Bos taurusgenome assembly (2009)
Liu, Yue, Qin, Xiang, Song, Xing-Zhi, Jiang, Huaiyang, Shen, Yufeng, Durbin, K James, ...
Abstract Background We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS)...
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...
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...
Bourgogne, Agathe, Garsin, Danielle A, Qin, Xiang, Singh, Kavindra V, Sillanpaa, Jouko, Yerrapragada, Shailaja, ...
Abstract Background Enterococcus faecalis has emerged as a major hospital pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF, which is commonly used for molecular manipulation...
Matějková, Petra, Strouhal, Michal, Šmajs, David, Norris, Steven J, Palzkill, Timothy, Petrosino, Joseph F, ...
Abstract Background Syphilis spirochete Treponema pallidum ssp. pallidum remains the enigmatic pathogen, since no virulence factors have been identified and the pathogenesis of the disease is poorly...
Table 1. Whole-genome sequencing of bacterial pathogensa Bacterium Status (ref.) (2008)
Twenty-five years ago, the development of molecular biology and recombinant DNA technology promised breakthroughs in infectious disease research. Since then, these methods have slowly teased out...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A, Weinstock, George M, Brown, Susan J, Denell, Robin, Beeman, Richard W, ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
Somatic mutations affect key pathways in lung adenocarcinoma (2008)
Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, ...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A., Weinstock, George M., Brown, Susan J., Denell, Robin, Beeman, Richard W., ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
Wang, Xiaohu, Gao, Haichun, Shen, Yufeng, Weinstock, George M., Zhou, Jizhong, Palzkill, Timothy
Quantifying the binding energy in DNA–protein interactions is of critical importance to understand transcriptional regulation. Based on a simple computational model, this study describes a...
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...
Highlander, Sarah K, Hultén, Kristina G, Qin, Xiang, Jiang, Huaiyang, Yerrapragada, Shailaja, Mason, Edward O, ...
Abstract Background Community acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) increasingly causes disease worldwide. USA300 has emerged as the predominant clone causing superficial...
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 genome of Apis mellifera: dialog between linkage mapping and sequence assembly (2007)
Solignac, Michel, Zhang, Lan, Mougel, Florence, Li, Bingshan, Vautrin, Dominique, Monnerot, Monique, ...
Abstract Two independent genome projects for the honey bee, a microsatellite linkage map and a genome sequence assembly, interactively produced an almost complete organization of the euchromatic...
Creating a honey bee consensus gene set (2007)
Elsik, Christine G, Mackey, Aaron J, Reese, Justin T, Milshina, Natalia V, Roos, David S, Weinstock, George M
Abstract Background We wished to produce a single reference gene set for honey bee ( Apis mellifera ). Our motivation was twofold. First, we wished to obtain an improved set of gene models with...
Characterizing the cancer genome in lung adenocarcinoma (2007)
Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, ...
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome (2007)
Rogers, Jeffrey, Katze, Michael G., Gibbs, Richard A., Burmgarner, Roger, Weinstock, George M., Prüfer, Kay
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser (2007)
Miller, Webb, Rosenbloom, Kate, Hardison, Ross C., Hou, Minmei, Taylor, James, Raney, Brian, ...
This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006...
Community annotation: Procedures, protocols, and supporting tools (2006)
Elsik, Christine G., Worley, Kim C., Zhang, Lan, Milshina, Natalia V., Jiang, Huaiyang, Reese, Justin T., ...
Investigators at the Baylor College of Medicine Human Genome Sequencing Center (BCM–HGSC) and BeeBase organized a community-wide effort to manually annotate the honey bee (Apis mellifera) genome....
Savard, Joël, Tautz, Diethard, Richards, Stephen, Weinstock, George M., Gibbs, Richard A., Werren, John H., ...
Comparative studies require knowledge of the evolutionary relationships between taxa. However, neither morphological nor paleontological data have been able to unequivocally resolve the major groups...
Savard, Joël, Tautz, Diethard, Richards, Stephen, Weinstock, George M., Gibbs, Richard A., Werren, John H., ...
Comparative studies require knowledge of the evolutionary relationships between taxa. However, neither morphological nor paleontological data have been able to unequivocally resolve the major groups...
Community annotation: Procedures, protocols, and supporting tools (2006)
Elsik, Christine G., Worley, Kim C., Zhang, Lan, Milshina, Natalia V., Jiang, Huaiyang, Reese, Justin T., ...
Investigators at the Baylor College of Medicine Human Genome Sequencing Center (BCM–HGSC) and BeeBase organized a community-wide effort to manually annotate the honey bee (Apis mellifera) genome....
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
Pooled genomic indexing of rhesus macaque (2005)
Milosavljevic, Aleksandar, Harris, Ronald A., Sodergren, Erica J., Jackson, Andrew R., Kalafus, Ken J., Hodgson, Anne, ...
Pooled genomic indexing (PGI) is a method for mapping collections of bacterial artificial chromosome (BAC) clones between species by using a combination of clone pooling and DNA sequencing. PGI has...
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...
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...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have...
Michael P. Mcleod, Xiang Qin, Or E. Karpathy, Jason Gioia, Sarah K. Highl, George E. Fox, ...
Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome...
Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project (2004)
Chen, Rui, Sodergren, Erica, Weinstock, George M., Gibbs, Richard A.
CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome...
The Atlas Genome Assembly System (2004)
Havlak, Paul, Chen, Rui, Durbin, K. James, Egan, Amy, Ren, Yanru, Song, Xing-Zhi, ...
Atlas is a suite of programs developed for assembly of genomes by a “combined approach” that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford...
McKevitt, Matthew, Patel, Krupa, Smajs, David, Marsh, Michael, McLoughlin, Melanie, Norris, Steven J., ...
A topoisomerase-based method was used to clone PCR products encoding 991 of the 1041 open reading frames identified in the genome sequence of the bacterium that causes syphilis, Treponema pallidum...
McKevitt, Matthew, Patel, Krupa, Smajs, David, Marsh, Michael, McLoughlin, Melanie, Norris, Steven J., ...
A topoisomerase-based method was used to clone PCR products encoding 991 of the 1041 open reading frames identified in the genome sequence of the bacterium that causes syphilis, Treponema pallidum...
BAC Library of T. pallidum DNA in E. coli (2002)
Smajs, David, McKevitt, Matthew, Wang, Ling, Howell, Jerrilyn K., Norris, Steven J., Palzkill, Timothy, ...
Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome (2001)
Chen, Rui, Bouck, John B., Weinstock, George M., Gibbs, Richard A.
Sfil genomic cleavage map of Escherichia coli K-12 strain MG1655 (1992)
Perkins, Jeffrey D., Heath, Joe Don, Sharma, Baldev R., Weinstock, George M.
An Sfil restriction map of Escherichia coli K-12 strain MG1655 Is presented. The map contains thirty-one cleavage sites separating fragments ranging in size from 407 kb to 3.7 kb. Several techniques...
Coque, Teresa M., Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
Enterococci are usually susceptible in vitro to trimethoprim; however, high-level resistance (HLR) (MICs, >1,024 μg/ml) has been reported. We studied Enterococcus faecalis DEL, for which the...
Jonas, Brandie M., Murray, Barbara E., Weinstock, George M.
We hypothesized that multidrug resistance efflux pumps (MDRs) may be contributing to the drug resistance of enterococci. We recently identified potential MDR-encoding genes in the Enterococcus...
Genetic Organization of Plasmid ColJs, Encoding Colicin Js Activity, Immunity, and Release Genes
Šmajs, David, Weinstock, George M.
The 5.2-kb ColJs plasmid of a colicinogenic strain of Shigella sonnei (colicin type 7) was isolated and sequenced. pColJs was partly homologous to pColE1 and to pesticin-encoding plasmid pPCP1,...
Šmajs, David, Weinstock, George M.
A cosmid library of DNA from colicin Js-sensitive enteroinvasive Escherichia coli (EIEC) strain O164 was made in colicin Js-resistant strain E. coli VCS257, and colicin Js-sensitive clones were...
Analysis of a Gene Cluster of Enterococcus faecalis Involved in Polysaccharide Biosynthesis
Xu, Yi, Singh, Kavindra V., Qin, Xiang, Murray, Barbara E., Weinstock, George M.
Previously, we described a gene cluster of Enterococcus faecalis OG1RF that produced an antigenic polysaccharide when cloned in Escherichia coli. The polysaccharide antigen was not detectable in E....
Qin, Xiang, Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
Three agr-like genes (fsrA, fsrB, and fsrC, for Enterococcus faecalis regulator) were found upstream of the previously reported gelatinase gene (gelE) and a downstream putative serine protease gene...
Qin, Xiang, Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
We have previously identified a locus, fsr, a homologue of staphylococcal agr loci, which positively regulates the expression of gelatinase and serine protease (encoded by gelE and sprE,...
Nallapareddy, Sreedhar R., Singh, Kavindra V., Duh, Ruay-Wang, Weinstock, George M., Murray, Barbara E.
Our previous work reported that most Enterococcus faecalis strains adhered to the extracellular matrix proteins collagen types I and IV and laminin after growth at 46°C, but not 37°C, and we...
Nallapareddy, Sreedhar R., Qin, Xiang, Weinstock, George M., Höök, Magnus, Murray, Barbara E.
Adhesin-mediated binding to extracellular matrix (ECM) proteins is thought to be a crucial step in the pathogenic process of many bacterial infections. We have previously reported conditional...
Effect of Disruption of a Gene Encoding an Autolysin of Enterococcus faecalis OG1RF
Qin, Xiang, Singh, Kavindra V., Xu, Yi, Weinstock, George M., Murray, Barbara E.
A mutant (TX5127) of Enterococcus faecalis OG1RF was generated by disruption mutagenesis of a previously described autolysin gene. TX5127 formed longer chains (2 to 10 cells per chain) than wild-type...
A Cluster of Genes Involved in Polysaccharide Biosynthesis from Enterococcus faecalis OG1RF
Xu, Yi, Murray, Barbara E., Weinstock, George M.
Our previous work identified a cosmid clone containing a 43-kb insert from Enterococcus faecalis OG1RF that produced a nonprotein antigen in Escherichia coli. In the present work, we studied this...
Malathum, Kumthorn, Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
Repetitive sequence-based PCR was compared to pulsed-field gel electrophoresis (PFGE) for the ability to discriminate Enterococcus faecalis isolates at the subspecies level. The BOXA2R primer,...
Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
Enterococcus faecalis isolates are resistant to clindamycin (CLI) and quinupristin-dalfopristin (Q-D), and this is thought to be a species characteristic. Disruption of a gene (abc-23, now designated...
Involvement of PhoP-PhoS Homologs in Enterococcus faecalis Virulence
Teng, Fang, Wang, Ling, Singh, Kavindra V., Murray, Barbara E., Weinstock, George M.
Eleven PhoP-PhoS homolog pairs were identified by searching the Enterococcus faecalis V583 genome sequence database at The Institute for Genomic Research with the Bacillus subtilis PhoP-PhoS...
Teng, Fang, Jacques-Palaz, Karen D., Weinstock, George M., Murray, Barbara E.
In previous studies, we cloned a cluster of genes involved in polysaccharide biosynthesis (epa) from Enterococcus faecalis strain OG1RF and showed that this gene cluster mediated synthesis of a...
Teng, Fang, Kawalec, Magdalena, Weinstock, George M., Hryniewicz, Waleria, Murray, Barbara E.
A gene encoding a major secreted antigen, SagA, was identified in Enterococcus faecium by screening an E. faecium genomic expression library with sera from patients with E. faecium-associated...
Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome
Chen, Rui, Bouck, John B., Weinstock, George M., Gibbs, Richard A.
Multi-species sequence comparisons are a very efficient way to reveal conserved genes. Because sequence finishing is expensive and time consuming, many genome sequences are likely to stay incomplete....
Zeng, Jing, Teng, Fang, Weinstock, George M., Murray, Barbara E.
We used a two-chamber system to study transcytosis of Enterococcus faecalis across monolayers of human colon carcinoma-derived T84 cells, which show structural resemblance to the native intestine....
Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project
Chen, Rui, Sodergren, Erica, Weinstock, George M., Gibbs, Richard A.
CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome...
The Atlas Genome Assembly System
Havlak, Paul, Chen, Rui, Durbin, K. James, Egan, Amy, Ren, Yanru, Song, Xing-Zhi, ...
Atlas is a suite of programs developed for assembly of genomes by a “combined approach” that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford...
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
Seshadri, Rekha, Myers, Garry S. A., Tettelin, Hervé, Eisen, Jonathan A., Heidelberg, John F., Dodson, Robert J., ...
We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors...
McKevitt, Matthew, Patel, Krupa, Smajs, David, Marsh, Michael, McLoughlin, Melanie, Norris, Steven J., ...
A topoisomerase-based method was used to clone PCR products encoding 991 of the 1041 open reading frames identified in the genome sequence of the bacterium that causes syphilis, Treponema pallidum...
Complete Genome Sequence of Rickettsia typhi and Comparison with Sequences of Other Rickettsiae
McLeod, Michael P., Qin, Xiang, Karpathy, Sandor E., Gioia, Jason, Highlander, Sarah K., Fox, George E., ...
Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome...
Pooled genomic indexing of rhesus macaque
Milosavljevic, Aleksandar, Harris, Ronald A., Sodergren, Erica J., Jackson, Andrew R., Kalafus, Ken J., Hodgson, Anne, ...
Pooled genomic indexing (PGI) is a method for mapping collections of bacterial artificial chromosome (BAC) clones between species by using a combination of clone pooling and DNA sequencing. PGI has...
Transcriptome of Treponema pallidum: Gene Expression Profile during Experimental Rabbit Infection†
Šmajs, David, McKevitt, Matthew, Howell, Jerrilyn K., Norris, Steven J., Cai, Wei-Wen, Palzkill, Timothy, ...
RNA transcript levels in the syphilis spirochete Treponema pallidum subsp. pallidum (Nichols) isolated from experimentally infected rabbits were determined by the use of DNA microarray technology....
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...
Nallapareddy, Sreedhar R., Wenxiang, Huang, Weinstock, George M., Murray, Barbara E.
Enterococcus faecalis, a common cause of endocarditis and known for its capacity to transfer antibiotic resistance to other pathogens, has recently emerged as an important, multidrug-resistant...
BAC Library of T. pallidum DNA in E. coli
Šmajs, David, McKevitt, Matthew, Wang, Ling, Howell, Jerrilyn K., Norris, Steven J., Palzkill, Timothy, ...
Treponema pallidum subspecies pallidum (Nichols) chromosomal DNA was used to construct a large insert bacterial artificial chromosome (BAC) library in Escherichia coli DH10B using the pBeloBAC11...
Genome Scale Identification of Treponema pallidum Antigens
McKevitt, Matthew, Brinkman, Mary Beth, McLoughlin, Melanie, Perez, Carla, Howell, Jerrilyn K., Weinstock, George M., ...
Antibody responses for 882 of the 1,039 proteins in the proteome of Treponema pallidum were examined. Sera collected from infected rabbits were used to systematically identify 106 antigenic proteins,...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
Brinkman, Mary Beth, McKevitt, Matthew, McLoughlin, Melanie, Perez, Carla, Howell, Jerrilyn, Weinstock, George M., ...
To identify antigens important in the human immune response to syphilis, the serum antibody reactivity of syphilitic patients was examined with 908 of the 1,039 proteins in the proteome of Treponema...
Weinstock, George M., Susskind, Miriam M., Botstein, David
Insertions of the translocatable ampicillin-resistance element Tn1 were selected in the genome of the temperate Salmonella phage P22 by growing the phage on hosts carrying the resistance plasmid RP4....
Coque, Teresa M., Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
Enterococci are usually susceptible in vitro to trimethoprim; however, high-level resistance (HLR) (MICs, >1,024 μg/ml) has been reported. We studied Enterococcus faecalis DEL, for which the...
Jonas, Brandie M., Murray, Barbara E., Weinstock, George M.
We hypothesized that multidrug resistance efflux pumps (MDRs) may be contributing to the drug resistance of enterococci. We recently identified potential MDR-encoding genes in the Enterococcus...
Genetic Organization of Plasmid ColJs, Encoding Colicin Js Activity, Immunity, and Release Genes
Šmajs, David, Weinstock, George M.
The 5.2-kb ColJs plasmid of a colicinogenic strain of Shigella sonnei (colicin type 7) was isolated and sequenced. pColJs was partly homologous to pColE1 and to pesticin-encoding plasmid pPCP1,...
Šmajs, David, Weinstock, George M.
A cosmid library of DNA from colicin Js-sensitive enteroinvasive Escherichia coli (EIEC) strain O164 was made in colicin Js-resistant strain E. coli VCS257, and colicin Js-sensitive clones were...
Analysis of a Gene Cluster of Enterococcus faecalis Involved in Polysaccharide Biosynthesis
Xu, Yi, Singh, Kavindra V., Qin, Xiang, Murray, Barbara E., Weinstock, George M.
Previously, we described a gene cluster of Enterococcus faecalis OG1RF that produced an antigenic polysaccharide when cloned in Escherichia coli. The polysaccharide antigen was not detectable in E....
Qin, Xiang, Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
Three agr-like genes (fsrA, fsrB, and fsrC, for Enterococcus faecalis regulator) were found upstream of the previously reported gelatinase gene (gelE) and a downstream putative serine protease gene...
Qin, Xiang, Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
We have previously identified a locus, fsr, a homologue of staphylococcal agr loci, which positively regulates the expression of gelatinase and serine protease (encoded by gelE and sprE,...
Nallapareddy, Sreedhar R., Singh, Kavindra V., Duh, Ruay-Wang, Weinstock, George M., Murray, Barbara E.
Our previous work reported that most Enterococcus faecalis strains adhered to the extracellular matrix proteins collagen types I and IV and laminin after growth at 46°C, but not 37°C, and we...
Nallapareddy, Sreedhar R., Qin, Xiang, Weinstock, George M., Höök, Magnus, Murray, Barbara E.
Adhesin-mediated binding to extracellular matrix (ECM) proteins is thought to be a crucial step in the pathogenic process of many bacterial infections. We have previously reported conditional...
Effect of Disruption of a Gene Encoding an Autolysin of Enterococcus faecalis OG1RF
Qin, Xiang, Singh, Kavindra V., Xu, Yi, Weinstock, George M., Murray, Barbara E.
A mutant (TX5127) of Enterococcus faecalis OG1RF was generated by disruption mutagenesis of a previously described autolysin gene. TX5127 formed longer chains (2 to 10 cells per chain) than wild-type...
A Cluster of Genes Involved in Polysaccharide Biosynthesis from Enterococcus faecalis OG1RF
Xu, Yi, Murray, Barbara E., Weinstock, George M.
Our previous work identified a cosmid clone containing a 43-kb insert from Enterococcus faecalis OG1RF that produced a nonprotein antigen in Escherichia coli. In the present work, we studied this...
Malathum, Kumthorn, Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
Repetitive sequence-based PCR was compared to pulsed-field gel electrophoresis (PFGE) for the ability to discriminate Enterococcus faecalis isolates at the subspecies level. The BOXA2R primer,...
Singh, Kavindra V., Weinstock, George M., Murray, Barbara E.
Enterococcus faecalis isolates are resistant to clindamycin (CLI) and quinupristin-dalfopristin (Q-D), and this is thought to be a species characteristic. Disruption of a gene (abc-23, now designated...
Involvement of PhoP-PhoS Homologs in Enterococcus faecalis Virulence
Teng, Fang, Wang, Ling, Singh, Kavindra V., Murray, Barbara E., Weinstock, George M.
Eleven PhoP-PhoS homolog pairs were identified by searching the Enterococcus faecalis V583 genome sequence database at The Institute for Genomic Research with the Bacillus subtilis PhoP-PhoS...
Teng, Fang, Jacques-Palaz, Karen D., Weinstock, George M., Murray, Barbara E.
In previous studies, we cloned a cluster of genes involved in polysaccharide biosynthesis (epa) from Enterococcus faecalis strain OG1RF and showed that this gene cluster mediated synthesis of a...
BAC Library of T. pallidum DNA in E. coli
Šmajs, David, McKevitt, Matthew, Wang, Ling, Howell, Jerrilyn K., Norris, Steven J., Palzkill, Timothy, ...
Treponema pallidum subspecies pallidum (Nichols) chromosomal DNA was used to construct a large insert bacterial artificial chromosome (BAC) library in Escherichia coli DH10B using the pBeloBAC11...
Teng, Fang, Kawalec, Magdalena, Weinstock, George M., Hryniewicz, Waleria, Murray, Barbara E.
A gene encoding a major secreted antigen, SagA, was identified in Enterococcus faecium by screening an E. faecium genomic expression library with sera from patients with E. faecium-associated...
Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome
Chen, Rui, Bouck, John B., Weinstock, George M., Gibbs, Richard A.
Multi-species sequence comparisons are a very efficient way to reveal conserved genes. Because sequence finishing is expensive and time consuming, many genome sequences are likely to stay incomplete....
Zeng, Jing, Teng, Fang, Weinstock, George M., Murray, Barbara E.
We used a two-chamber system to study transcytosis of Enterococcus faecalis across monolayers of human colon carcinoma-derived T84 cells, which show structural resemblance to the native intestine....
Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project
Chen, Rui, Sodergren, Erica, Weinstock, George M., Gibbs, Richard A.
CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome...
The Atlas Genome Assembly System
Havlak, Paul, Chen, Rui, Durbin, K. James, Egan, Amy, Ren, Yanru, Song, Xing-Zhi, ...
Atlas is a suite of programs developed for assembly of genomes by a “combined approach” that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford...
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
Seshadri, Rekha, Myers, Garry S. A., Tettelin, Hervé, Eisen, Jonathan A., Heidelberg, John F., Dodson, Robert J., ...
We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors...
McKevitt, Matthew, Patel, Krupa, Smajs, David, Marsh, Michael, McLoughlin, Melanie, Norris, Steven J., ...
A topoisomerase-based method was used to clone PCR products encoding 991 of the 1041 open reading frames identified in the genome sequence of the bacterium that causes syphilis, Treponema pallidum...
Complete Genome Sequence of Rickettsia typhi and Comparison with Sequences of Other Rickettsiae
McLeod, Michael P., Qin, Xiang, Karpathy, Sandor E., Gioia, Jason, Highlander, Sarah K., Fox, George E., ...
Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
Pooled genomic indexing of rhesus macaque
Milosavljevic, Aleksandar, Harris, Ronald A., Sodergren, Erica J., Jackson, Andrew R., Kalafus, Ken J., Hodgson, Anne, ...
Pooled genomic indexing (PGI) is a method for mapping collections of bacterial artificial chromosome (BAC) clones between species by using a combination of clone pooling and DNA sequencing. PGI has...
Transcriptome of Treponema pallidum: Gene Expression Profile during Experimental Rabbit Infection†
Šmajs, David, McKevitt, Matthew, Howell, Jerrilyn K., Norris, Steven J., Cai, Wei-Wen, Palzkill, Timothy, ...
RNA transcript levels in the syphilis spirochete Treponema pallidum subsp. pallidum (Nichols) isolated from experimentally infected rabbits were determined by the use of DNA microarray technology....
Genome Scale Identification of Treponema pallidum Antigens
McKevitt, Matthew, Brinkman, Mary Beth, McLoughlin, Melanie, Perez, Carla, Howell, Jerrilyn K., Weinstock, George M., ...
Antibody responses for 882 of the 1,039 proteins in the proteome of Treponema pallidum were examined. Sera collected from infected rabbits were used to systematically identify 106 antigenic proteins,...
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...
Nallapareddy, Sreedhar R., Wenxiang, Huang, Weinstock, George M., Murray, Barbara E.
Enterococcus faecalis, a common cause of endocarditis and known for its capacity to transfer antibiotic resistance to other pathogens, has recently emerged as an important, multidrug-resistant...
Weinstock, George M., Susskind, Miriam M., Botstein, David
Insertions of the translocatable ampicillin-resistance element Tn1 were selected in the genome of the temperate Salmonella phage P22 by growing the phage on hosts carrying the resistance plasmid RP4....
Brinkman, Mary Beth, McKevitt, Matthew, McLoughlin, Melanie, Perez, Carla, Howell, Jerrilyn, Weinstock, George M., ...
To identify antigens important in the human immune response to syphilis, the serum antibody reactivity of syphilitic patients was examined with 908 of the 1,039 proteins in the proteome of Treponema...
Petrosino, Joseph F., Xiang, Qin, Karpathy, Sandor E., Jiang, Huaiyang, Yerrapragada, Shailaja, Liu, Yamei, ...
The γ-proteobacterium Francisella tularensis is one of the most infectious human pathogens, and the highly virulent organism F. tularensis subsp. tularensis (type A) and less virulent organism F....
Gioia, Jason, Qin, Xiang, Jiang, Huaiyang, Clinkenbeard, Kenneth, Lo, Reggie, Liu, Yamei, ...
The draft genome sequence of Mannheimia haemolytica A1, the causative agent of bovine respiratory disease complex (BRDC), is presented. Strain ATCC BAA-410, isolated from the lung of a calf with...
Creating a honey bee consensus gene set
Elsik, Christine G, Mackey, Aaron J, Reese, Justin T, Milshina, Natalia V, Roos, David S, Weinstock, George M
A high-quality consensus gene set for the honey bee (Apis mellifera) created using a new algorithm (GLEAN) is described.
Savard, Joël, Tautz, Diethard, Richards, Stephen, Weinstock, George M., Gibbs, Richard A., Werren, John H., ...
Comparative studies require knowledge of the evolutionary relationships between taxa. However, neither morphological nor paleontological data have been able to unequivocally resolve the major groups...
Karpathy, Sandor E., Qin, Xiang, Gioia, Jason, Jiang, Huaiyang, Liu, Yamei, Petrosino, Joseph F., ...
Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and...
Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032
Gioia, Jason, Yerrapragada, Shailaja, Qin, Xiang, Jiang, Huaiyang, Igboeli, Okezie C., Muzny, Donna, ...
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,...
Highlander, Sarah K, Hultén, Kristina G, Qin, Xiang, Jiang, Huaiyang, Yerrapragada, Shailaja, Mason, Edward O, ...
Strouhal, Michal, Šmajs, David, Matějková, Petra, Sodergren, Erica, Amin, Anita G., Howell, Jerrilyn K., ...
The genome of Treponema paraluiscuniculi strain Cuniculi A was compared to the genome of the syphilis spirochete Treponema pallidum subsp. pallidum strain Nichols using DNA microarray hybridization,...
Matějková, Petra, Strouhal, Michal, Šmajs, David, Norris, Steven J, Palzkill, Timothy, Petrosino, Joseph F, ...
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
Miller, Webb, Rosenbloom, Kate, Hardison, Ross C., Hou, Minmei, Taylor, James, Raney, Brian, ...
This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006...
Durfee, Tim, Nelson, Richard, Baldwin, Schuyler, Plunkett, Guy, Burland, Valerie, Mau, Bob, ...
Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and...
Gao, Haichun, Pattison, Donna, Yan, Tingfen, Klingeman, Dawn M., Wang, Xiaohu, Petrosino, Joseph, ...
A comprehensive gene collection for S. oneidensis was constructed using the lambda recombinase (Gateway) cloning system. A total of 3584 individual ORFs (85%) have been successfully cloned into the...
Brinkman, Mary Beth, McGill, Melanie A., Pettersson, Jonas, Rogers, Arthur, Matějková, Petra, Šmajs, David, ...
The antigenicity, structural location, and function of the predicted lipoprotein TP0136 of Treponema pallidum subsp. pallidum were investigated based on previous screening studies indicating that...
Wang, Xiaohu, Gao, Haichun, Shen, Yufeng, Weinstock, George M., Zhou, Jizhong, Palzkill, Timothy
Quantifying the binding energy in DNA–protein interactions is of critical importance to understand transcriptional regulation. Based on a simple computational model, this study describes a...
Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF
Bourgogne, Agathe, Garsin, Danielle A, Qin, Xiang, Singh, Kavindra V, Sillanpaa, Jouko, Yerrapragada, Shailaja, ...
A comparison of two strains of the hospital pathogen Enterococcus faecalis suggests that mediators of virulence differ between strains and that virulence does not depend on mobile gene elements