Curating Genetic Association Literature for Common Diseases (2009)
Elana Silver, Eran Halperin, Kord M. Kober, Badri Padhukasahasram, Nila Patil, Michelle Sommargren, ...
Papers describing genetic associations with common diseases are currently being published at a rapid rate. These new papers add to an already large body of literature which includes candidate gene...
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...
Fast-evolving noncoding sequences in the human genome (2007)
Bird, Christine P, Stranger, Barbara E, Liu, Maureen, Thomas, Daryl J, Ingle, Catherine E, Beazley, Claude, ...
Abstract Background Gene regulation is considered one of the driving forces of evolution. Although protein-coding DNA sequences and RNA genes have been subject to recent evolutionary events in the...
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
The ENCODE Project at UC Santa Cruz (2007)
Thomas, Daryl J., Rosenbloom, Kate R., Clawson, Hiram, Hinrichs, Angie S., Trumbower, Heather, Raney, Brian J., ...
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development...
Variation resources at UC Santa Cruz (2007)
Thomas, Daryl J., Trumbower, Heather, Kern, Andrew D., Rhead, Brooke L., Kuhn, Robert M., Haussler, David, ...
The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in...
doi:10.1093/nar/gkl1017 The ENCODE Project at UC Santa Cruz (2006)
Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, ...
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development...
doi:10.1093/nar/gkl953 Variation resources at UC Santa Cruz (2006)
Daryl J. Thomas, Heather Trumbower, Andrew D. Kern, Brooke L. Rhead, Robert M. Kuhn, David Haussler, ...
The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in...
The ENCODE Project at UC Santa Cruz (2006)
Thomas, Daryl J., Rosenbloom, Kate R., Clawson, Hiram, Hinrichs, Angie S., Trumbower, Heather, Raney, Brian J., ...
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development...
Variation resources at UC Santa Cruz (2006)
Thomas, Daryl J., Trumbower, Heather, Kern, Andrew D., Rhead, Brooke L., Kuhn, Robert M., Haussler, David, ...
The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in...
The ENCODE Project at UC Santa Cruz (2006)
Thomas, Daryl J., Rosenbloom, Kate R., Clawson, Hiram, Hinrichs, Angie S., Trumbower, Heather, Raney, Brian J., ...
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development...
Variation resources at UC Santa Cruz (2006)
Thomas, Daryl J., Trumbower, Heather, Kern, Andrew D., Rhead, Brooke L., Kuhn, Robert M., Haussler, David, ...
The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in...
Sequence features in regions of weak and strong linkage disequilibrium (2005)
Smith, Albert V., Thomas, Daryl J., Munro, Heather M., Abecasis, Gonçalo R.
We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation...
Genomic regions exhibiting positive selection identified from dense genotype data (2005)
Carlson, Christopher S., Thomas, Daryl J., Eberle, Michael A., Swanson, Johanna E., Livingston, Robert J., Rieder, Mark J., ...
The allele frequency spectrum of polymorphisms in DNA sequences can be used to test for signatures of natural selection that depart from the expected frequency spectrum under the neutral theory. We...
Karchin, Rachel, Diekhans, Mark, Kelly, Libusha, Thomas, Daryl J., Pieper, Ursula, Eswar, Narayanan, ...
Motivation: The NCBI dbSNP database lists over 9 million single nucleotide polymorphisms (SNPs) in the human genome, but currently contains limited annotation information. SNPs that result in amino...
Karchin, Rachel, Diekhans, Mark, Kelly, Libusha, Thomas, Daryl J., Pieper, Ursula, Eswar, Narayanan, ...
Motivation: The NCBI dbSNP database lists over 9 million SNPs in the human genome, but currently contains limited annotation information. SNPs that result in amino-acid residue changes (nsSNPs) are...
Sequence features in regions of weak and strong linkage disequilibrium
Smith, Albert V., Thomas, Daryl J., Munro, Heather M., Abecasis, Gonçalo R.
We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation...
Genomic regions exhibiting positive selection identified from dense genotype data
Carlson, Christopher S., Thomas, Daryl J., Eberle, Michael A., Swanson, Johanna E., Livingston, Robert J., Rieder, Mark J., ...
The allele frequency spectrum of polymorphisms in DNA sequences can be used to test for signatures of natural selection that depart from the expected frequency spectrum under the neutral theory. We...
Sequence features in regions of weak and strong linkage disequilibrium
Smith, Albert V., Thomas, Daryl J., Munro, Heather M., Abecasis, Gonçalo R.
We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation...
Genomic regions exhibiting positive selection identified from dense genotype data
Carlson, Christopher S., Thomas, Daryl J., Eberle, Michael A., Swanson, Johanna E., Livingston, Robert J., Rieder, Mark J., ...
The allele frequency spectrum of polymorphisms in DNA sequences can be used to test for signatures of natural selection that depart from the expected frequency spectrum under the neutral theory. We...
The ENCODE Project at UC Santa Cruz
Thomas, Daryl J., Rosenbloom, Kate R., Clawson, Hiram, Hinrichs, Angie S., Trumbower, Heather, Raney, Brian J., ...
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development...
Variation resources at UC Santa Cruz
Thomas, Daryl J., Trumbower, Heather, Kern, Andrew D., Rhead, Brooke L., Kuhn, Robert M., Haussler, David, ...
The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in...
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Fast-evolving noncoding sequences in the human genome
Bird, Christine P, Stranger, Barbara E, Liu, Maureen, Thomas, Daryl J, Ingle, Catherine E, Beazley, Claude, ...
Over 1,300 conserved non-coding sequences were identified that appear to have undergone dramatic human-specific changes in selective pressures; these are enriched in recent segmental duplications,...