Wu, Chengcang, Proestou, Dina, Carter, Dorothy, Nicholson, Erica, Santos, Filippe, Zhao, Shaying, ...
Abstract Background Manduca sexta, Heliothis virescens , and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC...
Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao (2009)
Li, Xuanyang, Slife, Jennifer, Patel, Neil, Zhao, Shaying
Abstract Background We recently discovered two composite long terminal repeat (LTR)-retrotransposon-like elements which we named DA (~300 kb) and Xiao (~30 kb), meaning big and small in Chinese...
BAC Library Construction (2009)
Shaying Zhao, Marvin Stodolsky, Kazutoyo Osoegawa
DNA cloning, especially large DNA cloning, is the first step in contemporary complex genome analysis. Cloning technology of high-molecular-weight DNA has been developed mainly using yeast and...
Comparative analysis of Alu repeats in primate genomes (2009)
Liu, George E., Alkan, Can, Jiang, Lu, Zhao, Shaying, Eichler, Evan E.
Using bacteria artificial chromosome (BAC) end sequences (16.9 Mb) and high-quality alignments of genomic sequences (17.4 Mb), we performed a global assessment of the divergence distributions,...
A physical map of the bovine genome (2007)
Snelling, Warren M, Chiu, Readman, Schein, Jacqueline E, Hobbs, Matthew, Abbey, Colette A, Adelson, David L, ...
Abstract Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify...
Using comparative genomics to reorder the human genome sequence into a virtual sheep genome (2007)
Dalrymple, Brian P, Kirkness, Ewen F, Nefedov, Mikhail, McWilliam, Sean, Ratnakumar, Abhirami, Barris, Wes, ...
Abstract Background Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the...
A physical map of the bovine genome (2007)
Chiu, Readman, Schein, Jacqueline, Hobbs, Matthew, Abbey, Colette, Adelson, David, ...
ABSTRACT: BACKGROUND: Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify...
Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle (2007)
Wheeler, Thomas T, Hood, Kylie A, Maqbool, Nauman J, McEwan, John C, Bingle, Colin D, Zhao, Shaying
Abstract Background Cattle and other ruminants have evolved the ability to derive most of their metabolic energy requirement from otherwise indigestible plant matter through a symbiotic relationship...
Using Comparative Genomics to Reorder the Human Genome Sequence into a Virtual Sheep Genome (2007)
Dalrymple, Brian, Kirkness, Ewen, Nefedov, Mikhail, McWilliam, Sean, Ratnakumar, Abhirami, Barris, Wes, ...
Background: Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Chris T. Yohn, Zhaoshi Jiang, Sean D. McGrath, Karen E. Hayden, Philipp Khaitovich, Matthew E. Johnson, ...
Comparison of human and other primate genomes provides evidence for a retroviral infection that bombarded the genomes of chimpanzees and gorillas 3-4 million years ago.
Chris T. Yohn, Zhaoshi Jiang, Sean D. McGrath, Karen E. Hayden, Philipp Khaitovich, Matthew E. Johnson, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Yohn, Chris T., Jiang, Zhaoshi, McGrath, Sean D., Hayden, Karen E., Khaitovich, Philipp, Johnson, Matthew E., ...
Yohn, Chris T, Jiang, Zhaoshi, McGrath, Sean D, Hayden, Karen E, Khaitovich, Philipp, Johnson, Matthew E, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome (2004)
Krzywinski,Martin, Wallis,John, Goesele,Claudia, Bosdet,Ian, Chiu,Readman, Graves,Tina, ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC...
Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome (2004)
Krzywinski,Martin, Wallis,John, Goesele,Claaudia, Bosdet,Ian, Chiu,Readman, Graves,Tina, ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC...
Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome (2004)
Krzywinski, Martin, Wallis, John, Goesele, Claaudia, Bosdet, Ian, Chiu, Readman, Graves, Tina, ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC...
Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome (2004)
Krzywinski, Martin, Wallis, John, Goesele, Claudia, Bosdet, Ian, Chiu, Readman, Graves, Tina, ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC...
Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation (2004)
Zhao, Shaying, Shetty, Jyoti, Hou, Lihua, Delcher, Arthur, Zhu, Baoli, Osoegawa, Kazutoyo, ...
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300...
Greshock, Joel, Naylor, Tara L., Margolin, Adam, Diskin, Sharon, Cleaver, Stephen H., Futreal, P. Andrew, ...
Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for...
Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome (2004)
Krzywinski, Martin, Wallis, John, Gösele, Claudia, Bosdet, Ian, Chiu, Readman, Graves, Tina, ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC...
BAC Resources for the Rat Genome Project (2004)
Osoegawa, Kazutoyo, Zhu, Baoli, Shu, Chung Li, Ren, Teresa, Cao, Qing, Vessere, Gery M., ...
Two 11-fold redundant bacterial artificial chromosome (BAC) libraries (RPCI-32 and CHORI-230) have been constructed to support the rat genome project. The first library was constructed using a male...
A set of BAC clones spanning the human genome (2004)
Krzywinski, Martin, Bosdet, Ian, Smailus, Duane, Chiu, Readman, Mathewson, Carrie, Wye, Natasja, ...
Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC...
Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation (2004)
Zhao, Shaying, Shetty, Jyoti, Hou, Lihua, Delcher, Arthur, Zhu, Baoli, Osoegawa, Kazutoyo, ...
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300...
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. (2003)
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Greshock, Joel, Naylor, Tara L., Margolin, Adam, Diskin, Sharon, Cleaver, Stephen H., Futreal, P. Andrew, ...
Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome (2003)
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
A comprehensive BAC resource (2001)
The Human Genome Project has generated extensive map and sequence data for a large number of Bacterial Artificial Chromosome (BAC) clones. In order to maximize the efficient use of the data and to...
Mouse BAC Ends Quality Assessment and Sequence Analyses (2001)
Zhao, Shaying, Shatsman, Sofiya, Ayodeji, Bola, Geer, Keita, Tsegaye, Getahun, Krol, Margaret, ...
Mouse BAC Ends Quality Assessment and Sequence Analyses (2001)
Zhao, Shaying, Shatsman, Sofiya, Ayodeji, Bola, Geer, Keita, Tsegaye, Getahun, Krol, Margaret, ...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5 (2001)
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
Mouse BAC Ends Quality Assessment and Sequence Analyses (2001)
Zhao, Shaying, Shatsman, Sofiya, Ayodeji, Bola, Geer, Keita, Tsegaye, Getahun, Krol, Margaret, ...
The Human BAC Ends database includes all non-redundant human BAC end sequences (BESs) generated by The Institute for Genomic Research (TIGR), the University of Washington (UW) and California...
A methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase (MeTr) from Clostridium thermoaceticum catalyzes the transfer of the N$\sp5$-methyl group from (6S)-methyltetrahydrofolate...
Thesis (Ph. D.)--University of Nebraska--Lincoln, 1996.
Sequence-tagged connectors: A sequence approach to mapping and scanning the human genome
Mahairas, Gregory G., Wallace, James C., Smith, Kim, Swartzell, Steven, Holzman, Ted, Keller, Andrew, ...
The sequence-tagged connector (STC) strategy proposes to generate sequence tags densely scattered (every 3.3 kilobases) across the human genome by arraying 450,000 bacterial artificial chromosomes...
The Human Genome Project has generated extensive map and sequence data for a large number of Bacterial Artificial Chromosome (BAC) clones. In order to maximize the efficient use of the data and to...
The Human BAC Ends database includes all non-redundant human BAC end sequences (BESs) generated by The Institute for Genomic Research (TIGR), the University of Washington (UW) and California...
End-sequence profiling: Sequence-based analysis of aberrant genomes
Volik, Stanislav, Zhao, Shaying, Chin, Koei, Brebner, John H., Herndon, David R., Tao, Quanzhou, ...
Genome rearrangements are important in evolution, cancer, and other diseases. Precise mapping of the rearrangements is essential for identification of the involved genes, and many techniques have...
Mouse BAC Ends Quality Assessment and Sequence Analyses
Zhao, Shaying, Shatsman, Sofiya, Ayodeji, Bola, Geer, Keita, Tsegaye, Getahun, Krol, Margaret, ...
A large-scale BAC end-sequencing project at The Institute for Genomic Research (TIGR) has generated one of the most extensive sets of sequence markers for the mouse genome to date. With a sequencing...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
The current strategy for sequencing the mouse genome involves the combination of a whole-genome shotgun approach with clone-based sequencing. High-resolution physical maps will provide a foundation...
Greshock, Joel, Naylor, Tara L., Margolin, Adam, Diskin, Sharon, Cleaver, Stephen H., Futreal, P. Andrew, ...
Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for...
Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome
Krzywinski, Martin, Wallis, John, Gösele, Claudia, Bosdet, Ian, Chiu, Readman, Graves, Tina, ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC...
BAC Resources for the Rat Genome Project
Osoegawa, Kazutoyo, Zhu, Baoli, Shu, Chung Li, Ren, Teresa, Cao, Qing, Vessere, Gery M., ...
Two 11-fold redundant bacterial artificial chromosome (BAC) libraries (RPCI-32 and CHORI-230) have been constructed to support the rat genome project. The first library was constructed using a male...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
A set of BAC clones spanning the human genome
Krzywinski, Martin, Bosdet, Ian, Smailus, Duane, Chiu, Readman, Mathewson, Carrie, Wye, Natasja, ...
Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC...
Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation
Zhao, Shaying, Shetty, Jyoti, Hou, Lihua, Delcher, Arthur, Zhu, Baoli, Osoegawa, Kazutoyo, ...
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300...
Yohn, Chris T, Jiang, Zhaoshi, McGrath, Sean D, Hayden, Karen E, Khaitovich, Philipp, Johnson, Matthew E, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Kouprina, Natalay, Leem, Sun-Hee, Solomon, Greg, Ly, Albert, Koriabine, Maxim, Otstot, John, ...
The reported draft human genome sequence includes many contigs that are separated by gaps of unknown sequence. These gaps may be due to chromosomal regions that are not present in the Escherichia...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Sequence-tagged connectors: A sequence approach to mapping and scanning the human genome
Mahairas, Gregory G., Wallace, James C., Smith, Kim, Swartzell, Steven, Holzman, Ted, Keller, Andrew, ...
The sequence-tagged connector (STC) strategy proposes to generate sequence tags densely scattered (every 3.3 kilobases) across the human genome by arraying 450,000 bacterial artificial chromosomes...
The Human Genome Project has generated extensive map and sequence data for a large number of Bacterial Artificial Chromosome (BAC) clones. In order to maximize the efficient use of the data and to...
The Human BAC Ends database includes all non-redundant human BAC end sequences (BESs) generated by The Institute for Genomic Research (TIGR), the University of Washington (UW) and California...
End-sequence profiling: Sequence-based analysis of aberrant genomes
Volik, Stanislav, Zhao, Shaying, Chin, Koei, Brebner, John H., Herndon, David R., Tao, Quanzhou, ...
Genome rearrangements are important in evolution, cancer, and other diseases. Precise mapping of the rearrangements is essential for identification of the involved genes, and many techniques have...
Mouse BAC Ends Quality Assessment and Sequence Analyses
Zhao, Shaying, Shatsman, Sofiya, Ayodeji, Bola, Geer, Keita, Tsegaye, Getahun, Krol, Margaret, ...
A large-scale BAC end-sequencing project at The Institute for Genomic Research (TIGR) has generated one of the most extensive sets of sequence markers for the mouse genome to date. With a sequencing...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
The current strategy for sequencing the mouse genome involves the combination of a whole-genome shotgun approach with clone-based sequencing. High-resolution physical maps will provide a foundation...
Greshock, Joel, Naylor, Tara L., Margolin, Adam, Diskin, Sharon, Cleaver, Stephen H., Futreal, P. Andrew, ...
Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for...
Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome
Krzywinski, Martin, Wallis, John, Gösele, Claudia, Bosdet, Ian, Chiu, Readman, Graves, Tina, ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC...
BAC Resources for the Rat Genome Project
Osoegawa, Kazutoyo, Zhu, Baoli, Shu, Chung Li, Ren, Teresa, Cao, Qing, Vessere, Gery M., ...
Two 11-fold redundant bacterial artificial chromosome (BAC) libraries (RPCI-32 and CHORI-230) have been constructed to support the rat genome project. The first library was constructed using a male...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
A set of BAC clones spanning the human genome
Krzywinski, Martin, Bosdet, Ian, Smailus, Duane, Chiu, Readman, Mathewson, Carrie, Wye, Natasja, ...
Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC...
Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation
Zhao, Shaying, Shetty, Jyoti, Hou, Lihua, Delcher, Arthur, Zhu, Baoli, Osoegawa, Kazutoyo, ...
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300...
Yohn, Chris T, Jiang, Zhaoshi, McGrath, Sean D, Hayden, Karen E, Khaitovich, Philipp, Johnson, Matthew E, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Kouprina, Natalay, Leem, Sun-Hee, Solomon, Greg, Ly, Albert, Koriabine, Maxim, Otstot, John, ...
The reported draft human genome sequence includes many contigs that are separated by gaps of unknown sequence. These gaps may be due to chromosomal regions that are not present in the Escherichia...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle
Wheeler, Thomas T, Hood, Kylie A, Maqbool, Nauman J, McEwan, John C, Bingle, Colin D, Zhao, Shaying
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome
Shedlock, Andrew M., Botka, Christopher W., Zhao, Shaying, Shetty, Jyoti, Zhang, Tingting, Liu, Jun S., ...
We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard...
Using comparative genomics to reorder the human genome sequence into a virtual sheep genome
Dalrymple, Brian P, Kirkness, Ewen F, Nefedov, Mikhail, McWilliam, Sean, Ratnakumar, Abhirami, Barris, Wes, ...
Using BAC-end sequences, a sparse marker map and the sequences of the human, dog and cow genomes, an accurate and detailed sub-gene level map of the sheep genome has been constructed.
A physical map of the bovine genome
Snelling, Warren M, Chiu, Readman, Schein, Jacqueline E, Hobbs, Matthew, Abbey, Colette A, Adelson, David L, ...
A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly.
Wu, Chengcang, Proestou, Dina, Carter, Dorothy, Nicholson, Erica, Santos, Filippe, Zhao, Shaying, ...
Comparative analysis of Alu repeats in primate genomes
Liu, George E., Alkan, Can, Jiang, Lu, Zhao, Shaying, Eichler, Evan E.
Using bacteria artificial chromosome (BAC) end sequences (16.9 Mb) and high-quality alignments of genomic sequences (17.4 Mb), we performed a global assessment of the divergence distributions,...