Yu, Yiting, Kim, H Stanley, Chua, Hui, Lin, Chi, Sim, Siew, Lin, Daoxun, ...
Abstract Background The Gram-negative bacterium Burkholderia pseudomallei (Bp) is the causative agent of the human disease melioidosis. To understand the evolutionary mechanisms contributing to Bp...
Yu, Yiting, Kim, H. S., Chua, Hui H., Lin, Chi H., Sim, Siew H., Lin, Daoxun, ...
The Gram-negative bacterium Burkholderia pseudomallei (Bp) is the causative agent of the human disease melioidosis. To understand the evolutionary mechanisms contributing to Bp virulence, we...
Uneven chromosome contraction and expansion in the maize genome (2006)
Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...
Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...
Uneven chromosome contraction and expansion in the maize genome (2006)
Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...
Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...
Genomics of the fungal kingdom: Insights into eukaryotic biology (2005)
Galagan, James E., Henn, Matthew R., Ma, Li-Jun, Cuomo, Christina A., Birren, Bruce
The last decade has witnessed a revolution in the genomics of the fungal kingdom. Since the sequencing of the first fungus in 1996, the number of available fungal genome sequences has increased by an...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi (2005)
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
Patterns of Intron Gain and Loss in Fungi (2004)
Cydney B. Nielsen, Brad Friedman, Bruce Birren, Christopher B. Burge, James E. Galagan
A comparative study of four fungal genomes reveals the patterns of intron gain and loss over several hundred million years of evolution.
Patterns of Intron Gain and Loss in Fungi (2004)
Cydney B. Nielsen, Brad Friedman, Bruce Birren, Christopher B. Burge, James E. Galagan
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. L
In Kellis et al. (2003), we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genome-wide...
The Complete Genome and Proteome of Mycoplasma mobile (2004)
Jaffe, Jacob D., Stange-Thomann, Nicole, Smith, Cherylyn, DeCaprio, David, Fisher, Sheila, Butler, Jonathan, ...
Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete...
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric L
In [13] we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genome-wide comparative analysis...
MacMurray, Armand J., Moralejo, Daniel H., Kwitek, Anne E., Rutledge, Elizabeth A., Van Yserloo, Brian, Gohlke, Paul, ...
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, ...
Inoue, Ken, Dewar, Ken, Katsanis, Nicholas, Reiter, Lawrence T., Lander, Eric S., Devon, Keri L., ...
Footz, Tim K., Brinkman-Mills, Polly, Banting, Graham S., Maier, Stephanie A., Riazi, M. Ali, Bridgland, Lindsay, ...
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, ...
Transformation of Escherichia coli with large DNA molecules by electroporation (1995)
Sheng, YuLing, Mancino, Valeria, Birren, Bruce
We have examined bacterial electroporation with a specific Interest in the transformation of large DNA, I.e. molecules >100 kb. We have used DNA from bacterial artificial chromosomes (BACs) ranging...
Rapid pulsed field separation of DNA molecules up to 250 kb (1994)
Pulsed field gel electrophoresis (PFGE) Is capable of resolving a wide size range of DNA molecules which would all co-migrate in conventional agarose gels. We describe pulsed field gel conditions...
Stable propagation of cosmid sized human DNA inserts in an F factor based vector (1992)
Kim, Ung-Jin, Shizuya, Hiroaki, De Jong, Pieter J., Birren, Bruce, Simon, Melvin I.
Instability of complex mammalian genomic DNA inserts is commonplace in cosmid libraries constructed in conventional multicopy vectors. To develop a means to construct stable libraries, we have...
Stable propagation of cosmid sized human DNA inserts in an F factor based vector (1992)
Kim, Ung-Jin, Shizuya, Hiroaki, De Jong, Pieter J., Birren, Bruce, Simon, Melvin I.
Instability of complex mammalian genomic DNA inserts is commonplace in cosmid libraries constructed in conventional multicopy vectors. To develop a means to construct stable libraries, we have...
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,...
MacMurray, Armand J., Moralejo, Daniel H., Kwitek, Anne E., Rutledge, Elizabeth A., Van Yserloo, Brian, Gohlke, Paul, ...
The BB (BioBreeding) rat is one of the best models of spontaneous autoimmune diabetes and is used to study non-MHC loci contributing to Type 1 diabetes. Type 1 diabetes in the diabetes-prone BB...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
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...
Footz, Tim K., Brinkman-Mills, Polly, Banting, Graham S., Maier, Stephanie A., Riazi, M. Ali, Bridgland, Lindsay, ...
We have sequenced a 1.1-Mb region of human chromosome 22q containing the dosage-sensitive gene(s) responsible for cat eye syndrome (CES) as well as the 450-kb homologous region on mouse chromosome 6....
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...
The Complete Genome and Proteome of Mycoplasma mobile
Jaffe, Jacob D., Stange-Thomann, Nicole, Smith, Cherylyn, DeCaprio, David, Fisher, Sheila, Butler, Jonathan, ...
Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete...
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
Patterns of Intron Gain and Loss in Fungi
Nielsen, Cydney B, Friedman, Brad, Birren, Bruce, Burge, Christopher B, Galagan, James E
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
Structure and Architecture of the Maize Genome1[W]
Haberer, Georg, Young, Sarah, Bharti, Arvind K., Gundlach, Heidrun, Raymond, Christina, Fuks, Galina, ...
Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of...
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,...
MacMurray, Armand J., Moralejo, Daniel H., Kwitek, Anne E., Rutledge, Elizabeth A., Van Yserloo, Brian, Gohlke, Paul, ...
The BB (BioBreeding) rat is one of the best models of spontaneous autoimmune diabetes and is used to study non-MHC loci contributing to Type 1 diabetes. Type 1 diabetes in the diabetes-prone BB...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
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...
Footz, Tim K., Brinkman-Mills, Polly, Banting, Graham S., Maier, Stephanie A., Riazi, M. Ali, Bridgland, Lindsay, ...
We have sequenced a 1.1-Mb region of human chromosome 22q containing the dosage-sensitive gene(s) responsible for cat eye syndrome (CES) as well as the 450-kb homologous region on mouse chromosome 6....
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...
The Complete Genome and Proteome of Mycoplasma mobile
Jaffe, Jacob D., Stange-Thomann, Nicole, Smith, Cherylyn, DeCaprio, David, Fisher, Sheila, Butler, Jonathan, ...
Although often considered “minimal” organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete...
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
Patterns of Intron Gain and Loss in Fungi
Nielsen, Cydney B, Friedman, Brad, Birren, Bruce, Burge, Christopher B, Galagan, James E
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
Structure and Architecture of the Maize Genome1[W]
Haberer, Georg, Young, Sarah, Bharti, Arvind K., Gundlach, Heidrun, Raymond, Christina, Fuks, Galina, ...
Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of...
Uneven chromosome contraction and expansion in the maize genome
Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...
Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...
Dynamics of Pseudomonas aeruginosa genome evolution
Mathee, Kalai, Narasimhan, Giri, Valdes, Camilo, Qiu, Xiaoyun, Matewish, Jody M., Koehrsen, Michael, ...
One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety of debilitating diseases or immune...
Champion, Mia D., Zeng, Qiandong, Nix, Eli B., Nano, Francis E., Keim, Paul, Kodira, Chinnappa D., ...
Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to...