Ralph, Steven G, Chun, Hye, Kolosova, Natalia, Cooper, Dawn, Oddy, Claire, Ritland, Carol E, ...
Abstract Background Members of the pine family (Pinaceae), especially species of spruce ( Picea spp.) and pine ( Pinus spp.), dominate many of the world's temperate and boreal forests. These conifer...
Identification of a set of genes showing regionally enriched expression in the mouse brain (2008)
D'Souza, Cletus A, Chopra, Vikramjit, Varhol, Richard, Xie, Yuan-Yun, Bohacec, Slavita, Zhao, Yongjun, ...
Abstract Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of...
Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags (2008)
Shin, Heesun, Hirst, Martin, Bainbridge, Matthew N, Magrini, Vincent, Mardis, Elaine, Moerman, Donald G, ...
Abstract Background We have applied a high-throughput pyrosequencing technology for transcriptome profiling of Caenorhabditis elegans in its first larval stage. Using this approach, we have generated...
Identification of transcripts with enriched expression in the developing and adult pancreas (2008)
Hoffman, Brad G, Zavaglia, Bogard, Witzsche, Joy, Ruiz De Algara, Teresa, Beach, Mike, Hoodless, Pamela A, ...
Abstract Background Despite recent advances, the transcriptional hierarchy driving pancreas organogenesis remains largely unknown, in part due to the paucity of comprehensive analyses. To address...
Ralph, Steven G, Chun, Hye Jung E, Cooper, Dawn, Kirkpatrick, Robert, Kolosova, Natalia, Gunter, Lee, ...
Abstract Background The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree...
Baross, Ágnes, Delaney, Allen D, Li, H Irene, Nayar, Tarun, Flibotte, Stephane, Qian, Hong, ...
Abstract Background Genomic deletions and duplications are important in the pathogenesis of diseases, such as cancer and mental retardation, and have recently been shown to occur frequently in...
High-Throughput In Vivo Analysis of Gene Expression in Caenorhabditis elegans (2007)
Rebecca Hunt-Newbury, Ryan Viveiros, Robert Johnsen, Allan Mah, Dina Anastas, Lily Fang, ...
Using DNA sequences 5′ to open reading frames, we have constructed green fluorescent protein (GFP) fusions and generated spatial and temporal tissue expression profiles for 1,886 specific genes in...
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...
Hou, Juan, Charters, Anita M, Lee, Sam C, Zhao, Yongjun, Wu, Mona K, Jones, Steven JM, ...
Abstract Background The embryonic definitive endoderm (DE) gives rise to organs of the gastrointestinal and respiratory tract including the liver, pancreas and epithelia of the lung and colon....
Pugh, Trevor J, Bebb, Gwyn, Barclay, Lorena, Sutcliffe, Margaret, Fee, John, Salski, Chris, ...
Abstract Background Gefitinib, a small molecule tyrosine kinase inhibitor of the Epidermal Growth Factor Receptor ( EGFR ), has shown limited efficacy in the treatment of lung cancer. Recognized...
LongSAGE profiling of nine human embryonic stem cell lines (2007)
Hirst, Martin, Delaney, Allen, Rogers, Sean A, Schnerch, Angelique, Persaud, Deryck R, O'Connor, Michael D, ...
Abstract To facilitate discovery of novel human embryonic stem cell (ESC) transcripts, we generated 2.5 million LongSAGE tags from 9 human ESC lines. Analysis of this data revealed that ESCs express...
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...
Bainbridge, Matthew N, Warren, René L, Hirst, Martin, Romanuik, Tammy, Zeng, Thomas, Go, Anne, ...
Abstract Background High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can...
High-throughput sequencing: a failure mode analysis (2005)
Yang, George S, Stott, Jeffery M, Smailus, Duane, Barber, Sarah A, Balasundaram, Miruna, Marra, Marco A, ...
Abstract Background Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase...
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...
A Public Database for Gene Expression in Human Cancers (2002)
Anita Lal, Alex E. Lash, Stephen F. Altschul, Victor Velculescu, Lin Zhang, Roger E. Mclendon, ...
A public database, SAGEmap, was created as a component of the Cancer Genome Anatomy Project to provide a central location for depositing, retrieving, and analyzing human gene expression data. This...
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...
Systematic sequencing of cDNA clones using the transposon Tn5
Shevchenko, Yuriy, Bouffard, Gerard G., Butterfield, Yaron S. N., Blakesley, Robert W., Hartley, James L., Young, Alice C., ...
In parallel with the production of genomic sequence data, attention is being focused on the generation of comprehensive cDNA-sequence resources. Such efforts are increasingly emphasizing the...
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...
High Throughput Fingerprint Analysis of Large-Insert Clones
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
As part of the Human Genome Project, the Washington University Genome Sequencing Center has commenced systematic sequencing of human chromsome 7. To organize and supply the effort, we have undertaken...
Thacker, Colin, Marra, Marco A., Jones, Alana, Baillie, David L., Rose, Ann M.
Comparative genomic analysis was used to investigate the gene structure of the bli-4 locus from two related Caenorhabditis species, C. elegans and C. briggsae. In C. elegans, bli-4 is a complex gene...
The CMT2D Locus: Refined Genetic Position and Construction of a Bacterial Clone-Based Physical Map
Ellsworth, Rachel E., Ionasescu, Victor, Searby, Charles, Sheffield, Val C., Braden, Valerie V., Kucaba, Tamara A., ...
Charcot-Marie-Tooth (CMT) disease is a progressive neuropathy of the peripheral nervous system, typically characterized by muscle weakness of the distal limbs. CMT is noted for its genetic...
Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening
Loging, W. Troy, Lal, Anita, Siu, I-Mei, Loney, Tania L., Wikstrand, Carol J., Marra, Marco A., ...
Genes expressed specifically in malignant tissue may have potential as therapeutic targets but have been difficult to locate for most cancers. The information hidden within certain public databases...
Theories and Applications for Sequencing Randomly Selected Clones
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
The zebrafish is a powerful system for understanding the vertebrate genome, allowing the combination of genetic, molecular, and embryological analysis. Expressed sequence tags (ESTs) provide a rapid...
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...
Assessment of SAGE in Transcript Identification
Pleasance, Erin D., Marra, Marco A., Jones, Steven J.M.
An essential step in Serial Analysis of Gene Expression (SAGE) is tag mapping, which refers to the unambiguous determination of the gene represented by a SAGE tag. Current resources for tag mapping...
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 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...
Warren, René, Hsiao, William W. L., Kudo, Hisashi, Myhre, Matt, Dosanjh, Manisha, Petrescu, Anca, ...
Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we...
Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
Baross, Ágnes, Butterfield, Yaron S.N., Coughlin, Shaun M., Zeng, Thomas, Griffith, Malachi, Griffith, Obi L., ...
The Mammalian Gene Collection (MGC) consortium (http://mgc.nci.nih.gov) seeks to establish publicly available collections of full-ORF cDNAs for several organisms of significance to biomedical...
High-throughput sequencing: a failure mode analysis
Yang, George S, Stott, Jeffery M, Smailus, Duane, Barber, Sarah A, Balasundaram, Miruna, Marra, Marco A, ...
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression
Halaschek-Wiener, Julius, Khattra, Jaswinder S., McKay, Sheldon, Pouzyrev, Anatoli, Stott, Jeff M., Yang, George S., ...
We have identified longevity-associated genes in a long-lived Caenorhabditis elegans daf-2 (insulin/IGF receptor) mutant using serial analysis of gene expression (SAGE), a method that efficiently...
Simple, robust methods for high-throughput nanoliter-scale DNA sequencing
Smailus, Duane E., Marziali, Andre, Dextras, Philip, Marra, Marco A., Holt, Robert A.
We have developed high-throughput DNA sequencing methods that generate high quality data from reactions as small as 400 nL, providing an approximate order of magnitude reduction in reagent use...
Siddiqui, Asim S., Khattra, Jaswinder, Delaney, Allen D., Zhao, Yongjun, Astell, Caroline, Asano, Jennifer, ...
We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing...
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...
Wilson, Gary M., Flibotte, Stephane, Missirlis, Perseus I., Marra, Marco A., Jones, Steven, Thornton, Kevin, ...
Duplication of chromosomal segments and associated genes is thought to be a primary mechanism for generating evolutionary novelty. By comparative genome hybridization using a full-coverage (tiling)...
Sequence biases in large scale gene expression profiling data
Siddiqui, Asim S., Delaney, Allen D., Schnerch, Angelique, Griffith, Obi L., Jones, Steven J. M., Marra, Marco A.
We present the results of a simple, statistical assay that measures the G+C content sensitivity bias of gene expression experiments without the requirement of a duplicate experiment. We analyse five...
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...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
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...
Systematic sequencing of cDNA clones using the transposon Tn5
Shevchenko, Yuriy, Bouffard, Gerard G., Butterfield, Yaron S. N., Blakesley, Robert W., Hartley, James L., Young, Alice C., ...
In parallel with the production of genomic sequence data, attention is being focused on the generation of comprehensive cDNA-sequence resources. Such efforts are increasingly emphasizing the...
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...
High Throughput Fingerprint Analysis of Large-Insert Clones
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
As part of the Human Genome Project, the Washington University Genome Sequencing Center has commenced systematic sequencing of human chromsome 7. To organize and supply the effort, we have undertaken...
Thacker, Colin, Marra, Marco A., Jones, Alana, Baillie, David L., Rose, Ann M.
Comparative genomic analysis was used to investigate the gene structure of the bli-4 locus from two related Caenorhabditis species, C. elegans and C. briggsae. In C. elegans, bli-4 is a complex gene...
The CMT2D Locus: Refined Genetic Position and Construction of a Bacterial Clone-Based Physical Map
Ellsworth, Rachel E., Ionasescu, Victor, Searby, Charles, Sheffield, Val C., Braden, Valerie V., Kucaba, Tamara A., ...
Charcot-Marie-Tooth (CMT) disease is a progressive neuropathy of the peripheral nervous system, typically characterized by muscle weakness of the distal limbs. CMT is noted for its genetic...
Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening
Loging, W. Troy, Lal, Anita, Siu, I-Mei, Loney, Tania L., Wikstrand, Carol J., Marra, Marco A., ...
Genes expressed specifically in malignant tissue may have potential as therapeutic targets but have been difficult to locate for most cancers. The information hidden within certain public databases...
Theories and Applications for Sequencing Randomly Selected Clones
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
The zebrafish is a powerful system for understanding the vertebrate genome, allowing the combination of genetic, molecular, and embryological analysis. Expressed sequence tags (ESTs) provide a rapid...
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...
Assessment of SAGE in Transcript Identification
Pleasance, Erin D., Marra, Marco A., Jones, Steven J.M.
An essential step in Serial Analysis of Gene Expression (SAGE) is tag mapping, which refers to the unambiguous determination of the gene represented by a SAGE tag. Current resources for tag mapping...
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...