ABySS: A parallel assembler for short read sequence data (2009)
Simpson, Jared T., Wong, Kim, Jackman, Shaun D., Schein, Jacqueline E., Jones, Steven J.M., Birol, Inanç
Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the...
De novo transcriptome assembly with ABySS (2009)
Birol, Inanç, Jackman, Shaun D., Nielsen, Cydney B., Qian, Jenny Q., Varhol, Richard, Stazyk, Greg, ...
Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using...
AUTOMATED IMAGE ANALYSIS FOR DNA FINGERPRINTING (2007)
Daniel R. Fuhrmann, Readman Chiu, Jacqueline E. Schein, Robert H. Waterston, John D. Mcpherson, Marco A. Marra
Methods for automated detection of DNA restriction fragments resolved on agarose fingerprinting gels are described. We present a mathematical model for the location and shape of the restriction...
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...
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Novel expressed sequences identified in a model of androgen independent prostate cancer (2007)
Quayle, Steven N, Hare, Heidi, Delaney, Allen D, Hirst, Martin, Hwang, Dorothy, Schein, Jacqueline E, ...
Abstract Background Prostate cancer is the most frequently diagnosed cancer in American men, and few effective treatment options are available to patients who develop hormone-refractory prostate...
Physical map-assisted whole-genome shotgun sequence assemblies (2006)
Warren, René L., Varabei, Dmitry, Platt, Darren, Huang, Xiaoqiu, Messina, David, Yang, Shiaw-Pyng, ...
We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical...
A BAC-based physical map of the Drosophila buzzatii genome (2005)
Gonzalez, Josefa, Nefedov, Michael, Bosdet, Ian, Casals, Ferran, Calvete, Oriol, Delprat, Alejandra, ...
Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps and provide useful resources for sequencing entire genomes. Drosophila...
A BAC-based physical map of the Drosophila buzzatii genome (2005)
González, Josefa, Nefedov, Michael, Bosdet, Ian, Casals, Ferran, Calvete, Oriol, Delprat, Alejandra, ...
Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps, and provide useful resources for sequencing entire genomes. Drosophila...
Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics (2004)
Matthew L. Rise, Gordon D. Brown, Melanie A. Mawer, Robert H. Devlin, Nathanael Kuipers, ...
service
Rise, Matthew L., Von Schalburg, Kristian R., Brown, Gordon D., Mawer, Melanie A., Devlin, Robert H., Kuipers, Nathanael, ...
We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus...
Automated ordering of fingerprinted clones (2004)
Flibotte, Stephane, Chiu, Readman, Fjell, Chris, Krzywinski, Martin, Schein, Jacqueline E., Shin, Heesun, ...
Motivation: A considerable amount of human intervention is currently required to produce high quality fingerprint based physical maps for genomic studies. Results: An algorithm has been developed and...
Rise, Matthew L., Von Schalburg, Kristian R., Brown, Gordon D., Mawer, Melanie A., Devlin, Robert H., Kuipers, Nathanael, ...
We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus...
Automated ordering of fingerprinted clones (2004)
Flibotte, Stephane, Chiu, Readman, Fjell, Chris, Krzywinski, Martin, Schein, Jacqueline E., Shin, Heesun, ...
Motivation: A considerable amount of human intervention is currently required to produce high-quality fingerprint-based physical maps for genomic studies. Results: An algorithm has been developed and...
Automated ordering of fingerprinted clones (2004)
Flibotte, Stephane, Chiu, Readman, Fjell, Chris, Krzywinski, Martin, Schein, Jacqueline E., Shin, Heesun, ...
Motivation: A considerable amount of human intervention is currently required to produce high quality fingerprint based physical maps for genomic studies. Results: An algorithm has been developed and...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003)
Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, ...
With the Caenorhabditis briggsae genome now in hand, C. elegans biologists have a powerful new research tool to refine their knowledge of gene function in C. elegans and to study the path of genome...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003)
Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
Internet Contig Explorer (iCE)--A Tool for Visualizing Clone Fingerprint Maps (2003)
Fjell, Christopher D., Bosdet, Ian, Schein, Jacqueline E., Jones, Steven J.M., Marra, Marco A.
Fingerprinted clone physical maps have proven useful in various applications, supporting both whole-genome and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have...
Software for Automated Analysis of DNA Fingerprinting Gels (2003)
Fuhrmann, Daniel R., Krzywinski, Martin I., Chiu, Readman, Saeedi, Parvaneh, Schein, Jacqueline E., Bosdet, Ian E., ...
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the...
Schein, Jacqueline E., Tangen, Kristin L., Chiu, Readman, Shin, Heesun, Lengeler, Klaus B., MacDonald, William Kim, ...
Schein, Jacqueline E., Tangen, Kristin L., Chiu, Readman, Shin, Heesun, Lengeler, Klaus B., MacDonald, William Kim, ...
Butterfield, Yaron S. N., Marra, Marco A., Asano, Jennifer K., Chan, Susanna Y., Guin, Ranabir, Krzywinski, Martin I., ...
We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing...
Interpreting a Sequenced Genome: Toward a Cosmid Transgenic Library of Caenorhabditis elegans (1997)
Janke, Diana L., Schein, Jacqueline E., Ha, Thê, Franz, Norman W., O'Neil, Nigel J., Vatcher, Greg P., ...
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones
Butterfield, Yaron S. N., Marra, Marco A., Asano, Jennifer K., Chan, Susanna Y., Guin, Ranabir, Krzywinski, Martin I., ...
We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing...
Schein, Jacqueline E., Tangen, Kristin L., Chiu, Readman, Shin, Heesun, Lengeler, Klaus B., MacDonald, William Kim, ...
The basidiomycete fungus Cryptococcus neoformans is an important opportunistic pathogen of humans that poses a significant threat to immunocompromised individuals. Isolates of C. neoformans are...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
Rise, Matthew L., Von Schalburg, Kristian R., Brown, Gordon D., Mawer, Melanie A., Devlin, Robert H., Kuipers, Nathanael, ...
We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus...
Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps
Fjell, Christopher D., Bosdet, Ian, Schein, Jacqueline E., Jones, Steven J.M., Marra, Marco A.
Fingerprinted clone physical maps have proven useful in various applications, supporting both whole-genome and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have...
Software for Automated Analysis of DNA Fingerprinting Gels
Fuhrmann, Daniel R., Krzywinski, Martin I., Chiu, Readman, Saeedi, Parvaneh, Schein, Jacqueline E., Bosdet, Ian E., ...
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the...
A BAC-based physical map of the Drosophila buzzatii genome
González, Josefa, Nefedov, Michael, Bosdet, Ian, Casals, Ferran, Calvete, Oriol, Delprat, Alejandra, ...
Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps, and provide useful resources for sequencing entire genomes. Drosophila...
Larkin, Denis M., Green, Cheryl A., Elliott, Janice S., Olmstead, Colleen A., Chiu, Readman, ...
Approximately 3,000 cattle bacterial artificial chromosome (BAC)-end sequences were added to the Illinois–Texas 5,000-rad RH (RH, radiation hybrid) map. The BAC-end sequences selected for mapping...
Physical map-assisted whole-genome shotgun sequence assemblies
Warren, René L., Varabei, Dmitry, Platt, Darren, Huang, Xiaoqiu, Messina, David, Yang, Shiaw-Pyng, ...
We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical...
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones
Butterfield, Yaron S. N., Marra, Marco A., Asano, Jennifer K., Chan, Susanna Y., Guin, Ranabir, Krzywinski, Martin I., ...
We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing...
Schein, Jacqueline E., Tangen, Kristin L., Chiu, Readman, Shin, Heesun, Lengeler, Klaus B., MacDonald, William Kim, ...
The basidiomycete fungus Cryptococcus neoformans is an important opportunistic pathogen of humans that poses a significant threat to immunocompromised individuals. Isolates of C. neoformans are...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
Rise, Matthew L., Von Schalburg, Kristian R., Brown, Gordon D., Mawer, Melanie A., Devlin, Robert H., Kuipers, Nathanael, ...
We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus...
Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps
Fjell, Christopher D., Bosdet, Ian, Schein, Jacqueline E., Jones, Steven J.M., Marra, Marco A.
Fingerprinted clone physical maps have proven useful in various applications, supporting both whole-genome and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have...
Software for Automated Analysis of DNA Fingerprinting Gels
Fuhrmann, Daniel R., Krzywinski, Martin I., Chiu, Readman, Saeedi, Parvaneh, Schein, Jacqueline E., Bosdet, Ian E., ...
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the...
A BAC-based physical map of the Drosophila buzzatii genome
González, Josefa, Nefedov, Michael, Bosdet, Ian, Casals, Ferran, Calvete, Oriol, Delprat, Alejandra, ...
Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps, and provide useful resources for sequencing entire genomes. Drosophila...
Larkin, Denis M., Green, Cheryl A., Elliott, Janice S., Olmstead, Colleen A., Chiu, Readman, ...
Approximately 3,000 cattle bacterial artificial chromosome (BAC)-end sequences were added to the Illinois–Texas 5,000-rad RH (RH, radiation hybrid) map. The BAC-end sequences selected for mapping...
Physical map-assisted whole-genome shotgun sequence assemblies
Warren, René L., Varabei, Dmitry, Platt, Darren, Huang, Xiaoqiu, Messina, David, Yang, Shiaw-Pyng, ...
We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical...
Novel expressed sequences identified in a model of androgen independent prostate cancer
Quayle, Steven N, Hare, Heidi, Delaney, Allen D, Hirst, Martin, Hwang, Dorothy, Schein, Jacqueline E, ...
Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation
Friedman, J. M., Baross, Ágnes, Delaney, Allen D., Ally, Adrian, Arbour, Laura, Asano, Jennifer, ...
The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically detectable chromosomal abnormalities are the most frequently recognized cause, but...
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse
McLeod, Michael P., Warren, René L., Hsiao, William W. L., Araki, Naoto, Myhre, Matthew, Fernandes, Clinton, ...
Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest....
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
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.
ABySS: A parallel assembler for short read sequence data
Simpson, Jared T., Wong, Kim, Jackman, Shaun D., Schein, Jacqueline E., Jones, Steven J.M., Birol, İnanç
Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the...