The theory of discovering rare variants via DNA sequencing (2009)
Wendl, Michael C, Wilson, Richard K
Abstract Background Rare population variants are known to have important biomedical implications, but their systematic discovery has only recently been enabled by advances in DNA sequencing. The...
Statistical aspects of discerning indel-type structural variation via DNA sequence alignment (2009)
Wendl, Michael C, Wilson, Richard K
Abstract Background Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown...
Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophoraTTO1 (2009)
Bai, Xiaodong, Adams, Byron J, Ciche, Todd A, Clifton, Sandra, Gaugler, Randy, Hogenhout, Saskia A, ...
Abstract Background The entomopathogenic nematode Heterorhabditis bacteriophora and its symbiotic bacterium, Photorhabdus luminescens , are important biological control agents of insect pests. This...
Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1 (2009)
Bai, Xiaodong, Adams, Byron J., Ciche, Todd A., Clifton, Sandra, Gaugler, Randy, Hogenhout, Saskia A., ...
Background: The entomopathogenic nematode Heterorhabditis bacteriophora and its symbiotic bacterium, Photorhabdus luminescens, are important biological control agents of insect pests. This...
Molecular determinants archetypical to the phylum Nematoda (2009)
Yin, Yong, Martin, John, Abubucker, Sahar, Wang, Zhengyuan, Wyrwicz, Lucjan, Rychlewski, Leszek, ...
Abstract Background Nematoda diverged from other animals between 600–1,200 million years ago and has become one of the most diverse animal phyla on earth. Most nematodes are free-living animals,...
A burst of segmental duplications in the genome of the African great ape ancestor (2009)
Marqués-Bonet, Tomàs, Kidd, Jeffrey M., Ventura, Mario, Graves, Tina A., Cheng, Ze, Hillier, LaDeana W., ...
5 pages, 4 figures.-- Supplementary information (3 files) available at: http://www.nature.com/nature/journal/v457/n7231/suppinfo/nature07744.html
Girirajan, Santhosh, Chen, Lin, Graves, Tina, Marques-Bonet, Tomas, Ventura, Mario, Fronick, Catrina, ...
The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of...
VarScan: variant detection in massively parallel sequencing of individual and pooled samples (2009)
Koboldt, Daniel C., Chen, Ken, Wylie, Todd, Larson, David E., McLellan, Michael D., Mardis, Elaine R., ...
Summary: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The...
Cancer genome sequencing: a review (2009)
Mardis, Elaine R., Wilson, Richard K.
A genomic era of cancer studies is developing rapidly, fueled by the emergence of next-generation sequencing technologies that provide exquisite sensitivity and resolution. This article discusses...
Somatic mutations affect key pathways in lung adenocarcinoma (2008)
Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, ...
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well- classified primary tumours. Here we report the results of a collaborative...
Article Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2008)
Adam Siepel, Gill Bejerano, Jakob S. Pedersen, Angie S. Hinrichs, Minmei Hou, Kate Rosenbloom, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Patel, Vidushi S, Cooper, Steven JB, Deakin, Janine E, Fulton, Bob, Graves, Tina, Warren, Wesley C, ...
Abstract Background Vertebrate alpha (α)- and beta (β)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin...
Aspects of coverage in medical DNA sequencing (2008)
Wendl, Michael C, Wilson, Richard K
Abstract Background DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used...
Marks, Jennifer L., Gong, Yixuan X., Chitale, Dhananjay, Golas, Ben, McLellan, Michael D., Kasai, Yumi, ...
Somatic mutations affect key pathways in lung adenocarcinoma (2008)
Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, ...
Genome analysis of the platypus reveals unique signatures of evolution (2008)
Warren, Wesley C., Hillier, LaDeana W., Marshall Graves, Jennifer A., Birney, Ewan, Ponting, Chris P., Grützner, Frank, ...
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a...
Haplotype sorting using human fosmid clone end-sequence pairs (2008)
Kidd, Jeffrey M., Cheng, Ze, Graves, Tina, Fulton, Bob, Wilson, Richard K., Eichler, Evan E.
An important goal of human genetics and genomics is to understand the complete spectrum of genetic variation across a specific human haplotype. By combining information from a dense SNP map with...
Patel, Vidushi S., Cooper, Steven John Baynard, Deakin, Janine E., Fulton, Bob, Graves, Tina, Warren, Wesley, ...
Background: Vertebrate alpha (α)- and beta (β)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the...
Patel, Vidushi S., Cooper, Steven John Baynard, Deakin, Janine E., Fulton, Bob, Graves, Tina, Warren, Wesley, ...
Background: Vertebrate alpha (α)- and beta (β)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the...
Characterizing the cancer genome in lung adenocarcinoma (2007)
Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, ...
Somatic alterations in cellular DNA underlie almost all human cancers(1). The prospect of targeted therapies(2) and the development of high-resolution, genome-wide approaches(3-8) are now spurring...
Design and implementation of a generalized laboratory data model (2007)
Wendl, Michael C, Smith, Scott, Pohl, Craig S, Dooling, David J, Chinwalla, Asif T, Crouse, Kevin, ...
Abstract Background Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many...
Evolution of Symbiotic Bacteria in the Distal Human Intestine (2007)
Jian Xu, Michael A. Mahowald, Ruth E. Ley, Catherine A. Lozupone, Micah Hamady, Eric C. Martens, ...
The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping...
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,...
Chen, Ken, McLellan, Michael D., Ding, Li, Wendl, Michael C., Kasai, Yumi, Wilson, Richard K., ...
Small insertions and deletions (indels) and single nucleotide polymorphisms (SNPs) are common genetic variants that are thought to be associated with a wide variety of human diseases. Owing to the...
Characterizing the cancer genome in lung adenocarcinoma (2007)
Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, ...
Design and implementation of a generalized laboratory data model (2007)
Michael C Wendl, Scott Smith, Craig S Pohl, David J Dooling, Asif T Chinwalla, Kevin Crouse, ...
Application of a superword array in genome assembly (2006)
Huang, Xiaoqiu, Yang, Shiaw-Pyng, Chinwalla, Asif T., Hillier, LaDeana W., Minx, Patrick, Mardis, Elaine R., ...
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array....
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...
Molecular refinement of gibbon genome rearrangement (2006)
Roberto, Roberta, Capozzi, Oronzo, Wilson, Richard K., Mardis, Elaine R., Lomiento, Mariana, Tuzun, Eray, ...
The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and...
Investigating hookworm genomes by comparative analysis of two Ancylostomaspecies (2005)
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
Abstract Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans . Applying genomics techniques to...
AFGWC Automated Meteorological Data Processing (2005)
The present 'state of the art' in automated meteorological data processing as practiced at Air Force Global Weather Central is discussed. This includes major activities from interface with the...
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
Punctuated duplication seeding events during the evolution of human chromosome 2p11. (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
Susan K. Flowers, Carla Easter, Andrea Holmes, Brian Cohen, Z April E, Elaine R. Mardis, ...
Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other...
Application of a superword array in genome assembly (2005)
Xiaoqiu Huang, Shiaw-pyng Yang, Asif T. Chinwalla, Ladeana W. Hillier, Patrick Minx, Elaine R. Mardis, ...
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array....
Punctuated duplication seeding events during the evolution of human chromosome 2p11 (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
The repetitive landscape of the chicken genome (2005)
Wicker, Thomas, Robertson, Jon S., Schulze, Stefan R., Feltus, F. Alex, Magrini, Vincent, Morrison, Jason A., ...
Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005)
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Punctuated duplication seeding events during the evolution of human chromosome 2p11 (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005)
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms (2004)
Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, ...
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken...
A physical map of the chicken genome (2004)
Wallis, John W, Aerts, Jan, Groenen, Martien A M, Layman, Dan, Graves, Tina A, ...
Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can...
EAnnot: A genome annotation tool using experimental evidence (2004)
Ding, Li, Sabo, Aniko, Berkowicz, Nicolas, Meyer, Rekha R., Shotland, Yoram, Johnson, Mark R., ...
The sequence of any genome becomes most useful for biological experimentation when a complete and accurate gene set is available. Gene prediction programs offer an efficient way to generate an...
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes (2004)
Wylie, Todd, Martin, John C., Dante, Michael, Mitreva, Makedonka Dautova, Clifton, Sandra W., Chinwalla, Asif, ...
Nematode.net (www.nematode.net) is a web‐ accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at...
The Repetitive Landscape of the Chicken Genome (2004)
Wicker, Thomas, Robertson, Jon S., Schulze, Stefan R., Feltus, F. Alex, Magrini, Vincent, Morrison, Jason A., ...
Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation...
The Repetitive Landscape of the Chicken Genome (2004)
Wicker, Thomas, Robertson, Jon S., Schulze, Stefan R., Feltus, F. Alex, Magrini, Vincent, Morrison, Jason A., ...
Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation...
Furey, Terrence S., Diekhans, Mark, Lu, Yontao, Graves, Tina A., Oddy, Lachlan, Randall-Maher, Jennifer, ...
The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of ∼30,000 nonredundant human mRNA sequences with identified coding regions...
Viral Discovery and Sequence Recovery Using DNA Microarrays (2003)
David Wang, Anatoly Urisman, Yu-Tsueng Liu, Michael Springer, Thomas G. Ksiazek, Dean D. Erdman, ...
Know your enemy. Description of the ‘virus gene chip’ that helped to classify the SARS virus as a novel coronavirus.
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...
Viral Discovery and Sequence Recovery Using DNA Microarrays (2003)
David Wang, Anatoly Urisman, Yu-Tsueng Liu, Michael Springer, Thomas G. Ksiazek, Dean D. Erdman, ...
Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods...
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...
Robert H. Waterston, Sean Eddy, Richard K. Wilson, Genome Sequencing
The value of Caenorhabditis elegans as a model organism for biomedical research is unquestioned. The interpretation of its 100.2 Mb complete genome sequence has been enhanced by a high quality, 98 %...
What is Finished, and Why Does it Matter (2002)
Mardis, Elaine, McPherson, John, Martienssen, Robert, Wilson, Richard K., McCombie, W. Richard
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.
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.
McClelland, Michael, Florea, Liliana, Sanderson, Ken, Clifton, Sandra W., Parkhill, Julian, Churcher, Carol, ...
The Escherichia coli K-12 genome (ECO) was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A (collectively referred to as SAL)...
A Pneumatic Device for Rapid Loading of DNA Sequencing Gels (1998)
Panussis, Dimitrios A., Cook, Mark W., Rifkin, Lisa L., Snider, Jacqueline E., Strong, Joseph T., McGrane, Rebecca M., ...
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., ...
A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes (1997)
Devine, Scott E., Chissoe, Stephanie L., Eby, Yolanda, Wilson, Richard K., Boeke, Jef D.
The construction and analysis of M13 libraries prepared from YAC DNA (1995)
Vaudin, Mark, Hillier, LaDeana, Brinkman, Ryan, Sulston, John, Wilson, Richard K., Waterston, Robert H.
Yeast artificial chromosomes (YACs) provide a powerful way to isolate and map large regions of genomlc DNA and their use In genome analysis is now extensive. We modified a series of procedures to...
Lee, Linda G., Connell, Charles R., Woo, Sam L., Cheng, Richard D., McArdle, Bernard F., Fuller, Carl W., ...
The incorporation of fluorescently labeled dideoxynucleotides by T7 DNA polymerase is optimized by the use of Mn2+, fluorescein analogs and four 2′-deoxyribonucleoside 5′-O-(1-thiotriphosphates)...
Low pressure DNA shearing: a method for random DNA sequence analysis (1990)
Schriefer, Lawrence A., Gebauer, Beth K., Qiu, Lisa Q.Q., Waterston, Robert H., Wilson, Richard K.
Wilson, Richard K., Roe, Bruce A.
The overall structure of transfer RNA is optimized for its various functions by a series of unique post-transcriptional nucleotide modifications. Since many of these modifications are conserved from...
Business progressivism in Omaha, 1900-1917 / (1977)
Thesis (M.A.)--Creighton University, 1977.
Ellsworth, Rachel E., Jamison, D. Curtis, Touchman, Jeffrey W., Chissoe, Stephanie L., Braden Maduro, Valerie V., Bouffard, Gerard G., ...
The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous...
McClelland, Michael, Wilson, Richard K.
Raw sequence data representing the majority of a bacterial genome can be obtained at a tiny fraction of the cost of a completed sequence. To demonstrate the utility of such a resource, 870...
McClelland, Michael, Florea, Liliana, Sanderson, Ken, Clifton, Sandra W., Parkhill, Julian, Churcher, Carol, ...
The Escherichia coli K-12 genome (ECO) was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A (collectively referred to as SAL)...
Viral Discovery and Sequence Recovery Using DNA Microarrays
Wang, David, Urisman, Anatoly, Liu, Yu-Tsueng, Springer, Michael, Ksiazek, Thomas G, Erdman, Dean D, ...
Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods...
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...
Ley, Timothy J., Minx, Patrick J., Walter, Matthew J., Ries, Rhonda E., Sun, Hui, McLellan, Michael, ...
In this pilot study, we used primary human acute myeloid leukemia (AML) cell genomes as templates for exonic PCR amplification, followed by high-throughput resequencing, analyzing ≈7 million base...
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
Wylie, Todd, Martin, John C., Dante, Michael, Mitreva, Makedonka Dautova, Clifton, Sandra W., Chinwalla, Asif, ...
Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington...
A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes
Devine, Scott E., Chissoe, Stephanie L., Eby, Yolanda, Wilson, Richard K., Boeke, Jef D.
Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using...
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...
A Pneumatic Device for Rapid Loading of DNA Sequencing Gels
Panussis, Dimitrios A., Cook, Mark W., Rifkin, Lisa L., Snider, Jacqueline E., Strong, Joseph T., McGrane, Rebecca M., ...
This work describes the design and construction of a device that facilitates the loading of DNA samples onto polyacrylamide gels for detection in the Perkin Elmer/Applied Biosystems (PE/ABI) 373 and...
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...
Sequence and Comparative Analysis of the Maize NB Mitochondrial Genome1[w]
Clifton, Sandra W., Minx, Patrick, Fauron, Christiane M.-R., Gibson, Michael, Allen, James O., Sun, Hui, ...
The NB mitochondrial genome found in most fertile varieties of commercial maize (Zea mays subsp. mays) was sequenced. The 569,630-bp genome maps as a circle containing 58 identified genes encoding 33...
Furey, Terrence S., Diekhans, Mark, Lu, Yontao, Graves, Tina A., Oddy, Lachlan, Randall-Maher, Jennifer, ...
The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of ∼30,000 nonredundant human mRNA sequences with identified coding regions...
EAnnot: A genome annotation tool using experimental evidence
Ding, Li, Sabo, Aniko, Berkowicz, Nicolas, Meyer, Rekha R., Shotland, Yoram, Johnson, Mark R., ...
The sequence of any genome becomes most useful for biological experimentation when a complete and accurate gene set is available. Gene prediction programs offer an efficient way to generate an...
The repetitive landscape of the chicken genome
Wicker, Thomas, Robertson, Jon S., Schulze, Stefan R., Feltus, F. Alex, Magrini, Vincent, Morrison, Jason A., ...
Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation...
Katari, Manpreet S., Balija, Vivekanand, Wilson, Richard K., Martienssen, Robert A., McCombie, W. Richard
Since the completion of the Arabidopsis thaliana genome sequence, there is an ongoing effort to annotate the genome as accurately as possible. Comparing genome sequences of related species...
Investigating hookworm genomes by comparative analysis of two Ancylostoma species
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
Punctuated duplication seeding events during the evolution of human chromosome 2p11
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Walter, Matthew J., Park, John S., Ries, Rhonda E., Lau, Steven K. M., McLellan, Michael, Jaeger, Sara, ...
PU.1 is a member of the ETS family of transcription factors that is known to be important for hematopoietic development. Recently, haploinsufficiency for PU.1 has been shown to cause a shift in...
Flowers, Susan K, Easter, Carla, Holmes, Andrea, Cohen, Brian, Bednarski, April E, Mardis, Elaine R, ...
Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other...
Application of a superword array in genome assembly
Huang, Xiaoqiu, Yang, Shiaw-Pyng, Chinwalla, Asif T., Hillier, LaDeana W., Minx, Patrick, Mardis, Elaine R., ...
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array....
After the Duplication: Gene Loss and Adaptation in Saccharomyces Genomes
Cliften, Paul F., Fulton, Robert S., Wilson, Richard K., Johnston, Mark
The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before...
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...
Ellsworth, Rachel E., Jamison, D. Curtis, Touchman, Jeffrey W., Chissoe, Stephanie L., Braden Maduro, Valerie V., Bouffard, Gerard G., ...
The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous...
McClelland, Michael, Wilson, Richard K.
Raw sequence data representing the majority of a bacterial genome can be obtained at a tiny fraction of the cost of a completed sequence. To demonstrate the utility of such a resource, 870...
McClelland, Michael, Florea, Liliana, Sanderson, Ken, Clifton, Sandra W., Parkhill, Julian, Churcher, Carol, ...
The Escherichia coli K-12 genome (ECO) was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A (collectively referred to as SAL)...
Viral Discovery and Sequence Recovery Using DNA Microarrays
Wang, David, Urisman, Anatoly, Liu, Yu-Tsueng, Springer, Michael, Ksiazek, Thomas G, Erdman, Dean D, ...
Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods...
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...
Ley, Timothy J., Minx, Patrick J., Walter, Matthew J., Ries, Rhonda E., Sun, Hui, McLellan, Michael, ...
In this pilot study, we used primary human acute myeloid leukemia (AML) cell genomes as templates for exonic PCR amplification, followed by high-throughput resequencing, analyzing ≈7 million base...
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
Wylie, Todd, Martin, John C., Dante, Michael, Mitreva, Makedonka Dautova, Clifton, Sandra W., Chinwalla, Asif, ...
Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington...
A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes
Devine, Scott E., Chissoe, Stephanie L., Eby, Yolanda, Wilson, Richard K., Boeke, Jef D.
Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using...
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...
A Pneumatic Device for Rapid Loading of DNA Sequencing Gels
Panussis, Dimitrios A., Cook, Mark W., Rifkin, Lisa L., Snider, Jacqueline E., Strong, Joseph T., McGrane, Rebecca M., ...
This work describes the design and construction of a device that facilitates the loading of DNA samples onto polyacrylamide gels for detection in the Perkin Elmer/Applied Biosystems (PE/ABI) 373 and...
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...
Sequence and Comparative Analysis of the Maize NB Mitochondrial Genome1[w]
Clifton, Sandra W., Minx, Patrick, Fauron, Christiane M.-R., Gibson, Michael, Allen, James O., Sun, Hui, ...
The NB mitochondrial genome found in most fertile varieties of commercial maize (Zea mays subsp. mays) was sequenced. The 569,630-bp genome maps as a circle containing 58 identified genes encoding 33...
Furey, Terrence S., Diekhans, Mark, Lu, Yontao, Graves, Tina A., Oddy, Lachlan, Randall-Maher, Jennifer, ...
The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of ∼30,000 nonredundant human mRNA sequences with identified coding regions...
EAnnot: A genome annotation tool using experimental evidence
Ding, Li, Sabo, Aniko, Berkowicz, Nicolas, Meyer, Rekha R., Shotland, Yoram, Johnson, Mark R., ...
The sequence of any genome becomes most useful for biological experimentation when a complete and accurate gene set is available. Gene prediction programs offer an efficient way to generate an...
The repetitive landscape of the chicken genome
Wicker, Thomas, Robertson, Jon S., Schulze, Stefan R., Feltus, F. Alex, Magrini, Vincent, Morrison, Jason A., ...
Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation...
Katari, Manpreet S., Balija, Vivekanand, Wilson, Richard K., Martienssen, Robert A., McCombie, W. Richard
Since the completion of the Arabidopsis thaliana genome sequence, there is an ongoing effort to annotate the genome as accurately as possible. Comparing genome sequences of related species...
Investigating hookworm genomes by comparative analysis of two Ancylostoma species
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
Punctuated duplication seeding events during the evolution of human chromosome 2p11
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Walter, Matthew J., Park, John S., Ries, Rhonda E., Lau, Steven K. M., McLellan, Michael, Jaeger, Sara, ...
PU.1 is a member of the ETS family of transcription factors that is known to be important for hematopoietic development. Recently, haploinsufficiency for PU.1 has been shown to cause a shift in...
Flowers, Susan K, Easter, Carla, Holmes, Andrea, Cohen, Brian, Bednarski, April E, Mardis, Elaine R, ...
Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other...
Application of a superword array in genome assembly
Huang, Xiaoqiu, Yang, Shiaw-Pyng, Chinwalla, Asif T., Hillier, LaDeana W., Minx, Patrick, Mardis, Elaine R., ...
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array....
After the Duplication: Gene Loss and Adaptation in Saccharomyces Genomes
Cliften, Paul F., Fulton, Robert S., Wilson, Richard K., Johnston, Mark
The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before...
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...
Marks, Jenifer L., McLellan, Michael D., Zakowski, Maureen F., Lash, Alex E., Kasai, Yumi, Broderick, Stephen, ...
Evolution of Symbiotic Bacteria in the Distal Human Intestine
Xu, Jian, Mahowald, Michael A, Ley, Ruth E, Lozupone, Catherine A, Hamady, Micah, Martens, Eric C, ...
The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping...
Molecular refinement of gibbon genome rearrangements
Roberto, Roberta, Capozzi, Oronzo, Wilson, Richard K., Mardis, Elaine R., Lomiento, Mariana, Tuzun, Eray, ...
The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and...
PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data
Chen, Ken, McLellan, Michael D., Ding, Li, Wendl, Michael C., Kasai, Yumi, Wilson, Richard K., ...
Small insertions and deletions (indels) and single nucleotide polymorphisms (SNPs) are common genetic variants that are thought to be associated with a wide variety of human diseases. Owing to the...
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,...
Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut
Samuel, Buck S., Hansen, Elizabeth E., Manchester, Jill K., Coutinho, Pedro M., Henrissat, Bernard, Fulton, Robert, ...
The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as hydrogen-consuming methanogenic archaea. Studies in gnotobiotic mice indicate that Methanobrevibacter...
Design and implementation of a generalized laboratory data model
Wendl, Michael C, Smith, Scott, Pohl, Craig S, Dooling, David J, Chinwalla, Asif T, Crouse, Kevin, ...
Yin, Yong, Martin, John, Abubucker, Sahar, Scott, Alan L., McCarter, James P., Wilson, Richard K., ...
Biological properties of the nematode intestine warrant in-depth investigation, the results of which can be utilized in the control of parasitic nematodes that infect humans, livestock, and plants....
Link, Daniel C., Kunter, Ghada, Kasai, Yumi, Zhao, Yu, Miner, Tracie, McLellan, Michael D., ...
Severe congenital neutropenia (SCN) is an inborn disorder of granulopoiesis. Like most other bone marrow failure syndromes, it is associated with a marked propensity to transform into a...
Patel, Vidushi S, Cooper, Steven JB, Deakin, Janine E, Fulton, Bob, Graves, Tina, Warren, Wesley C, ...
Welsh, Eric A., Liberton, Michelle, Stöckel, Jana, Loh, Thomas, Elvitigala, Thanura, Wang, Chunyan, ...
Unicellular cyanobacteria have recently been recognized for their contributions to nitrogen fixation in marine environments, a function previously thought to be filled mainly by filamentous...
Molecular determinants archetypical to the phylum Nematoda
Yin, Yong, Martin, John, Abubucker, Sahar, Wang, Zhengyuan, Wyrwicz, Lucjan, Rychlewski, Leszek, ...
Tomasson, Michael H., Xiang, Zhifu, Walgren, Richard, Zhao, Yu, Kasai, Yumi, Miner, Tracie, ...
Activating mutations in tyrosine kinase (TK) genes (eg, FLT3 and KIT) are found in more than 30% of patients with de novo acute myeloid leukemia (AML); many groups have speculated that mutations in...
Identification of somatic JAK1 mutations in patients with acute myeloid leukemia
Xiang, Zhifu, Zhao, Yu, Mitaksov, Vesselin, Fremont, Daved H., Kasai, Yumi, Molitoris, AnnaLynn, ...
Somatic mutations in JAK2 are frequently found in myeloproliferative diseases, and gain-of-function JAK3 alleles have been identified in M7 acute myeloid leukemia (AML), but a role for JAK1 in AML...
Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1
Bai, Xiaodong, Adams, Byron J, Ciche, Todd A, Clifton, Sandra, Gaugler, Randy, Hogenhout, Saskia A, ...
Haplotype sorting using human fosmid clone end-sequence pairs
Kidd, Jeffrey M., Cheng, Ze, Graves, Tina, Fulton, Bob, Wilson, Richard K., Eichler, Evan E.
An important goal of human genetics and genomics is to understand the complete spectrum of genetic variation across a specific human haplotype. By combining information from a dense SNP map with...
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
Mahowald, Michael A., Rey, Federico E., Seedorf, Henning, Turnbaugh, Peter J., Fulton, Robert S., Wollam, Aye, ...
The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the...
Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
Girirajan, Santhosh, Chen, Lin, Graves, Tina, Marques-Bonet, Tomas, Ventura, Mario, Fronick, Catrina, ...
The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of...
Acquired copy number alterations in adult acute myeloid leukemia genomes
Walter, Matthew J., Payton, Jacqueline E., Ries, Rhonda E., Shannon, William D., Deshmukh, Hrishikesh, Zhao, Yu, ...
Cytogenetic analysis of acute myeloid leukemia (AML) cells has accelerated the identification of genes important for AML pathogenesis. To complement cytogenetic studies and to identify genes altered...