Response to comment on "Human-specific gain of function in a developmental enhancer" (2009)
Prabhakar, Shyam, Visel, Axel, Akiyama, Jennifer A., Shoukry, Malak, Lewis, Keith D., Holt, Amy, ...
Duret and Galtier argue that human-specific sequence divergence and gain of function in the HACNS1 enhancer result from deleterious biased gene conversion (BGC) with no contribution from positive...
Response to comment on "Human-specific gain of function in a developmental enhancer" (2009)
Prabhakar, Shyam, Visel, Axel, Akiyama, Jennifer A., Shoukry, Malak, Lewis, Keith D., Holt, Amy, ...
Duret and Galtier argue that human-specific sequence divergence and gain of function in the HACNS1 enhancer result from deleterious biased gene conversion (BGC) with no contribution from positive...
Gill Bejerano, Craig Lowe, Nadav Ahituv, Bryan King, Adam Siepel, Sofie Salama, ...
An enhancer near ISL1 and an ultraconserved PCBP2 exon are
Human-specific gain of function in a developmental enhancer (2008)
Prabhakar, Shyam, Visel, Axel, Akiyama, Jennifer A., Shoukry, Malak, Lewis, Keith D., Holt, Amy, ...
Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive....
Martinez, Diego, Berka, Randy M., Henrissat, Bernard, Saloheimo, Markku, Arvas, Mikko, Baker, Scott E., ...
Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as...
* Corresponding authors Summary (2008)
Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, Wes Bethel, ...
The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing...
Identification of ancient remains through genomic sequencing (2008)
Blow, Matthew J., Zhang, Tao, Woyke, Tanja, Speller, Camilla F., Krivoshapkin, Andrei, Yang, Dongya Y., ...
Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In...
Deletion of Ultraconserved Elements Yields Viable Mice (2007)
Nadav Ahituv, Yiwen Zhu, Axel Visel, Amy Holt, Veena Afzal, Len A. Pennacchio, ...
Ultraconserved elements have been suggested to retain extended perfect sequence identity between the human, mouse, and rat genomes due to essential functional properties. To investigate the...
Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene (2007)
Ward, Robert D., Cho, MinChul, Camper, S. A., Davis, Shannon W., Raetzman, Lori T., Smith, Timothy P. L., ...
Mutations in PROP1 are a common genetic cause of multiple pituitary hormone deficiency (MPHD). We used a comparative genomics approach to predict the transcriptional regulatory domains of Prop1 and...
Deletion of ultraconserved elements yields viable mice (2007)
Ahituv, Nadav, Zhu, Yiwen, Visel, Axel, Holt, Amy, Afzal, Veena, Pennacchio, Len A., ...
Ultraconserved elements have been suggested to retain extended perfect sequence identity between the human, mouse, and rat genomes due to essential functional properties. To investigate the...
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons (2007)
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M, Boffelli, Dario
Abstract Background Genomic comparisons between human and distant, non-primate mammals are commonly used to identify cis -regulatory elements based on constrained sequence evolution. However, these...
Sequencing and analysis of Neanderthal genomic DNA (2006)
Coop, Graham, Kudaravalli, Sridhar, Smith, Doug, Krause, Johannes, Alessi, Joe, ...
Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe...
Symbiosis insights through metagenomic analysis of a microbial consortium (2006)
Woyke, Tanja, Teeling, Hanno, Ivanova, Natalia N., Hunteman, Marcel, Richter, Michael, Gloeckner, Frank Oliver, ...
Primate-specific evolution of an LDLR enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Background Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. Results In this...
Accelerated Evolution of Conserved Noncoding Sequences in the Human Genome (2006)
Prambhakar, Shyam, Noonan, James P., Paabo, Svante, Rubin, Edward M.
Genomic comparisons between human and distant, non-primate mammals are commonly used to identify cis-regulatory elements based on constrained sequence evolution. However, these methods fail to detect...
Primate-Specific Evolution of an LDLR Enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. In this study, we...
Sequencing and Analysis of Neanderthal Genomic DNA (2006)
Noonan, James P., Coop, Graham, Kudaravalli, Sridhar, Smith, Doug, Krause, Johannes, Alessi, Joe, ...
Recovery and analysis of multiple Neanderthal autosomal sequences using a metagenomic approach reveals that modern humans and Neanderthals split ~;400,000 years ago, without significant evidence of...
Detection of Weakly Conserved Ancestral Mammalian Regulatory Sequences by Primate Comparisons (2006)
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M., Boffelli, Dario
Genomic comparisons between human and distant, non-primate mammals are commonly used to identify cis-regulatory elements based on constrained sequence evolution. However, these methods fail to detect...
In Vivo Enhancer Analysis Chromosome 16 Conserved Noncoding Sequences (2006)
Pennacchio, Len A., Ahituv, Nadav, Moses, Alan M., Nobrega, Marcelo, Prabhakar, Shyam, Shoukry, Malak, ...
The identification of enhancers with predicted specificities in vertebrate genomes remains a significant challenge that is hampered by a lack of experimentally validated training sets. In this study,...
Accelerated Evolution of Conserved Noncoding Sequences in Humans (2006)
Prabhakar, Shyam, Noonan, James, Pääbo, Svante, Rubin, Edward M.
Application of sequence-based methods in human microbial ecology (2006)
Weng, Li, Rubin, Edward M., Bristow, James
Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods,...
Close sequence comparisons are sufficient to identify human cis-regulatory elements (2006)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Application of sequence-based methods in human microbial ecology (2006)
Weng, Li, Rubin, Edward M., Bristow, James
Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods,...
Close sequence comparisons are sufficient to identify human cis-regulatory elements (2006)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Close Sequence Comparisons are Sufficient to Identify Human cis-Regulatory Elements (2005)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Primate-specific evolution of an LDLR enhancer (2005)
Wang, Qian-Fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 are Derived from a Retroposon (2005)
Bejerano, Gill, Lowe, Craig, Ahituv, Nadav, King, Bryan, Siepel, Adam, Salama, Sofie, ...
Hundreds of highly conserved distal cis-regulatory elements have been characterized to date in vertebrate genomes1. Many thousands more are predicted based on comparative genomics2,3. Yet, in stark...
Metagenomics: DNA sequencing of environmental samples (2005)
Tringe, Susannah Green, Rubin, Edward M.
While genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent but a fraction of the...
Application of Sequence-based Methods in Human Microbial Ecology (2005)
Weng, Li, Rubin, Edward M., Bristow, James
Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods,...
Ahituv, Nadav, Prabhakar, Shyam, Poulin, Francis, Rubin, Edward M., Couronne, Olivier
Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major...
Sequence-based Methods in Human Microbial Ecology: A The 2nd Human Genome Comes of Age (2005)
Weng, Li, Rubin, Edward M., Bristow, James
Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease (2005)
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can negatively impact human development and health, yet due to the difficulty of detecting these critical sequences we predominantly focus on coding sequences...
Genomic sequencing of Pleistocene cave bears (2005)
Noonan, James P., Hofreiter, Michael, Smith, Doug, Priest, James R., Rohland, Nadin, Rabeder, Gernot, ...
Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and...
Genomic sequencing of Pleistocene Cave Bears (2005)
Noonan, James P., Hofreiter, Michael, Smith, Doug, Priest, James R., Rohland, Nadin, Rabeder, Gernot, ...
Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease (2005)
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can have a negative impact on human development and health, yet because of the difficulty of detecting these critical sequences, we predominantly focus on...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease (2005)
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can have a negative impact on human development and health, yet because of the difficulty of detecting these critical sequences, we predominantly focus on...
Ahituv, Nadav, Prabhakar, Shyam, Poulin, Francis, Rubin, Edward M., Couronne, Olivier
Our inability to associate distant regulatory elements with the genes they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle...
Ahituv, Nadav, Prabhakar, Shyam, Poulin, Francis, Rubin, Edward M., Couronne, Olivier
Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major...
Comparative metagenomics of microbial communities (2004)
Tringe, Susannah Green, Von Mering, Christian, Kobayashi, Arthur, Salamov, Asaf A., Chen, Kevin, Chang, Hwai W., ...
The predicted proteins encoded in DNA isolated from environmental microbial community samples reveal habitat-specific metabolic demands.
In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer (2004)
Poulin, Francis, Nobrega, Marcelo A., Plajzer-Frick, Ingrid, Holt, Amy, Afzal, Veena, Rubin, Edward M., ...
Genomic sequence comparisons between human, mouse and pufferfish (Takifugu rubripes (Fugu))have revealed a set of extremely conserved noncoding sequences. While this high degree of sequence...
Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene (2004)
Baroukh, Nadine, Ahituv, Nadav, Chang, Jessie, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., ...
COUP-TFII is a central nuclear hormone receptor that tightly regulates the expression of numerous target lipid metabolism genes in vertebrates. However, it remains unclear how COUP-TFII itself is...
The sequence and analysis of duplication rich human chromosome 16 (2004)
Martin, Joel, Han, Cliff, Gordon, Laurie A., Terry, Astrid, Prabhakar, Shyam, She, Xinwei, ...
We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by...
Intra-species sequence comparisons for annotating genomes (2004)
Boffelli, Dario, Weer, Claire V., Weng, Li, Lewis, Keith D., Shoukry, Malak I., Pachter, Lior, ...
Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its...
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., ...
Human apoB contributes to increased serum total apo(a) level in LPAtransgenic mice (2004)
Teivainen, Päivi A, Eliassen, Knut A, Rubin, Edward M, Djurovic, Srdjan, Berg, Kåre
Abstract Background The Lp(a) lipoprotein (Lp(a)) consists of the polymorphic glycoprotein apolipoprotein(a) (apo(a)), which is attached by a disulfide bond to apolipoprotein B (apoB). Apo(a), which...
Megabase deletions of gene deserts result in viable mice (2004)
Nobrega, Marcelo A., Zhu, Yiwen, Plajzer-Frick, Ingrid, Afzal, Veena, Rubin, Edward M.
The functional importance of the approximately 98 percent of mammalian genomes not corresponding to protein coding sequences remain largely un-scrutinized 1. To test experimentally whether some...
The complete sequence of human chromosome 5 (2004)
Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, State, ...
Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding...
Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments (2004)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Bethel, E. Wes, ...
We have developed Phylo-VISTA (Shah et al., 2003), an interactive software tool for analyzing multiple alignments by visualizing a similarity measure for DNA sequences of multiple species. The...
Genoux, Annelise, Gervois, Philippe, Rommens, Corinne, Dehondt, Helene, Foulard, Michel, Dehennault, Maud, ...
Several epidemiological studies have established that elevated plasma triglyceride concentrations constitute an independent risk factor for cardiovascular diseases. In addition, systemic inflammation...
Phosphorylation-dependent down-regulation of apolipoprotein A5 by insulin (2004)
Nowak, Maxine, Helleboid-Chapman, Audrey, Jakel, Heidelinde, Rommens, Corinne, Martin, Genevieve, Duran-Sandoval, Daniel, ...
The apolipoprotein A5 (APOA5) gene has been shown to be important in lowering plasma triglyceride levels. Since several studies have shown that hyperinsulinemia is associated with...
Mechanism of lipid lowering in mice expressing human apolipoprotein A5 (2004)
Fruchart-Najib, Jamila, Bauge, Eric, Niculescu, Loredan-Stefan, Pham, Tatiana, Thomas, Benoit, Rommens, Corinne, ...
Recently, we reported that apoAV plays key role in triglycerides lowering. Here, we attempted to determine the mechanism underlying this hypotriglyceridemic effect. We showed that triglyceride...
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...
Haplotypes in the APOA1-C3-A4-A5 Gene Cluster affect Plasma Lipids in both Humans and Baboons (2004)
Qian-fei Wang, Xin Liu, Ze Peng, Ronald M. Krauss, David L, John L. V, ...
Copyright © 2004 Oxford University Press Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related...
Phylo-VISTA: Interactive Visualization of Multiple DNA Sequence Alignments (2004)
Nameeta Shah Olivier, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, Wes Bethel, ...
an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu. Contact phylovista@lbl.gov 1 Introduction Large-scale genome...
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...
Haplotypes in the APOA1-C3-A4-A5 Gene Cluster affect Plasma Lipids in both Humans and Baboons (2004)
Wang, Qian-fei, Liu, Xin, O'Connell, Jeff, Peng, Ze, Krauss, Ronald M., Rainwater, David L., ...
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however,...
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments (2004)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Wes Bethel, E., ...
Motivation The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by...
Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons (2004)
Wang, Qian-fei, Liu, Xin, O'Connell, Jeff, Peng, Ze, Krauss, Ronald M., Rainwater, David L., ...
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however,...
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...
Exploiting human-fish genome comparisons for deciphering gene regulation (2004)
Ahituv, Nadav, Rubin, Edward M., Nobrega, Marcelo A.
Comparative genomics has served as an essential guide in the identification of functional coding and non-coding sequences in vertebrate genomes. Human–mouse pair-wise comparisons have limited...
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...
Intraspecies sequence comparisons for annotating genomes (2004)
Boffelli, Dario, Weer, Claire V., Weng, Li, Lewis, Keith D., Shoukry, Malak I., Pachter, Lior, ...
Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its...
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments (2004)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Bethel, E. Wes, ...
Motivation: The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by...
Intraspecies sequence comparisons for annotating genomes (2004)
Boffelli, Dario, Weer, Claire V., Weng, Li, Lewis, Keith D., Shoukry, Malak I., Pachter, Lior, ...
Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its...
Haplotypes in the APOA1-C3-A4-A5 Gene Cluster affect Plasma Lipids in both Humans and Baboons (2004)
Wang, Qian-fei, Liu, Xin, O'Connell, Jeff, Peng, Ze, Krauss, Ronald M., Rainwater, David L., ...
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however,...
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments (2004)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Wes Bethel, E., ...
Motivation The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by...
Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons (2003)
Wang, Qian-fei, Liu, Xin, O'Connell, Jeff, Peng, Ze, Krauss, Ronald M., Rainwater, David L., ...
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however,...
Baroukh, Nadine N., Bauge, Eric, Akiyama, Jennifer, Chang, Jessie, Fruchart, Jean-Charles, Rubin, Edward M., ...
Both the apolipoprotein A5 and C3 genes have repeatedly been shown to play an important role in determining plasma triglyceride concentrations in humans and mice. In mice, transgenic and knockout...
Phylo-VISTA: An interactive visualization tool for multiple DNA sequence alignments (2003)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Bethel, E. Wes, ...
Motivation. The power of multi-sequence comparison for biological discovery is well established and sequence data from a growing list of organisms is becoming available. Thus, a need exists for...
Convergent evolution in primates and an insectivore (2003)
Boffelli, Dario, Cheng, Jan-Fang, Rubin, Edward M.
The cardiovascular risk factor apolipoprotein(a) (apo(a)) has a puzzling distribution among mammals, its presence being limited to a subset of primates and a member of the insectivore lineage, the...
Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments (2003)
Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, ...
We have developed Phylo-VISTA (Shah et al., 2003) , an interactive software tool for analyzing multiple alignments by visualizing a similarity measure for DNA sequences of multiple species. The...
Eichenbaum-Voline, Sophie, Olivier, Michael, Jones, Emma L., Naoumova, Rossitza P., Jones, Bethan, Gau, Brian, ...
Combined hyperlipidemia (CHL) is a common disorder of lipid metabolism that leads to an increased risk of cardiovascular disease. The lipid profile of CHL is characterised by high levels of...
Pennacchio, Len A., Rubin, Edward M.
Apolipoprotein A5 (APOA5) is a newly described member of the apolipoprotein gene family whose initial discovery arose from comparative sequence analysis of the mammalian APOA1/C3/A4 gene cluster....
Two independent apolipoprotein A5 haplotypes influence human plasma triglyceride levels (2002)
Pennacchio, Len A., Olivier, Michael, Hubacek, Jaroslav A., Krauss, Ronald M., Rubin, Edward M., Cohen, Jonathan C.
The recently identified apolipoprotein A5 gene (APOA5) has been shown to play an important role in determining plasma triglyceride concentrations in humans and mice. We previously identified an APOA5...
Talmud, Philippa J., Hawe, Emma, Martin, Steve, Olivier, Michael, Miller, George J., Rubin, Edward M., ...
Since triglycerides (TG) are a major independent risk factor for coronary heart disease, understanding their genetic and environmental determinants is of major importance. Mouse models indicate an...
Deletion of a coordinate regulator of type 2 cytokine expression in mice (2001)
Mohrs, Markus, Blankespoor, Catherine M., Wang, Zhi-En, Loots, Gaby G., Hadeiba, Husein, Shinkai, Kanade, ...
Mechanisms underlying the differentiation of stable T helper subsets will be important in understanding how discrete types of immunity develop in response to different pathogens. An evolutionarily...
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,...
Functional screening and complex traits: human 21q22.2 sequences affecting learning in mice (1997)
Desmond J. Smith, Edward M. Rubin
Libraries of the mammalian genome have generally been propagated in single cells and have been used for gene discovery through in vitro analyses. We have expanded upon this concept by the creation of...
Frazer, Kelly A., Ueda, Yukihiko, Zhu, Yiwen, Gifford, Vincent R., Garofalo, Maria R., Mohandas, Narla, ...
Transformation of Bacillus subtilis with cloned thymidylate synthetases. (1980)
Thesis (Ph. D.)--University of Rochester.
Reinforcement as a function of attractiveness of reinforcing agent and task complexity. (1970)
Thesis (M.A.)--Marquette University, 1970.
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...
Santamarina-Fojo, Silvia, Peterson, Katherine, Knapper, Catherine, Qiu, Yang, Freeman, Lita, Cheng, Jan-Fang, ...
The ABCA1 gene, a member of the ATP-binding cassette A (ABCA1) transporter superfamily, encodes a membrane protein that facilitates the cellular efflux of cholesterol and phospholipids. Mutations in...
Friddle, Carl J., Koga, Teiichiro, Rubin, Edward M., Bristow, James
Although cardiac hypertrophy has been the subject of intensive investigation, regression of hypertrophy has been significantly less studied, precluding large-scale analysis of the relationship...
Sago, Haruhiko, Carlson, Elaine J., Smith, Desmond J., Kilbridge, Joshua, Rubin, Edward M., Mobley, William C., ...
A mouse model for Down syndrome, Ts1Cje, has been developed. This model has made possible a step in the genetic dissection of the learning, behavioral, and neurological abnormalities associated with...
Endothelial lipase is a major determinant of HDL level
Ishida, Tatsuro, Choi, Sungshin, Kundu, Ramendra K., Hirata, Ken-ichi, Rubin, Edward M., Cooper, Allen D., ...
A new member of the lipase gene family, initially termed endothelial lipase (gene nomenclature, LIPG; protein, EL), is expressed in a variety of different tissues, suggesting a general role in lipid...
rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites
Loots, Gabriela G., Ovcharenko, Ivan, Pachter, Lior, Dubchak, Inna, Rubin, Edward M.
Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVISTA, for high-throughput...
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...
Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient Mice
Callow, Matthew J., Dudoit, Sandrine, Gong, Elaine L., Speed, Terence P., Rubin, Edward M.
Based on the assumption that severe alterations in the expression of genes known to be involved in high-density lipoprotein (HDL) metabolism may affect the expression of other genes, we screened an...
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...
Human apoB contributes to increased serum total apo(a) level in LPA transgenic mice
Teivainen, Päivi A, Eliassen, Knut A, Rubin, Edward M, Djurovic, Srdjan, Berg, Kåre
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...
Intraspecies sequence comparisons for annotating genomes
Boffelli, Dario, Weer, Claire V., Weng, Li, Lewis, Keith D., Shoukry, Malak I., Pachter, Lior, ...
Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its...
Nowak, Maxime, Helleboid-Chapman, Audrey, Jakel, Heidelinde, Martin, Geneviève, Duran-Sandoval, Daniel, Staels, Bart, ...
The apolipoprotein A5 gene (APOA5) has been repeatedly implicated in lowering plasma triglyceride levels. Since several studies have demonstrated that hyperinsulinemia is associated with...
The Ter mutation in the Dead-end gene causes germ cell loss and testicular germ cell tumours
Youngren, Kirsten K., Coveney, Douglas, Peng, Xiaoning, Bhattacharya, Chitralekha, Schmidt, Laura S., Nickerson, Michael L., ...
The Ter mutation causes primordial germ cell (PGC) loss on all mouse genetic backgrounds (Fig. 1a) with deficiency of PGCs1 starting at embryonic day 8. Ter is also a potent modifier of spontaneous...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can have a negative impact on human development and health, yet because of the difficulty of detecting these critical sequences, we predominantly focus on...
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...
Santamarina-Fojo, Silvia, Peterson, Katherine, Knapper, Catherine, Qiu, Yang, Freeman, Lita, Cheng, Jan-Fang, ...
The ABCA1 gene, a member of the ATP-binding cassette A (ABCA1) transporter superfamily, encodes a membrane protein that facilitates the cellular efflux of cholesterol and phospholipids. Mutations in...
Friddle, Carl J., Koga, Teiichiro, Rubin, Edward M., Bristow, James
Although cardiac hypertrophy has been the subject of intensive investigation, regression of hypertrophy has been significantly less studied, precluding large-scale analysis of the relationship...
Sago, Haruhiko, Carlson, Elaine J., Smith, Desmond J., Kilbridge, Joshua, Rubin, Edward M., Mobley, William C., ...
A mouse model for Down syndrome, Ts1Cje, has been developed. This model has made possible a step in the genetic dissection of the learning, behavioral, and neurological abnormalities associated with...
Endothelial lipase is a major determinant of HDL level
Ishida, Tatsuro, Choi, Sungshin, Kundu, Ramendra K., Hirata, Ken-ichi, Rubin, Edward M., Cooper, Allen D., ...
A new member of the lipase gene family, initially termed endothelial lipase (gene nomenclature, LIPG; protein, EL), is expressed in a variety of different tissues, suggesting a general role in lipid...
rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites
Loots, Gabriela G., Ovcharenko, Ivan, Pachter, Lior, Dubchak, Inna, Rubin, Edward M.
Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVISTA, for high-throughput...
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...
Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient Mice
Callow, Matthew J., Dudoit, Sandrine, Gong, Elaine L., Speed, Terence P., Rubin, Edward M.
Based on the assumption that severe alterations in the expression of genes known to be involved in high-density lipoprotein (HDL) metabolism may affect the expression of other genes, we screened an...
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...
Human apoB contributes to increased serum total apo(a) level in LPA transgenic mice
Teivainen, Päivi A, Eliassen, Knut A, Rubin, Edward M, Djurovic, Srdjan, Berg, Kåre
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...
Intraspecies sequence comparisons for annotating genomes
Boffelli, Dario, Weer, Claire V., Weng, Li, Lewis, Keith D., Shoukry, Malak I., Pachter, Lior, ...
Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its...
Nowak, Maxime, Helleboid-Chapman, Audrey, Jakel, Heidelinde, Martin, Geneviève, Duran-Sandoval, Daniel, Staels, Bart, ...
The apolipoprotein A5 gene (APOA5) has been repeatedly implicated in lowering plasma triglyceride levels. Since several studies have demonstrated that hyperinsulinemia is associated with...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can have a negative impact on human development and health, yet because of the difficulty of detecting these critical sequences, we predominantly focus on...
Close sequence comparisons are sufficient to identify human cis-regulatory elements
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Primate-specific evolution of an LDLR enhancer
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Analysis of primate-specific evolution of the LDL receptor enhancer demonstrates a molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions.
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M, Boffelli, Dario
Intra-primate genome comparisons identify functional modules that are undetected by comparisons with non-mammalian genomes.
Deletion of Ultraconserved Elements Yields Viable Mice
Ahituv, Nadav, Zhu, Yiwen, Visel, Axel, Holt, Amy, Afzal, Veena, Pennacchio, Len A, ...
Ultraconserved elements have been suggested to retain extended perfect sequence identity between the human, mouse, and rat genomes due to essential functional properties. To investigate the...
Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene
Ward, Robert D., Davis, Shannon W., Cho, MinChul, Esposito, Constance, Lyons, Robert H., Cheng, Jan-Fang, ...
Mutations in PROP1 are a common genetic cause of multiple pituitary hormone deficiency (MPHD). We used a comparative genomics approach to predict the transcriptional regulatory domains of Prop1 and...
The Airborne Metagenome in an Indoor Urban Environment
Tringe, Susannah G., Zhang, Tao, Liu, Xuguo, Yu, Yiting, Lee, Wah Heng, Yap, Jennifer, ...
The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested...
Identification of ancient remains through genomic sequencing
Blow, Matthew J., Zhang, Tao, Woyke, Tanja, Speller, Camilla F., Krivoshapkin, Andrei, Yang, Dongya Y., ...
Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In...