Radiation hybrid map of the mouse genome (9999)
William J. Van Etten, Robert G. Steen, Huy Nguyen, Andrew B. Castle, Donna K. Slonim, Bing Ge, ...
A YAC-based physical map of the mouse genome (9999)
Chad Nusbaum, Donna K. Slonim, Katrina L. Harris, Bruce W. Birren, Robert G. Steen, Lincoln D. Stein, ...
Levin, Joshua Z, Berger, Michael F, Adiconis, Xian, Rogov, Peter, Melnikov, Alexandre, Fennell, Timothy, ...
Abstract Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by...
MacCallum, Iain, Przybylski, Dariusz, Gnerre, Sante, Burton, Joshua, Shlyakhter, Ilya, Gnirke, Andreas, ...
Abstract We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes...
Closing gaps in the human genome using sequencing by synthesis (2009)
Garber, Manuel, Zody, Michael C, Arachchi, Harindra M, Berlin, Aaron, Gnerre, Sante, Green, Lisa M, ...
Abstract The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as...
Closing gaps in the human genome using sequencing by synthesis (2009)
Arachchi, Harindra M., Green, Lisa M., Zody, Michael C., Lennon, Niall, Gnerre, Sante, Berlin, Aaron, ...
The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as 'structural'...
Closing gaps in the human genome using sequencing by synthesis (2009)
Arachchi, Harindra M., Green, Lisa M., Zody, Michael C., Lennon, Niall, Gnerre, Sante, Berlin, Aaron, ...
The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as 'structural'...
Andreas Gnirke, Alexandre Melnikov, Jared Maguire, Peter Rogov, Emily M LeProust, William Brockman, ...
High-resolution mapping of copy-number alterations with massively parallel sequencing (2008)
Derek Y Chiang, Gad Getz, David B Jaffe, Michael J T O'Kelly, Xiaojun Zhao, Scott L Carter, ...
Short-term genome evolution of Listeria monocytogenesin a non-controlled environment (2008)
Orsi, Renato H, Borowsky, Mark L, Lauer, Peter, Young, Sarah K, Nusbaum, Chad, Galagan, James E, ...
Abstract Background While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus...
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment (2008)
Orsi, Renato H., Borowsky, Mark L., Lauer, Peter, Young, Sarah K., Nusbaum, Chad, Galagan, James E., ...
Background: While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus...
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment (2008)
Orsi, Renato H., Borowsky, Mark L., Lauer, Peter, Young, Sarah K., Nusbaum, Chad, Galagan, James E., ...
Background: While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus...
Quality scores and SNP detection in sequencing-by-synthesis systems (2008)
Brockman, William, Alvarez, Pablo, Young, Sarah, Garber, Manuel, Giannoukos, Georgia, Lee, William L., ...
Promising new sequencing technologies, based on sequencing-by-synthesis (SBS), are starting to deliver large amounts of DNA sequence at very low cost. Polymorphism detection is a key application. We...
ALLPATHS: De novo assembly of whole-genome shotgun microreads (2008)
Butler, Jonathan, MacCallum, Iain, Kleber, Michael, Shlyakhter, Ilya A., Belmonte, Matthew K., Lander, Eric S., ...
New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial,...
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells (2007)
Tarjei S. Mikkelsen, Manching Ku, David B. Jaffe, Biju Issac, Erez Lieberman, Georgia Giannoukos, ...
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis (2006)
Jörg Kämper, Regine Kahmann, Michael Bölker, Li-Jun Ma, Thomas Brefort, Barry J. Saville, ...
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis (2006)
Kämper, Jörg ; JFA; CORA, Kahmann, Regine, Bölker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J, ...
Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence...
Dostie, Josee, Richmond, Joann M., Arnaout, Ramy A., Selzer, Rebecca R., Lee, William L., Honan, Tracey A., ...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology....
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...
Dostie, Josée, Richmond, Todd A., Arnaout, Ramy A., Selzer, Rebecca R., Lee, William L., Honan, Tracey A., ...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology....
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...
Dostie, Josée, Richmond, Todd A., Arnaout, Ramy A., Selzer, Rebecca R., Lee, William L., Honan, Tracey A., ...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology....
DNA sequence and analysis of human chromosome 18 (2005)
Chad Nusbaum, Michael C. Zody, Mark L. Borowsky, Michael Kamal, Chinnappa D. Kodira, Todd D. Taylor, ...
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...
Olivier Jaillon, Jean-Marc Aury, Frédéric Brunet, Jean-Louis Petit, Nicole Stange-Thomann, Evan Mauceli, ...
Barbouti, Aikaterini, Stankiewicz, Pawel, Nusbaum, Chad, Cuomo, Christina, Cook, April, Höglund, Mattias, ...
Abstract is not available
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...
The genome sequence of the filamentous fungus Neurospora crassa (2003)
James E. Galagan, Sarah E. Calvo, Katherine A. Borkovich, Eric U. Selker, Nick D. Read, David Jaffe, ...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity (2002)
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Mapping of Myxococcus xanthus Social Motility dsp Mutations to the dif Genes
Lancero, Hope, Brofft, Jennifer E., Downard, John, Birren, Bruce W., Nusbaum, Chad, Naylor, Jerome, ...
Myxococcus xanthus dsp and dif mutants have similar phenotypes in that they are deficient in social motility and fruiting body development. We compared the two loci by genetic mapping,...
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...
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...
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...
Mapping of Myxococcus xanthus Social Motility dsp Mutations to the dif Genes
Lancero, Hope, Brofft, Jennifer E., Downard, John, Birren, Bruce W., Nusbaum, Chad, Naylor, Jerome, ...
Myxococcus xanthus dsp and dif mutants have similar phenotypes in that they are deficient in social motility and fruiting body development. We compared the two loci by genetic mapping,...
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...
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...
Barbouti, Aikaterini, Stankiewicz, Pawel, Nusbaum, Chad, Cuomo, Christina, Cook, April, Höglund, Mattias, ...
Although a great deal of information has accumulated regarding the mechanisms underlying constitutional DNA rearrangements associated with inherited disorders, virtually nothing is known about the...
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...
Dostie, Josée, Richmond, Todd A., Arnaout, Ramy A., Selzer, Rebecca R., Lee, William L., Honan, Tracey A., ...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology....
Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains
Ku, Manching, Koche, Richard P., Rheinbay, Esther, Mendenhall, Eric M., Endoh, Mitsuhiro, Mikkelsen, Tarjei S., ...
In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the...
ALLPATHS: De novo assembly of whole-genome shotgun microreads
Butler, Jonathan, MacCallum, Iain, Kleber, Michael, Shlyakhter, Ilya A., Belmonte, Matthew K., Lander, Eric S., ...
New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial,...
Quality scores and SNP detection in sequencing-by-synthesis systems
Brockman, William, Alvarez, Pablo, Young, Sarah, Garber, Manuel, Giannoukos, Georgia, Lee, William L., ...
Promising new sequencing technologies, based on sequencing-by-synthesis (SBS), are starting to deliver large amounts of DNA sequence at very low cost. Polymorphism detection is a key application. We...
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment
Orsi, Renato H, Borowsky, Mark L, Lauer, Peter, Young, Sarah K, Nusbaum, Chad, Galagan, James E, ...
Tsibris, Athe M. N., Korber, Bette, Arnaout, Ramy, Russ, Carsten, Lo, Chien-Chi, Leitner, Thomas, ...
High-throughput sequencing platforms provide an approach for detecting rare HIV-1 variants and documenting more fully quasispecies diversity. We applied this technology to the V3 loop-coding region...
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
Yassour, Moran, Kaplan, Tommy, Fraser, Hunter B., Levin, Joshua Z., Pfiffner, Jenna, Adiconis, Xian, ...
Defining the transcriptome, the repertoire of transcribed regions encoded in the genome, is a challenging experimental task. Current approaches, relying on sequencing of ESTs or cDNA libraries, are...
High-resolution profiling and discovery of planarian small RNAs
Friedländer, Marc R., Adamidi, Catherine, Han, Ting, Lebedeva, Svetlana, Isenbarger, Thomas A., Hirst, Martin, ...
Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue...
Closing gaps in the human genome using sequencing by synthesis
Garber, Manuel, Zody, Michael C, Arachchi, Harindra M, Berlin, Aaron, Gnerre, Sante, Green, Lisa M, ...
A novel method for closing non-structural gaps in the human genome assembly using 454 sequencing is presented here.
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
MacCallum, Iain, Przybylski, Dariusz, Gnerre, Sante, Burton, Joshua, Shlyakhter, Ilya, Gnirke, Andreas, ...
Allpaths2, a method for accurately assembling small genomes with high continuity using short paired reads.
Levin, Joshua Z, Berger, Michael F, Adiconis, Xian, Rogov, Peter, Melnikov, Alexandre, Fennell, Timothy, ...
Combining next-generation sequencing with capture of sequences from a relevant subset of a transcriptome produces an enhanced view of this subset