Letter Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes (2009)
Gregory M. Cooper, Michael Brudno, Eric A. Stone, Inna Dubchak, Serafim Batzoglou, Arend Sidow
We present an analysis of rates and patterns of microevolutionary phenomena that have shaped the human, mouse, and rat genomes since their last common ancestor. We find evidence for a shift in the...
Mefford, Heather C., Cooper, Gregory M., Zerr, Troy, Smith, Joshua D., Baker, Carl, Shafer, Neil, ...
Copy-number variants (CNVs) are substantial contributors to human disease. A central challenge in CNV-disease association studies is to characterize the pathogenicity of rare and possibly...
Article Distribution and intensity of constraint in mammalian genomic sequence (2008)
Gregory M. Cooper, Eric A. Stone, George Asimenos, Nisc Comparative, Sequencing Program, Eric D. Green, ...
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
for Large-Scale Multiple Alignment (2008)
Michael Brudno, Chuong B. Do, Gregory M. Cooper, Michael F. Kim, Eugene Davydov, ...
To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the...
Qualifying the relationship between sequence conservation and molecular function (2008)
Cooper, Gregory M., Brown, Christopher D.
Quantification of evolutionary constraints via sequence conservation can be leveraged to annotate genomic functional sequences. Recent efforts addressing the converse of this relationship have...
Clark, Taane G, Andrew, Toby, Cooper, Gregory M, Margulies, Elliott H, Mullikin, James C, Balding, David J
Abstract Background We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small...
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,...
Regulation of Craniofacial Bone Healing Using Noggin (2007)
In cases of craniosynostosis, defined as the premature fusion of the cranial sutures, there is a need to inhibit bone formation in small calvarial defects to avoid the occurrence of postoperative...
Regulation of Craniofacial Bone Healing Using Noggin (2007)
In cases of craniosynostosis, defined as the premature fusion of the cranial sutures, there is a need to inhibit bone formation in small calvarial defects to avoid the occurrence of postoperative...
Mefford, Heather C., Clauin, Séverine, Sharp, Andrew J., Moller, Rikke S., Ullmann, Reinhard, Kapur, Raj, ...
Most studies of genomic disorders have focused on patients with cognitive disability and/or peripheral nervous system defects. In an effort to broaden the phenotypic spectrum of this disease model,...
Distribution and intensity of constraint in mammalian genomic sequence (2005)
Cooper, Gregory M., Stone, Eric A., Asimenos, George, Green, Eric D., Batzoglou, Serafim, ...
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
Distribution and intensity of constraint in mammalian genomic sequence (2005)
Cooper, Gregory M., Stone, Eric A., Asimenos, George, Green, Eric D., Batzoglou, Serafim, ...
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
ABC: software for interactive browsing of genomic multiple sequence alignment data (2004)
Cooper, Gregory M, Singaravelu, Senthil AG, Sidow, Arend
Abstract Background Alignment and comparison of related genome sequences is a powerful method to identify regions likely to contain functional elements. Such analyses are data intensive, requiring...
Automated whole-genome multiple alignment of rat, mouse, and human (2004)
Brudno, Michael, Poliakov, Alexander, Salamov, Asaf, Cooper, Gregory M., Sidow, Arend, Rubin, Edward M., ...
Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes (2004)
Cooper, Gregory M., Brudno, Michael, Stone, Eric A., Dubchak, Inna, Batzoglou, Serafim, Sidow, Arend
We present an analysis of rates and patterns of microevolutionary phenomena that have shaped the human, mouse, and rat genomes since their last common ancestor. We find evidence for a shift in the...
Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human (2004)
Brudno, Michael, Poliakov, Alexander, Salamov, Asaf, Cooper, Gregory M., Sidow, Arend, Rubin, Edward M., ...
We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome...
Bmc Bioinformatics, Gregory M Cooper, Senthil Ag Singaravelu, Arend Sidow
Software ABC: software for interactive browsing of genomic multiple sequence alignment data
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (2003)
Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, ...
To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the...
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes (2003)
Cooper, Gregory M., Brudno, Michael, Program, NISC Comparative Sequencing, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of...
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (2003)
Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, ...
Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes
Cooper, Gregory M., Brudno, Michael, Stone, Eric A., Dubchak, Inna, Batzoglou, Serafim, Sidow, Arend
We present an analysis of rates and patterns of microevolutionary phenomena that have shaped the human, mouse, and rat genomes since their last common ancestor. We find evidence for a shift in the...
Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
Brudno, Michael, Poliakov, Alexander, Salamov, Asaf, Cooper, Gregory M., Sidow, Arend, Rubin, Edward M., ...
We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome...
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, ...
To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the...
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes
Cooper, Gregory M., Brudno, Michael, Program, NISC Comparative Sequencing, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of...
Distribution and intensity of constraint in mammalian genomic sequence
Cooper, Gregory M., Stone, Eric A., Asimenos, George, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes
Cooper, Gregory M., Brudno, Michael, Stone, Eric A., Dubchak, Inna, Batzoglou, Serafim, Sidow, Arend
We present an analysis of rates and patterns of microevolutionary phenomena that have shaped the human, mouse, and rat genomes since their last common ancestor. We find evidence for a shift in the...
Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
Brudno, Michael, Poliakov, Alexander, Salamov, Asaf, Cooper, Gregory M., Sidow, Arend, Rubin, Edward M., ...
We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome...
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
Brudno, Michael, Do, Chuong B., Cooper, Gregory M., Kim, Michael F., Davydov, Eugene, Program, NISC Comparative Sequencing, ...
To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the...
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes
Cooper, Gregory M., Brudno, Michael, Program, NISC Comparative Sequencing, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of...
Distribution and intensity of constraint in mammalian genomic sequence
Cooper, Gregory M., Stone, Eric A., Asimenos, George, Green, Eric D., Batzoglou, Serafim, Sidow, Arend
Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the...
Mammalian Comparative Sequence Analysis of the Agrp Locus
Kaelin, Christopher B., Cooper, Gregory M., Sidow, Arend, Barsh, Gregory S.
Agouti-related protein encodes a neuropeptide that stimulates food intake. Agrp expression in the brain is restricted to neurons in the arcuate nucleus of the hypothalamus and is elevated by states...
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,...
Functional constraint and small insertions and deletions in the ENCODE regions of the human genome
Clark, Taane G, Andrew, Toby, Cooper, Gregory M, Margulies, Elliott H, Mullikin, James C, Balding, David J
Indel rates were observed to be reduced approximately twenty-fold in exonic ENCODE regions, five-fold in sequence that exhibits high evolutionary constraint in mammals and up to two-fold in some...
A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose
Cooper, Gregory M., Johnson, Julie A., Langaee, Taimour Y., Feng, Hua, Stanaway, Ian B., Schwarz, Ute I., ...
Warfarin dosing is correlated with polymorphisms in vitamin K epoxide reductase complex 1 (VKORC1) and the cytochrome P450 2C9 (CYP2C9) genes. Recently, the FDA revised warfarin labeling to raise...
Reiner, Alexander P., Barber, Mathew J., Guan, Yongtao, Ridker, Paul M., Lange, Leslie A., Chasman, Daniel I., ...
Data from the Pharmacogenomics and Risk of Cardiovascular Disease (PARC) study and the Cardiovascular Health Study (CHS) provide independent and confirmatory evidence for association between common...
Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease
Itsara, Andy, Cooper, Gregory M., Baker, Carl, Girirajan, Santhosh, Li, Jun, Absher, Devin, ...
Copy number variants (CNVs) contribute to human genetic and phenotypic diversity. However, the distribution of larger CNVs in the general population remains largely unexplored. We identify large...