evolutionarily conserved sequences likely have biological function. Methods: To determine whether variation in conserved sequences in non-coding DNA contributes to risk for human disease,...
Fine-scale recombination patterns differ between chimpanzees and humans (2005)
Ptak, Susan E., Hinds, David A., Koehler, Kathrin, Nickel, Birgit, Patil, Nila, Ballinger, Dennis G., ...
The nature, pattern and function of human sequence variation (2004)
Eichler, Evan E, Frazer, Kelly A
Abstract A report on the 2004 Keystone Symposium 'Human Genome Sequence Variation and the Inherited Basis of Common Disease', Breckenridge, USA, 8-13 January 2004.
VISTA - computational tools for comparative genomics (2004)
Frazer, Kelly A., Pachter, Lior, Poliakov, Alexander, Rubin, Edward M., Dubchak, Inna
Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here we describe the VISTA family of tools created to assist biologists in...
Kelly A. Frazer, Heng Tao, Kazutoyo Osoegawa, Xiyin Chen, Mark F. Doherty, ...
data
VISTA: computational tools for comparative genomics (2004)
Kelly A. Frazer, Lior Pachter, Er Poliakov, Edward M. Rubin, Inna Dubchak
Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in...
Frazer, Kelly A., Tao, Heng, Osoegawa, Kazutoyo, De Jong, Pieter J., Chen, Xiyin, Doherty, Mark F., ...
Cross-species DNA sequence comparison is a fundamental method for identifying biologically important elements, because functional sequences are evolutionarily conserved, wheres nonfunctional...
Frazer, Kelly A., Wade, Claire M., Hinds, David A., Patil, Nila, Cox, David R., Daly, Mark J.
High-density SNP screening of panels of inbred mouse strains has been proposed as a method to accelerate the identification of genes associated with complex biomedical phenotypes. To evaluate the...
VISTA: computational tools for comparative genomics (2004)
Frazer, Kelly A., Pachter, Lior, Poliakov, Alexander, Rubin, Edward M., Dubchak, Inna
Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in...
Frazer, Kelly A., Tao, Heng, Osoegawa, Kazutoyo, De Jong, Pieter J., Chen, Xiyin, Doherty, Mark F., ...
Cross-species DNA sequence comparison is a fundamental method for identifying biologically important elements, because functional sequences are evolutionarily conserved, wheres nonfunctional...
Cross-Species Sequence Comparisons: A Review of Methods and Available Resources (2003)
Frazer, Kelly A., Elnitski, Laura, Church, Deanna M., Dubchak, Inna, Hardison, Ross C.
With the availability of whole-genome sequences for an increasing number of species, we are now faced with the challenge of decoding the information contained within these DNA sequences. Comparative...
Genomic DNA Insertions and Deletions Occur Frequently Between Humans and Nonhuman Primates (2003)
Frazer, Kelly A., Chen, Xiyin, Hinds, David A., Pant, P.V. Krishna, Patil, Nila, Cox, David R.
Genomic DNA Insertions and Deletions Occur Frequently Between Humans and Nonhuman Primates (2003)
Frazer, Kelly A., Chen, Xiyin, Hinds, David A., Pant, P.V. Krishna, Patil, Nila, Cox, David R.
Comparative DNA sequence studies between humans and nonhuman primates will be important for understanding the genetic basis of the phenotypic differences between these species. Here we compare ∼27...
Evolutionarily Conserved Sequences on Human Chromosome 21 (2001)
Frazer, Kelly A., Sheehan, John B., Stokowski, Renee P., Chen, Xiyin, Hosseini, Roya, Cheng, Jan-Fang, ...
Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons (2000)
Dubchak, Inna, Brudno, Michael, Loots, Gabriela G., Pachter, Lior, Mayor, Chris, Rubin, Edward M., ...
VISTA : visualizing global DNA sequence alignments of arbitrary length (2000)
Mayor, Chris, Brudno, Michael, Schwartz, Jody R., Poliakov, Alexander, Rubin, Edward M., Frazer, Kelly A., ...
Summary: VISTA is a program for visualizing global DNA sequence alignments of arbitrary length. It has a clean output, allowing for easy identification of similarity, and is easily configurable,...
PipMaker---A Web Server for Aligning Two Genomic DNA Sequences (2000)
Schwartz, Scott, Zhang, Zheng, Frazer, Kelly A., Smit, Arian, Riemer, Cathy, Bouck, John, ...
Frazer, Kelly A., Ueda, Yukihiko, Zhu, Yiwen, Gifford, Vincent R., Garofalo, Maria R., Mohandas, Narla, ...
Frazer, Kelly A., Boehnke, Michael, Budarf, Marcia L., Wolff, Roger K., Emanuel, Beverly S., Myers, Richard M., ...
We describe a high-resolution radiation hybrid map of the region on human chromosome 22 containing the neurofibromatosis type 2 (NF2) gene. Eighty-five hamster--human somatic cell hybrids generated...
Genomic interval engineering of mice identifies a novel modulator of triglyceride production
Zhu, Yiwen, Jong, Miek C., Frazer, Kelly A., Gong, Elaine, Krauss, Ronald M., Cheng, Jan-Fang, ...
To accelerate the biological annotation of novel genes discovered in sequenced regions of mammalian genomes, we are creating large deletions in the mouse genome targeted to include clusters of such...
PipMaker—A Web Server for Aligning Two Genomic DNA Sequences
Schwartz, Scott, Zhang, Zheng, Frazer, Kelly A., Smit, Arian, Riemer, Cathy, Bouck, John, ...
PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting...
Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons
Dubchak, Inna, Brudno, Michael, Loots, Gabriela G., Pachter, Lior, Mayor, Chris, Rubin, Edward M., ...
Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human–mouse DNA comparison studies have...
Evolutionarily Conserved Sequences on Human Chromosome 21
Frazer, Kelly A., Sheehan, John B., Stokowski, Renee P., Chen, Xiyin, Hosseini, Roya, Cheng, Jan-Fang, ...
Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide...
Frazer, Kelly A., Tao, Heng, Osoegawa, Kazutoyo, De Jong, Pieter J., Chen, Xiyin, Doherty, Mark F., ...
Cross-species DNA sequence comparison is a fundamental method for identifying biologically important elements, because functional sequences are evolutionarily conserved, wheres nonfunctional...
The nature, pattern and function of human sequence variation
Eichler, Evan E, Frazer, Kelly A
A report on the 2004 Keystone Symposium 'Human Genome Sequence Variation and the Inherited Basis of Common Disease', Breckenridge, USA, 8-13 January 2004.
Genomic DNA Insertions and Deletions Occur Frequently Between Humans and Nonhuman Primates
Frazer, Kelly A., Chen, Xiyin, Hinds, David A., Pant, P.V. Krishna, Patil, Nila, Cox, David R.
Comparative DNA sequence studies between humans and nonhuman primates will be important for understanding the genetic basis of the phenotypic differences between these species. Here we compare ∼27...
Cross-Species Sequence Comparisons: A Review of Methods and Available Resources
Frazer, Kelly A., Elnitski, Laura, Church, Deanna M., Dubchak, Inna, Hardison, Ross C.
With the availability of whole-genome sequences for an increasing number of species, we are now faced with the challenge of decoding the information contained within these DNA sequences. Comparative...
VISTA: computational tools for comparative genomics
Frazer, Kelly A., Pachter, Lior, Poliakov, Alexander, Rubin, Edward M., Dubchak, Inna
Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in...
Frazer, Kelly A., Wade, Claire M., Hinds, David A., Patil, Nila, Cox, David R., Daly, Mark J.
High-density SNP screening of panels of inbred mouse strains has been proposed as a method to accelerate the identification of genes associated with complex biomedical phenotypes. To evaluate the...
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy
Donfack, Joseph, Schneider, Daniel H, Tan, Zheng, Kurz, Thorsten, Dubchak, Inna, Frazer, Kelly A, ...
High-Resolution Whole-Genome Association Study of Parkinson Disease
Maraganore, Demetrius M., De Andrade, Mariza, Lesnick, Timothy G., Strain, Kari J., Farrer, Matthew J., Rocca, Walter A., ...
We performed a two-tiered, whole-genome association study of Parkinson disease (PD). For tier 1, we individually genotyped 198,345 uniformly spaced and informative single-nucleotide polymorphisms...
Allele-Specific KRT1 Expression Is a Complex Trait
Tao, Heng, Cox, David R, Frazer, Kelly A
The differential expression of alleles occurs commonly in humans and is likely an important genetic factor underlying heritable differences in phenotypic traits. Understanding the molecular basis of...
Analysis of allelic differential expression in human white blood cells
Pant, P.V. Krishna, Tao, Heng, Beilharz, Erica J., Ballinger, Dennis G., Cox, David R., Frazer, Kelly A.
Allelic variation of gene expression is common in humans, and is of interest because of its potential contribution to variation in heritable traits. To identify human genes with allelic expression...
Genomic interval engineering of mice identifies a novel modulator of triglyceride production
Zhu, Yiwen, Jong, Miek C., Frazer, Kelly A., Gong, Elaine, Krauss, Ronald M., Cheng, Jan-Fang, ...
To accelerate the biological annotation of novel genes discovered in sequenced regions of mammalian genomes, we are creating large deletions in the mouse genome targeted to include clusters of such...
PipMaker—A Web Server for Aligning Two Genomic DNA Sequences
Schwartz, Scott, Zhang, Zheng, Frazer, Kelly A., Smit, Arian, Riemer, Cathy, Bouck, John, ...
PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting...
Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons
Dubchak, Inna, Brudno, Michael, Loots, Gabriela G., Pachter, Lior, Mayor, Chris, Rubin, Edward M., ...
Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human–mouse DNA comparison studies have...
Evolutionarily Conserved Sequences on Human Chromosome 21
Frazer, Kelly A., Sheehan, John B., Stokowski, Renee P., Chen, Xiyin, Hosseini, Roya, Cheng, Jan-Fang, ...
Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide...
Frazer, Kelly A., Tao, Heng, Osoegawa, Kazutoyo, De Jong, Pieter J., Chen, Xiyin, Doherty, Mark F., ...
Cross-species DNA sequence comparison is a fundamental method for identifying biologically important elements, because functional sequences are evolutionarily conserved, wheres nonfunctional...
The nature, pattern and function of human sequence variation
Eichler, Evan E, Frazer, Kelly A
A report on the 2004 Keystone Symposium 'Human Genome Sequence Variation and the Inherited Basis of Common Disease', Breckenridge, USA, 8-13 January 2004.
Genomic DNA Insertions and Deletions Occur Frequently Between Humans and Nonhuman Primates
Frazer, Kelly A., Chen, Xiyin, Hinds, David A., Pant, P.V. Krishna, Patil, Nila, Cox, David R.
Comparative DNA sequence studies between humans and nonhuman primates will be important for understanding the genetic basis of the phenotypic differences between these species. Here we compare ∼27...
Cross-Species Sequence Comparisons: A Review of Methods and Available Resources
Frazer, Kelly A., Elnitski, Laura, Church, Deanna M., Dubchak, Inna, Hardison, Ross C.
With the availability of whole-genome sequences for an increasing number of species, we are now faced with the challenge of decoding the information contained within these DNA sequences. Comparative...
VISTA: computational tools for comparative genomics
Frazer, Kelly A., Pachter, Lior, Poliakov, Alexander, Rubin, Edward M., Dubchak, Inna
Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in...
Frazer, Kelly A., Wade, Claire M., Hinds, David A., Patil, Nila, Cox, David R., Daly, Mark J.
High-density SNP screening of panels of inbred mouse strains has been proposed as a method to accelerate the identification of genes associated with complex biomedical phenotypes. To evaluate the...
High-Resolution Whole-Genome Association Study of Parkinson Disease
Maraganore, Demetrius M., De Andrade, Mariza, Lesnick, Timothy G., Strain, Kari J., Farrer, Matthew J., Rocca, Walter A., ...
We performed a two-tiered, whole-genome association study of Parkinson disease (PD). For tier 1, we individually genotyped 198,345 uniformly spaced and informative single-nucleotide polymorphisms...
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy
Donfack, Joseph, Schneider, Daniel H, Tan, Zheng, Kurz, Thorsten, Dubchak, Inna, Frazer, Kelly A, ...
Analysis of allelic differential expression in human white blood cells
Pant, P.V. Krishna, Tao, Heng, Beilharz, Erica J., Ballinger, Dennis G., Cox, David R., Frazer, Kelly A.
Allelic variation of gene expression is common in humans, and is of interest because of its potential contribution to variation in heritable traits. To identify human genes with allelic expression...
Allele-Specific KRT1 Expression Is a Complex Trait
Tao, Heng, Cox, David R, Frazer, Kelly A
The differential expression of alleles occurs commonly in humans and is likely an important genetic factor underlying heritable differences in phenotypic traits. Understanding the molecular basis of...
In Vitro Human Keratinocyte Migration Rates Are Associated with SNPs in the KRT1 Interval
Tao, Heng, Berno, Anthony J., Cox, David R., Frazer, Kelly A.
Efforts to develop effective therapeutic treatments for promoting fast wound healing after injury to the epidermis are hindered by a lack of understanding of the factors involved....
Genetic determinants of phenotypic diversity in humans
Rahim, Nazli G, Harismendy, Olivier, Topol, Eric J, Frazer, Kelly A
New techniques are enabling the identification of genetic variants underlying complex diseases and phenotypic traits.
Evaluation of next generation sequencing platforms for population targeted sequencing studies
Harismendy, Olivier, Ng, Pauline C, Strausberg, Robert L, Wang, Xiaoyun, Stockwell, Timothy B, Beeson, Karen Y, ...
Human sequence generated from three next-generation sequencing platforms reveals systematic variability in sequence coverage due to local sequence characteristics.