Long-range regulation is a major driving force in maintaining genome integrity (2009)
Mongin, Emmanuel, Dewar, Ken, Blanchette, Mathieu
Abstract Background The availability of newly sequenced vertebrate genomes, along with more efficient and accurate alignment algorithms, have enabled the expansion of the field of comparative...
Feng, Jie, Lupien, Andréanne, Gingras, Hélène, Wasserscheid, Jessica, Dewar, Ken, Légaré, Danielle, ...
Linezolid is a member of a novel class of antibiotics, with resistance already being reported. We used whole-genome sequencing on three independent Streptococcus pneumoniae strains made resistant to...
Targeted screening of cis-regulatory variation in human haplotypes (2009)
Verlaan, Dominique J., Ge, Bing, Grundberg, Elin, Hoberman, Rose, Lam, Kevin C.L., Koka, Vonda, ...
Regulatory cis-acting variants account for a large proportion of gene expression variability in populations. Cis-acting differences can be specifically measured by comparing relative levels of...
A probabilistic approach for SNP discovery in high-throughput human resequencing data (2009)
Hoberman, Rose, Dias, Joana, Ge, Bing, Harmsen, Eef, Mayhew, Michael, Verlaan, Dominique J., ...
New high-throughput sequencing technologies are generating large amounts of sequence data, allowing the development of targeted large-scale resequencing studies. For these studies, accurate...
Satou, Yutaka, Mineta, Katsuhiko, Ogasawara, Michio, Sasakura, Yasunori, Shoguchi, Eiichi, Ueno, Keisuke, ...
Abstract Background The draft genome sequence of the ascidian Ciona intestinalis , along with associated gene models, has been a valuable research resource. However, recently accumulated expressed...
Identifying multiple alignment regions satisfying simple formulas and patterns
The Amphioxus Hox Cluster: Characterization, Comparative Genomics, and Evolution (2008)
Amemiya, Chris T., Prohaska, Sonja J., Hill-Force, Alicia, Cooke, April, Wasserscheid, Jessica, Ferrier, David E. K., ...
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution (2004)
Chiu, C-H., Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, ...
Identifying multiple alignment regions satisfying simple formulas and patterns (2004)
Stojanovic, Nikola, Dewar, Ken
Motivation: When studying multiple alignments of genomic sequences one frequently aims to locate and count regions which satisfy a set of constraints. These regions may be putatively functional, but...
Identifying multiple alignment regions satisfying simple formulas and patterns (2004)
Stojanovic, Nikola, Dewar, Ken
Motivation: When studying multiple alignments of genomic sequences one frequently aims to locate and count regions which satisfy a set of constraints. These regions may be putatively functional, but...
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution (2004)
Chiu, Chi-hua, Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, ...
The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish...
Identifying multiple alignment regions satisfying simple formulas and patterns (2004)
Stojanovic, Nikola, Dewar, Ken
Motivation: When studying multiple alignments of genomic sequences one frequently aims to locate and count regions which satisfy a set of constraints. These regions may be putatively functional, but...
Structure and Evolution of the Smith-Magenis Syndrome Repeat Gene Clusters, SMS-REPs (2002)
Park, Sung-Sup, Stankiewicz, Pawel, Bi, Weimin, Shaw, Christine, Lehoczky, Jessica, Dewar, Ken, ...
Identification of mixups among DNA sequencing plates (2002)
Stojanovic, Nikola, Chang, Jean L., Lehoczky, Jessica, Zody, Michael C., Dewar, Ken
Motivation: During the process of high-throughput genome sequencing there are opportunities for mixups of reagents and data associated with particular projects. The sequencing templates or sequence...
Inoue, Ken, Dewar, Ken, Katsanis, Nicholas, Reiter, Lawrence T., Lander, Eric S., Devon, Keri L., ...
Onyango, Patrick, Miller, Webb, Lehoczky, Jessica, Leung, Cheuk T., Birren, Bruce, Wheelan, Sarah, ...
Wiltshire, Tim, Pletcher, Mathew, Cole, Susan E., Villanueva, Melissa, Birren, Bruce, Lehoczky, Jessica, ...
Molecular evolution of the HoxA cluster in the three major gnathostome lineages
Chiu, Chi-hua, Amemiya, Chris, Dewar, Ken, Kim, Chang-Bae, Ruddle, Frank H., Wagner, Günter P.
The duplication of Hox clusters and their maintenance in a lineage has a prominent but little understood role in chordate evolution. Here we examined how Hox cluster duplication may influence changes...
Structure and Evolution of the Smith-Magenis Syndrome Repeat Gene Clusters, SMS-REPs
Park, Sung-Sup, Stankiewicz, Paweł, Bi, Weimin, Shaw, Christine, Lehoczky, Jessica, Dewar, Ken, ...
An ∼4-Mb genomic segment on chromosome 17p11.2, commonly deleted in patients with the Smith-Magenis syndrome (SMS) and duplicated in patients with dup(17)(p11.2p11.2) syndrome, is flanked by large,...
Wiltshire, Tim, Pletcher, Mathew, Cole, Susan E., Villanueva, Melissa, Birren, Bruce, Lehoczky, Jessica, ...
The distal end of human Chromosome (HSA) 21 from PDXK to the telomere shows perfect conserved linkage with mouse Chromosome (MMU) 10. This region is bounded on the proximal side by a segment of...
Inoue, Ken, Dewar, Ken, Katsanis, Nicholas, Reiter, Lawrence T., Lander, Eric S., Devon, Keri L., ...
Duplication and deletion of the 1.4-Mb region in 17p12 that is delimited by two 24-kb low copy number repeats (CMT1A–REPs) represent frequent genomic rearrangements resulting in two common...
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
Chiu, Chi-hua, Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, ...
The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish...
Molecular evolution of the HoxA cluster in the three major gnathostome lineages
Chiu, Chi-hua, Amemiya, Chris, Dewar, Ken, Kim, Chang-Bae, Ruddle, Frank H., Wagner, Günter P.
The duplication of Hox clusters and their maintenance in a lineage has a prominent but little understood role in chordate evolution. Here we examined how Hox cluster duplication may influence changes...
Structure and Evolution of the Smith-Magenis Syndrome Repeat Gene Clusters, SMS-REPs
Park, Sung-Sup, Stankiewicz, Paweł, Bi, Weimin, Shaw, Christine, Lehoczky, Jessica, Dewar, Ken, ...
An ∼4-Mb genomic segment on chromosome 17p11.2, commonly deleted in patients with the Smith-Magenis syndrome (SMS) and duplicated in patients with dup(17)(p11.2p11.2) syndrome, is flanked by large,...
Wiltshire, Tim, Pletcher, Mathew, Cole, Susan E., Villanueva, Melissa, Birren, Bruce, Lehoczky, Jessica, ...
The distal end of human Chromosome (HSA) 21 from PDXK to the telomere shows perfect conserved linkage with mouse Chromosome (MMU) 10. This region is bounded on the proximal side by a segment of...
Inoue, Ken, Dewar, Ken, Katsanis, Nicholas, Reiter, Lawrence T., Lander, Eric S., Devon, Keri L., ...
Duplication and deletion of the 1.4-Mb region in 17p12 that is delimited by two 24-kb low copy number repeats (CMT1A–REPs) represent frequent genomic rearrangements resulting in two common...
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
Chiu, Chi-hua, Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, ...
The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish...
Freimer, Nelson B., Service, Susan K., Ophoff, Roel A., Jasinska, Anna J., McKee, Kevin, Villeneuve, Amelie, ...
Non-human primates (NHP) provide crucial research models. Their strong similarities to humans make them particularly valuable for understanding complex behavioral traits and brain structure and...
Targeted screening of cis-regulatory variation in human haplotypes
Verlaan, Dominique J., Ge, Bing, Grundberg, Elin, Hoberman, Rose, Lam, Kevin C.L., Koka, Vonda, ...
Regulatory cis-acting variants account for a large proportion of gene expression variability in populations. Cis-acting differences can be specifically measured by comparing relative levels of...
Satou, Yutaka, Mineta, Katsuhiko, Ogasawara, Michio, Sasakura, Yasunori, Shoguchi, Eiichi, Ueno, Keisuke, ...
An improved assembly of the Ciona intestinalis genome reveals that it contains non-canonical introns and that about 20% of Ciona genes reside in operons.