Ivan Ovcharenko, Gabriela G. Loots, Ross C. Hardison, Webb Miller, Lisa Stubbs
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an...
Elso, Colleen, Lu, Xiaochen, Morrison, Stephanie, Tarver, Angela, Thompson, Heather, Thurkow, Hillary, ...
Translocations have provided invaluable tools for identifying both cancer-linked genes and loci associated with heritable human diseases, but heritable human translocations are rare and few mouse...
Gordon, Laurie, Yang, Shan, Tran-Gyamfi, Mary, Baggott, Dan, Christensen, Mari, Hamilton, Aaron, ...
The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However,...
Hamilton, Aaron T., Huntley, Stuart, Tran-Gyamfi, Mary, Baggott, Daniel M., Gordon, Laurie, Stubbs, Lisa
Most genes are conserved in mammals, but certain gene families have acquired large numbers of lineage-specific loci through repeated rounds of gene duplication, divergence, and loss that have...
Huntley, Stuart, Baggott, Daniel M., Hamilton, Aaron T., Tran-Gyamfi, Mary, Yang, Shan, Kim, Joomyeong, ...
Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array...
Identification of clustered YY1 binding sites in imprinting control regions (2006)
Do Kim, Jeong, Hinz, Angela K., Bergmann, Anne, Huang, Jennifer M., Ovcharenko, Ivan, Stubbs, Lisa, ...
Mammalian genomic imprinting is regulated by imprinting control regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In this study, the sequence...
Huntley, Stuart, Baggott, Daniel M., Hamilton, Aaron T., Tran-Gyamfi, Mary, Yang, Shan, Kim, Joomyeong, ...
Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array...
Hamilton, Aaron T., Huntley, Stuart, Tran-Gyamfi, Mary, Baggott, Daniel M., Gordon, Laurie, Stubbs, Lisa
Most genes are conserved in mammals, but certain gene families have acquired large numbers of lineage-specific loci through repeated rounds of gene duplication, divergence, and loss that have...
Identification of clustered YY1 binding sites in imprinting control region (2006)
Kim, Jeong Do, Hinz, Angela K., Bergmann, Anne, Huang, Jennifer M., Ovcharenko, Ivan, Stubbs, Lisa, ...
Mammalian genomic imprinting is regulated by imprinting control regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In this study, the sequence...
Allele-specific deposition of macroH2A1 in Imprinting Control Regions (2006)
Choo, Jung Ha, Kim, Jeong Do, Chung, Jae Hoon, Stubbs, Lisa, Kim, Joomyeong
In the current study, we analyzed the deposition patterns of macroH2A1 at a number of different genomic loci located in X chromosome and autosomes. MacroH2A1 is preferentially deposited at methylated...
Allele-specific deposition of macroH2A1 in imprinting control regions (2006)
Choo, Jung Ha, Kim, Jeong Do, Chung, Jae Hoon, Stubbs, Lisa, Kim, Joomyeong
In the current study, we analyzed the deposition patterns of macroH2A1 at a number of different genomic loci located in X chromosome and autosomes. MacroH2A1 is preferentially deposited at methylated...
Herron, Bruce J., Rao, Cherie, Liu, Shanming, Laprade, Lisa, Richardson, James A., Olivieri, Emily, ...
We have identified waved 3 (wa3), a novel recessive mutation that causes abnormalities of the heart and skin. The cardiac defect results in a severe and rapidly progressive dilated cardiomyopathy. We...
Evolution and functional classification of vertebrate gene deserts (2005)
Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct...
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...
Herron, Bruce J., Rao, Cherie, Liu, Shanming, Laprade, Lisa, Richardson, James A., Olivieri, Emily, ...
We have identified waved 3 (wa3), a novel recessive mutation that causes abnormalities of the heart and skin. The cardiac defect results in a severe and rapidly progressive dilated cardiomyopathy. We...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms (2004)
Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, ...
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken...
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles (2004)
Ovcharenko, Ivan, Loots, Gabriela G., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an...
Ovcharenko, Ivan, Nobrega, Marcelo A., Loots, Gabriela G., Stubbs, Lisa
With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have...
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...
Evolution and functional classification of vertebrate gene deserts (2004)
Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct...
Shannon, Mark, Hamilton, Aaron T., Gordon, Laurie, Branscomb, Elbert, Stubbs, Lisa
Mammalian genomes carry hundreds of Krüppel-type zinc finger (ZNF) genes, most of which reside in familial clusters. ZNF genes encoding Krüppel-associated box (KRAB) motifs are especially prone to...
Kim, Joomyeong, Kollhoff, Angela, Bergmann, Anne, Stubbs, Lisa
The 5′-ends of two paternally expressed mouse genes, Peg3 and Usp29, are jointly associated with a CpG island that exhibits allele-specific methylation. Sequence comparison of the regions derived...
Kim, Joomyeong, Noskov, Vladimir N., Lu, Xiaochen, Bergmann, Anne, Ren, Xiaojia, Warth, Tiffany, ...
Kim, Joomyeong, Ashworth, Linda, Branscomb, Elbert, Stubbs, Lisa
Peg3 (paternally expressed gene 3) is the first imprinted gene detected in the proximal region of mouse chromosome 7. Because imprinting is a trait that is generally conserved among mammals, and...
Kim, Joomyeong, Noskov, Vladimir N., Lu, Xiaochen, Bergmann, Anne, Ren, Xiaojia, Warth, Tiffany, ...
Using mouse BAC clones spanning an imprinted interval of proximal mouse chromosome 7 and the genomic sequence of the related interval of human chromosome 19q13.4, we have identified a novel mouse...
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
Ovcharenko, Ivan, Loots, Gabriela G., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an...
Shannon, Mark, Hamilton, Aaron T., Gordon, Laurie, Branscomb, Elbert, Stubbs, Lisa
Mammalian genomes carry hundreds of Krüppel-type zinc finger (ZNF) genes, most of which reside in familial clusters. ZNF genes encoding Krüppel-associated box (KRAB) motifs are especially prone to...
Ovcharenko, Ivan, Nobrega, Marcelo A., Loots, Gabriela G., Stubbs, Lisa
With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have...
Evolution and functional classification of vertebrate gene deserts
Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct...
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...
Huntley, Stuart, Baggott, Daniel M., Hamilton, Aaron T., Tran-Gyamfi, Mary, Yang, Shan, Kim, Joomyeong, ...
Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array...
Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes
Hamilton, Aaron T., Huntley, Stuart, Tran-Gyamfi, Mary, Baggott, Daniel M., Gordon, Laurie, Stubbs, Lisa
Most genes are conserved in mammals, but certain gene families have acquired large numbers of lineage-specific loci through repeated rounds of gene duplication, divergence, and loss that have...
Kim, Joomyeong, Ashworth, Linda, Branscomb, Elbert, Stubbs, Lisa
Peg3 (paternally expressed gene 3) is the first imprinted gene detected in the proximal region of mouse chromosome 7. Because imprinting is a trait that is generally conserved among mammals, and...
Kim, Joomyeong, Noskov, Vladimir N., Lu, Xiaochen, Bergmann, Anne, Ren, Xiaojia, Warth, Tiffany, ...
Using mouse BAC clones spanning an imprinted interval of proximal mouse chromosome 7 and the genomic sequence of the related interval of human chromosome 19q13.4, we have identified a novel mouse...
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
Ovcharenko, Ivan, Loots, Gabriela G., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an...
Shannon, Mark, Hamilton, Aaron T., Gordon, Laurie, Branscomb, Elbert, Stubbs, Lisa
Mammalian genomes carry hundreds of Krüppel-type zinc finger (ZNF) genes, most of which reside in familial clusters. ZNF genes encoding Krüppel-associated box (KRAB) motifs are especially prone to...
Ovcharenko, Ivan, Nobrega, Marcelo A., Loots, Gabriela G., Stubbs, Lisa
With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have...
Evolution and functional classification of vertebrate gene deserts
Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct...
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...
Huntley, Stuart, Baggott, Daniel M., Hamilton, Aaron T., Tran-Gyamfi, Mary, Yang, Shan, Kim, Joomyeong, ...
Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array...
Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes
Hamilton, Aaron T., Huntley, Stuart, Tran-Gyamfi, Mary, Baggott, Daniel M., Gordon, Laurie, Stubbs, Lisa
Most genes are conserved in mammals, but certain gene families have acquired large numbers of lineage-specific loci through repeated rounds of gene duplication, divergence, and loss that have...
Identification of clustered YY1 binding sites in imprinting control regions
Do Kim, Jeong, Hinz, Angela K., Bergmann, Anne, Huang, Jennifer M., Ovcharenko, Ivan, Stubbs, Lisa, ...
Mammalian genomic imprinting is regulated by imprinting control regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In this study, the sequence...
Gordon, Laurie, Yang, Shan, Tran-Gyamfi, Mary, Baggott, Dan, Christensen, Mari, Hamilton, Aaron, ...
The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However,...