Article Identification and Characterization of Multi-Species Conserved Sequences (2009)
Elliott H. Margulies, Mathieu Blanchette, David Haussler, Eric D. Green
Comparative sequence analysis has become an essential component of studies aiming to elucidate genome function. The increasing availability of genomic sequences from multiple vertebrates is creating...
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...
McCauley, Jacob L, Kenealy, Shannon J, Margulies, Elliott H, Schnetz-Boutaud, Nathalie, Gregory, Simon G, Hauser, Stephen L, ...
Abstract Background Although genes play a key role in many complex diseases, the specific genes involved in most complex diseases remain largely unidentified. Their discovery will hinge on 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,...
Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data (2007)
Sergey Nikolaev, Elliott H. Margulies, Jacques Rougemont, Bruno Nyffeler, ...
Understanding the early evolution of placental mammals is one of the most challenging issues in mammalian phylogeny. Here, we addressed this question by using the sequence data of the ENCODE...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Identification and Characterization of Multi-Species Conserved Sequences (2003)
Margulies, Elliott H., Blanchette, Mathieu, Haussler, David, Green, Eric D.
Comparative sequence analysis has become an essential component of studies aiming to elucidate genome function. The increasing availability of genomic sequences from multiple vertebrates is creating...
Identification and prevention of a GC content bias in SAGE libraries (2001)
Margulies, Elliott H., Kardia, Sharon L. R., Innis, Jeffrey W.
Serial Analysis of Gene Expression (SAGE) is becoming a widely used gene expression profiling method for the study of development, cancer and other human diseases. Investigators using SAGE rely...
eSAGE: managing and analysing data generated with Serial Analysis of Gene Expression (SAGE) (2000)
Margulies, Elliott H., Innis, Jeffrey W.
Summary: eSAGE is a comprehensive set of software tools for managing and analysing data generated with Serial Analysis of Gene Expression (SAGE). Availability: eSAGE is freely available for...
Identification and prevention of a GC content bias in SAGE libraries
Margulies, Elliott H., Kardia, Sharon L. R., Innis, Jeffrey W.
Serial Analysis of Gene Expression (SAGE) is becoming a widely used gene expression profiling method for the study of development, cancer and other human diseases. Investigators using SAGE rely...
Margulies, Elliott H., Kardia, Sharon L.R., Innis, Jeffrey W.
The analysis of differentially expressed genes is a powerful approach to elucidate the genetic mechanisms underlying the morphological and evolutionary diversity among serially homologous structures,...
Identification and Characterization of Multi-Species Conserved Sequences
Margulies, Elliott H., Blanchette, Mathieu, Haussler, David, Green, Eric D.
Comparative sequence analysis has become an essential component of studies aiming to elucidate genome function. The increasing availability of genomic sequences from multiple vertebrates is creating...
Angata, Takashi, Margulies, Elliott H., Green, Eric D., Varki, Ajit
Siglecs are a recently discovered family of animal lectins that belong to the Ig superfamily and recognize sialic acids (Sias). CD33-related Siglecs (CD33rSiglecs) are a subgroup with as-yet-unknown...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Identification and prevention of a GC content bias in SAGE libraries
Margulies, Elliott H., Kardia, Sharon L. R., Innis, Jeffrey W.
Serial Analysis of Gene Expression (SAGE) is becoming a widely used gene expression profiling method for the study of development, cancer and other human diseases. Investigators using SAGE rely...
Margulies, Elliott H., Kardia, Sharon L.R., Innis, Jeffrey W.
The analysis of differentially expressed genes is a powerful approach to elucidate the genetic mechanisms underlying the morphological and evolutionary diversity among serially homologous structures,...
Identification and Characterization of Multi-Species Conserved Sequences
Margulies, Elliott H., Blanchette, Mathieu, Haussler, David, Green, Eric D.
Comparative sequence analysis has become an essential component of studies aiming to elucidate genome function. The increasing availability of genomic sequences from multiple vertebrates is creating...
Angata, Takashi, Margulies, Elliott H., Green, Eric D., Varki, Ajit
Siglecs are a recently discovered family of animal lectins that belong to the Ig superfamily and recognize sialic acids (Sias). CD33-related Siglecs (CD33rSiglecs) are a subgroup with as-yet-unknown...
Margulies, Elliott H., Maduro, Valerie V. B., Thomas, Pamela J., Tomkins, Jeffery P., Amemiya, Chris T., Luo, Meizhong, ...
Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data
Nikolaev, Sergey, Montoya-Burgos, Juan I, Margulies, Elliott H, Program, NISC Comparative Sequencing, Rougemont, Jacques, Nyffeler, Bruno, ...
Understanding the early evolution of placental mammals is one of the most challenging issues in mammalian phylogeny. Here, we addressed this question by using the sequence data of the ENCODE...
McCauley, Jacob L, Kenealy, Shannon J, Margulies, Elliott H, Schnetz-Boutaud, Nathalie, Gregory, Simon G, Hauser, Stephen L, ...
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...
Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
Nikolaev, Sergey I., Montoya-Burgos, Juan I., Popadin, Konstantin, Parand, Leila, Margulies, Elliott H., Antonarakis, Stylianos E.
A comprehensive phylogenetic framework is indispensable for investigating the evolution of genomic features in mammals as a whole, and particularly in humans. Using the ENCODE sequence data, we...