Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries (2009)
Romanuik, Tammy L, Wang, Gang, Holt, Robert A, Jones, Steven JM, Marra, Marco A, Sadar, Marianne D
Abstract Background The development and maintenance of the prostate is dependent on androgens and the androgen receptor. The androgen pathway continues to be important in prostate cancer. Here, we...
DiGuistini, Scott, Liao, Nancy Y, Platt, Darren, Robertson, Gordon, Seidel, Michael, Chan, Simon K, ...
Abstract Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that...
Identification of genes expressed in the hermaphrodite germ line of C. elegansusing SAGE (2009)
Wang, Xin, Zhao, Yongjun, Wong, Kim, Ehlers, Peter, Kohara, Yuji, Jones, Steven J, ...
Abstract Background Germ cells must progress through elaborate developmental stages from an undifferentiated germ cell to a fully differentiated gamete. Some of these stages include exiting mitosis...
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans (2009)
Hillier, LaDeana W., Reinke, Valerie, Green, Philip, Hirst, Martin, Marra, Marco A., Waterston, Robert H.
Using massively parallel sequencing by synthesis methods, we have surveyed the polyA+ transcripts from four stages of the nematode Caenorhabditis elegans to an unprecedented depth. Using novel...
Circos: An information aesthetic for comparative genomics (2009)
Krzywinski, Martin, Schein, Jacqueline, Birol, Inanç, Connors, Joseph, Gascoyne, Randy, Horsman, Doug, ...
We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying...
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...
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...
Stephane Flibotte, Readman Chiu, Chris Fjell, Martin Krzywinski, Jacqueline E, Heesun Shin, ...
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...
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...
Wederell, Elizabeth D., Bilenky, Mikhail, Cullum, Rebecca, Thiessen, Nina, Dagpinar, Melis, Delaney, Allen, ...
Foxa2 (HNF3β) is a one of three, closely related transcription factors that are critical to the development and function of the mouse liver. We have used chromatin immunoprecipitation and massively...
Morin, Ryan D., OConnor, Michael D., Griffith, Malachi, Kuchenbauer, Florian, Delaney, Allen, Prabhu, Anna-Liisa, ...
MicroRNAs (miRNAs) are emerging as important, albeit poorly characterized, regulators of biological processes. Key to further elucidation of their roles is the generation of more complete lists of...
In-depth characterization of the microRNA transcriptome in a leukemia progression model (2008)
Kuchenbauer, Florian, Morin, Ryan D., Argiropoulos, Bob, Petriv, Oleh I., Griffith, Malachi, Heuser, Michael, ...
MicroRNAs (miRNAs) have been shown to play important roles in physiological as well as multiple malignant processes, including acute myeloid leukemia (AML). In an effort to gain further insight into...
Robertson, A. Gordon, Bilenky, Mikhail, Tam, Angela, Zhao, Yongjun, Zeng, Thomas, Thiessen, Nina, ...
We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different...
BMC Biology BioMed Central (2008)
Heesun Shin, Martin Hirst, Matthew N Bainbridge, Vincent Magrini, Elaine Mardis, Donald G Moerman, ...
Research article Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags
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...
Advances in Brief A Public Database for Gene Expression in Human Cancers 1 (2007)
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...
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...
Identification and analysis of internal promoters in Caenorhabditis elegans operons (2007)
Huang, Peiming, Pleasance, Erin D., Maydan, Jason S., Hunt-Newbury, Rebecca, ONeil, Nigel J., Mah, Allan, ...
The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoter∷GFP methodology, we have conducted the largest survey to date on...
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...
The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron (2007)
Etchberger, John F., Lorch, Adam, Sleumer, Monica C., Zapf, Richard, Jones, Steven J., Marra, Marco A., ...
Taste receptor cells constitute a highly specialized cell type that perceives and conveys specific sensory information to the brain. The detailed molecular composition of these cells and the...
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...
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...
Khattra, Jaswinder, Delaney, Allen D., Zhao, Yongjun, Siddiqui, Asim, Asano, Jennifer, McDonald, Helen, ...
We describe the details of a serial analysis of gene expression (SAGE) library construction and analysis platform that has enabled the generation of >298 high-quality SAGE libraries and >30 million...
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...
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...
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...
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...
Khattra, Jaswinder, Delaney, Allen D., Zhao, Yongjun, Siddiqui, Asim, Asano, Jennifer, McDonald, Helen, ...
We describe the details of a serial analysis of gene expression (SAGE) library construction and analysis platform that has enabled the generation of >298 high-quality SAGE libraries and >30 million...
Sequence biases in large scale gene expression profiling data (2006)
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...
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...
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression (2005)
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...
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression (2005)
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 (2005)
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...
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)...
Simple, robust methods for high-throughput nanoliter-scale DNA sequencing (2005)
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...
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, ...
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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...
Anglesio, Michael S., Evdokimova, Valentina, Melnyk, Nataliya, Zhang, Liyong, Fernandez, Conrad V., Grundy, Paul E., ...
We have analyzed the chromosome 6q21 breakpoint of a non-constitutional t(6;15)(q21;q21) rearrangement in sporadic Wilms' tumour. This identified a novel gene encoding a protein with six N-terminal...
Anglesio, Michael S., Evdokimova, Valentina, Melnyk, Nataliya, Zhang, Liyong, Fernandez, Conrad V., Grundy, Paul E., ...
We have analyzed the chromosome 6q21 breakpoint of a non-constitutional t(6;15)(q21;q21) rearrangement in sporadic Wilms' tumor. This identified a novel gene encoding a protein with six N-terminal...
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...
A set of BAC clones spanning the human genome (2004)
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...
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...
Systematic Recovery and Analysis of Full-ORF Human cDNA Clones (2004)
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...
Anglesio, Michael S., Evdokimova, Valentina, Melnyk, Nataliya, Zhang, Liyong, Fernandez, Conrad V., Grundy, Paul E., ...
We have analyzed the chromosome 6q21 breakpoint of a non-constitutional t(6;15)(q21;q21) rearrangement in sporadic Wilms' tumour. This identified a novel gene encoding a protein with six N-terminal...
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...
Functional Characterization of a Catabolic Plasmid from Polychlorinated- (2003)
Biphenyl-degrading Rhodococcus, Strain Rha, René Warren, Hisashi Kudo, Matt Myhre, ...
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...
Assessment of SAGE in Transcript Identification (2003)
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 (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...
Systematic sequencing of cDNA clones using the transposon Tn5 (2002)
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...
Theories and Applications for Sequencing Randomly Selected Clones (2001)
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Theories and Applications for Sequencing Randomly Selected Clones (2001)
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Jones, Steven J.M., Riddle, Donald L., Pouzyrev, Anatoli T., Velculescu, Victor E., Hillier, LaDeana, Eddy, Sean R., ...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
Jones, Steven J.M., Riddle, Donald L., Pouzyrev, Anatoli T., Velculescu, Victor E., Hillier, LaDeana, Eddy, Sean R., ...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
Theories and Applications for Sequencing Randomly Selected Clones (2001)
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Jones, Steven J.M., Riddle, Donald L., Pouzyrev, Anatoli T., Velculescu, Victor E., Hillier, LaDeana, Eddy, Sean R., ...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
Ellsworth, Rachel E., Ionasescu, Victor, Searby, Charles, Sheffield, Val C., Braden, Valerie V., Kucaba, Tamara A., ...
High Throughput Fingerprint Analysis of Large-Insert Clones (1997)
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
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...
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)...
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...
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...
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....
Molecular Profiling of Clinical Tissue Specimens : Feasibility and Applications
Emmert-Buck, Michael R., Strausberg, Robert L., Krizman, David B., Bonaldo, M. Fatima, Bonner, Robert F., Bostwick, David G., ...
Khattra, Jaswinder, Delaney, Allen D., Zhao, Yongjun, Siddiqui, Asim, Asano, Jennifer, McDonald, Helen, ...
We describe the details of a serial analysis of gene expression (SAGE) library construction and analysis platform that has enabled the generation of >298 high-quality SAGE libraries and >30 million...
Molecular Profiling of Clinical Tissue Specimens: Feasibility and Applications
Emmert-Buck, Michael R., Strausberg, Robert L., Krizman, David B., Bonaldo, M. Fatima, Bonner, Robert F., Bostwick, David G., ...
High-Throughput In Vivo Analysis of Gene Expression in Caenorhabditis elegans
Hunt-Newbury, Rebecca, Viveiros, Ryan, Johnsen, Robert, Mah, Allan, Anastas, Dina, Fang, Lily, ...
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...
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,...
The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron
Etchberger, John F., Lorch, Adam, Sleumer, Monica C., Zapf, Richard, Jones, Steven J., Marra, Marco A., ...
Taste receptor cells constitute a highly specialized cell type that perceives and conveys specific sensory information to the brain. The detailed molecular composition of these cells and the...
Ralph, Steven G, Chun, Hye Jung E, Cooper, Dawn, Kirkpatrick, Robert, Kolosova, Natalia, Gunter, Lee, ...
Identification and analysis of internal promoters in Caenorhabditis elegans operons
Huang, Peiming, Pleasance, Erin D., Maydan, Jason S., Hunt-Newbury, Rebecca, O’Neil, Nigel J., Mah, Allan, ...
The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoter∷GFP methodology, we have conducted the largest survey to date on the...
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.
LongSAGE profiling of nine human embryonic stem cell lines
Hirst, Martin, Delaney, Allen, Rogers, Sean A, Schnerch, Angelique, Persaud, Deryck R, O'Connor, Michael D, ...
Analysis of a 2.6 million longSAGE sequence tag resource generated from nine human embryonic stem cell lines reveals an enrichment of RNA binding proteins and novel ES-specific transcripts.
Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags
Shin, Heesun, Hirst, Martin, Bainbridge, Matthew N, Magrini, Vincent, Mardis, Elaine, Moerman, Donald G, ...
Identification of transcripts with enriched expression in the developing and adult pancreas
Hoffman, Brad G, Zavaglia, Bogard, Witzsche, Joy, Ruiz De Algara, Teresa, Beach, Mike, Hoodless, Pamela A, ...
The expression profile of different developmental stages of the murine pancreas and predictions of transcription factor interactions, provides a framework for pancreas regulatory networks and...
Identification of a set of genes showing regionally enriched expression in the mouse brain
D'Souza, Cletus A, Chopra, Vikramjit, Varhol, Richard, Xie, Yuan-Yun, Bohacec, Slavita, Zhao, Yongjun, ...
Wederell, Elizabeth D., Bilenky, Mikhail, Cullum, Rebecca, Thiessen, Nina, Dagpinar, Melis, Delaney, Allen, ...
Foxa2 (HNF3β) is a one of three, closely related transcription factors that are critical to the development and function of the mouse liver. We have used chromatin immunoprecipitation and massively...
Morin, Ryan D., O’Connor, Michael D., Griffith, Malachi, Kuchenbauer, Florian, Delaney, Allen, Prabhu, Anna-Liisa, ...
MicroRNAs (miRNAs) are emerging as important, albeit poorly characterized, regulators of biological processes. Key to further elucidation of their roles is the generation of more complete lists of...
Ralph, Steven G, Chun, Hye Jung E, Kolosova, Natalia, Cooper, Dawn, Oddy, Claire, Ritland, Carol E, ...
In-depth characterization of the microRNA transcriptome in a leukemia progression model
Kuchenbauer, Florian, Morin, Ryan D., Argiropoulos, Bob, Petriv, Oleh I., Griffith, Malachi, Heuser, Michael, ...
MicroRNAs (miRNAs) have been shown to play important roles in physiological as well as multiple malignant processes, including acute myeloid leukemia (AML). In an effort to gain further insight into...
Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE
Wang, Xin, Zhao, Yongjun, Wong, Kim, Ehlers, Peter, Kohara, Yuji, Jones, Steven J, ...
Robertson, A. Gordon, Bilenky, Mikhail, Tam, Angela, Zhao, Yongjun, Zeng, Thomas, Thiessen, Nina, ...
We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different...
Meissner, Barbara, Warner, Adam, Wong, Kim, Dube, Nicholas, Lorch, Adam, McKay, Sheldon J., ...
A crucial step in the development of muscle cells in all metazoan animals is the assembly and anchorage of the sarcomere, the essential repeat unit responsible for muscle contraction. In...
Genetic Variation in Healthy Oldest-Old
Halaschek-Wiener, Julius, Amirabbasi-Beik, Mahsa, Monfared, Nasim, Pieczyk, Markus, Sailer, Christian, Kollar, Anita, ...
Individuals who live to 85 and beyond without developing major age-related diseases may achieve this, in part, by lacking disease susceptibility factors, or by possessing resistance factors that...
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
Hillier, LaDeana W., Reinke, Valerie, Green, Philip, Hirst, Martin, Marra, Marco A., Waterston, Robert H.
Using massively parallel sequencing by synthesis methods, we have surveyed the polyA+ transcripts from four stages of the nematode Caenorhabditis elegans to an unprecedented depth. Using novel...
Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries
Romanuik, Tammy L, Wang, Gang, Holt, Robert A, Jones, Steven JM, Marra, Marco A, Sadar, Marianne D
DiGuistini, Scott, Liao, Nancy Y, Platt, Darren, Robertson, Gordon, Seidel, Michael, Chan, Simon K, ...
A method for de novo assembly of a eukaryotic genome using Illumina, 454 and Sanger generated sequence data