Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny (2009)
Vinař, Tomáš, Brejová, Broňa, Song, Giltae, Siepel, Adam
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding...
Reconstructing the Evolutionary History of Complex Human Gene Clusters (2009)
Yu Zhang, Giltae Song, Eric D. Green, Adam Siepel, Webb Miller
Abstract. Clusters of genes that evolved from single progenitors via repeated segmental duplications present significant challenges to the generation of a truly complete human genome sequence. Such...
Patterns of Positive Selection in Six Mammalian (2009)
Carolin Kosiol, Melissa J. Hubisz, Carlos D. Bustamante, Adam Siepel
Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight into the dynamics of genome evolution, the genetic basis of differences between species, and the functions of...
New Methods for Detecting Lineage-Specific Selection ⋆ (2009)
Adam Siepel, Katherine S. Pollard, David Haussler
Abstract. So far, most methods for identifying sequences under selection based on comparative sequence data have either assumed selectional pressures are the same across all branches of a phylogeny,...
Phylogenomics of primates and their ancestral populations (2009)
Genome assemblies are now available for nine primate species, and large-scale sequencing projects are underway or approved for six others. An explicitly evolutionary and phylogenetic approach to...
Gill Bejerano, Craig Lowe, Nadav Ahituv, Bryan King, Adam Siepel, Sofie Salama, ...
An enhancer near ISL1 and an ultraconserved PCBP2 exon are
Article Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2008)
Adam Siepel, Gill Bejerano, Jakob S. Pedersen, Angie S. Hinrichs, Minmei Hou, Kate Rosenbloom, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
ABSTRACT Computational Identification of Evolutionarily Conserved Exons (2008)
Phylogenetic hidden Markov models (phylo-HMMs) have recently been proposed as a means for addressing a multispecies version of the ab initio gene prediction problem. These models allow sequence...
New Methods for Detecting Lineage-Specific Selection (2008)
Adam Siepel, Katherine S. Pollard, David Haussler
Abstract. So far, most methods for identifying sequences under selection based on comparative sequence data have either assumed selectional pressures are the same across all branches of a phylogeny,...
ABSTRACT Computational Identification of Evolutionarily Conserved Exons (2008)
Phylogenetic hidden Markov models (phylo-HMMs) have recently been proposed as a means for addressing a multispecies version of the ab initio gene prediction problem. These models allow sequence...
Adam Siepel, Andrew Farmer, Andrew Tolopko, Peter Steadman, Dawn Perry, Faye Schilkey, ...
Abstract: Heterogeneity of databases and software resources continues to hamper the integration of biological information (Markowitz and Ritter, 1995; Davidson, et al., 1995; Baker, et al., 1998)....
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,...
Targeted discovery of novel human exons by comparative genomics (2007)
Siepel, Adam, Diekhans, Mark, Brejová, Brona, Langton, Laura, Stevens, Michael, Comstock, Charles L.G., ...
A complete and accurate set of human protein-coding gene annotations is perhaps the single most important resource for genomic research after the human-genome sequence itself, yet the major gene...
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser (2007)
Miller, Webb, Rosenbloom, Kate, Hardison, Ross C., Hou, Minmei, Taylor, James, Raney, Brian, ...
This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006...
Forces Shaping the Fastest Evolving Regions in the Human Genome (2006)
Katherine S. Pollard, Sofie R. Salama, Bryan King, Andrew D. Kern, Tim Dreszer, Sol Katzman, ...
Comparative genomics allow us to search the human genome for segments that were extensively changed in the last ~5 million years since divergence from our common ancestor with chimpanzee, but are...
Forces Shaping the Fastest Evolving Regions in the Human Genome (2006)
Katherine S. Pollard, Sofie R. Salama, Bryan King, Andrew Kern, Tim Dreszer, Sol Katzman, ...
Comparative genomics allows us to search the human genome for segments that were extensively changed in the last ~5 million years since divergence from our common ancestor with chimpanzee, but are...
Identification and classification of conserved RNA secondary structures in the human genome (2006)
Pedersen, Jakob Skou, Bejerano, Gill, Siepel, Adam, Rosenbloom, Kate, Lindblad-Toh, Kerstin, Lander, Eric S, ...
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed...
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006)
Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, ...
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed...
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006)
Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate R. Rosenbloom, Kerstin Lindblad-Toh, Eric S Lander, ...
The discovery of, e.g., microRNAs and riboswitches have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general...
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...
Phylogenetic hidden Markov models (2005)
Adam Siepel, David Haussler, Adam Siepel, David Haussler
Phylogenetic hidden Markov models, or phylo-HMMs, are probabilistic models that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005)
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005)
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Combining phylogenetic and hidden Markov models in biosequence analysis (2004)
A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process changes from one site...
Combining phylogenetic and hidden Markov models in biosequence analysis (2004)
A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process changes from one site...
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood (2004)
Nucleotide substitution in both coding and noncoding regions is context-dependent, in the sense that substitution rates depend on the identity of neighboring bases. Context-dependent substitution has...
Efficient approximations for learning phylogenetic HMM models from data (2004)
Jojic, Vladimir, Jojic, Nebojsa, Meek, Chris, Geiger, Dan, Siepel, Adam, Haussler, David, ...
Motivation: We consider models useful for learning an evolutionary or phylogenetic tree from data consisting of DNA sequences corresponding to the leaves of the tree. In particular, we consider a...
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood (2003)
Nucleotide substitution in both coding and non-coding regions is context-dependent, in the sense that substitution rates depend on the identity of neighboring bases. Context-dependent substitution...
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood (2003)
Nucleotide substitution in both coding and non-coding regions is context-dependent, in the sense that substitution rates depend on the identity of neighboring bases. Context-dependent substitution...
Expectation Maximization for Combined Phylogenetic and Hidden Markov Models (2002)
An expectation maximization (EM) algorithm is derived to estimate the parameters of a phylogenetic model, a probabilistic model of molecular evolution that considers the phylogeny, or evolutionary...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
Pedersen, Jakob Skou, Bejerano, Gill, Siepel, Adam, Rosenbloom, Kate, Lindblad-Toh, Kerstin, Lander, Eric S, ...
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed...
Forces Shaping the Fastest Evolving Regions in the Human Genome
Pollard, Katherine S, Salama, Sofie R, King, Bryan, Kern, Andrew D, Dreszer, Tim, Katzman, Sol, ...
Comparative genomics allow us to search the human genome for segments that were extensively changed in the last ~5 million years since divergence from our common ancestor with chimpanzee, but are...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
Pedersen, Jakob Skou, Bejerano, Gill, Siepel, Adam, Rosenbloom, Kate, Lindblad-Toh, Kerstin, Lander, Eric S, ...
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed...
Forces Shaping the Fastest Evolving Regions in the Human Genome
Pollard, Katherine S, Salama, Sofie R, King, Bryan, Kern, Andrew D, Dreszer, Tim, Katzman, Sol, ...
Comparative genomics allow us to search the human genome for segments that were extensively changed in the last ~5 million years since divergence from our common ancestor with chimpanzee, but are...
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,...
Targeted discovery of novel human exons by comparative genomics
Siepel, Adam, Diekhans, Mark, Brejová, Broňa, Langton, Laura, Stevens, Michael, Comstock, Charles L.G., ...
A complete and accurate set of human protein-coding gene annotations is perhaps the single most important resource for genomic research after the human-genome sequence itself, yet the major gene...
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
Miller, Webb, Rosenbloom, Kate, Hardison, Ross C., Hou, Minmei, Taylor, James, Raney, Brian, ...
This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006...
Patterns of Positive Selection in Six Mammalian Genomes
Kosiol, Carolin, Vinař, Tomáš, Da Fonseca, Rute R., Hubisz, Melissa J., Bustamante, Carlos D., Nielsen, Rasmus, ...
Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight into the dynamics of genome evolution, the genetic basis of differences between species, and the functions of...
Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae
Wang, Ying, Diehl, Adam, Wu, Feinan, Vrebalov, Julia, Giovannoni, James, Siepel, Adam, ...
Comparative genomics is a powerful tool for gaining insight into genomic function and evolution. However, in plants, sequence data that would enable detailed comparisons of both coding and noncoding...
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
Holloway, Alisha K., Begun, David J., Siepel, Adam, Pollard, Katherine S.
Recent genomic sequencing of 10 additional Drosophila genomes provides a rich resource for comparative genomics analyses aimed at understanding the similarities and differences between species and...