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...
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm048 Sequence analysis (2008)
Minmei Hou, Piotr Berman, Chih-hao Hsu, Robert S. Harris
HomologMiner: looking for homologous genomic groups in whole genomes
Algorithms for Aligning and Clustering Genomic Sequences that Contain Duplications (2007)
Genomes of advanced organisms contain numerous repeated sequences, including gene clusters, tandem repeats, interspersed repeats, and segmental duplications. Among these, gene clusters are the class...
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,...
Algorithms for aligning and clustering genomic sequences that contain duplications (2007)
Thesis (Ph.D.)--Pennsylvania State University, 2007.
C. Thach Nguyen, Jian Shen, Minmei Hou, Li Sheng, Webb Miller, Louxin Zhang
Abstract. This paper studies the algorithmic issues of the spanning star forest problem. We prove the following results: (1) There is a polynomial-time approximation scheme for planar graphs; (2)...
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...
HomologMiner: looking for homologous genomic groups in whole genomes (2007)
Hou, Minmei, Berman, Piotr, Hsu, Chih-Hao, Harris, Robert S.
Motivation: Complex genomes contain numerous repeated sequences, and genomic duplication is believed to be a main evolutionary mechanism to obtain new functions. Several tools are available for de...
Controlling size when aligning multiple genomic sequences with duplications (2006)
Minmei Hou, Louxin Zhang, Webb Miller
Abstract. For a genomic region containing a tandem gene cluster, a proper set of alignments needs to align only orthologous segments, i.e., those separated by a speciation event. Otherwise, methods...
Ovcharenko, Ivan, Loots, Gabriela G., Giardine, Belinda M., Hou, Minmei, Ma, Jian, Hardison, Ross C., ...
Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of...
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...
Ovcharenko, Ivan, Loots, Gabriela G., Giardine, Belinda M., Hou, Minmei, Ma, Jian, Hardison, Ross C., ...
Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of...
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Ovcharenko, Ivan, Loots, Gabriela G., Giardine, Belinda M., Hou, Minmei, Ma, Jian, Hardison, Ross C., ...
Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of...
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...
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Ovcharenko, Ivan, Loots, Gabriela G., Giardine, Belinda M., Hou, Minmei, Ma, Jian, Hardison, Ross C., ...
Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of...
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...
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,...
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...