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)...
Working together: Farnesyl transferase inhibitors and statins block protein prenylation (2009)
Jonathan W. Wojtkowiak, Richard A. Gibbs, Raymond R. Mattingly
Farnesyl transferase inhibitors (FTIs) have so far proved to have limited value as single agents in clinical trials. This PharmSight will focus on the use of a novel group of FTIs that are most...
Hampton, Oliver A., Den Hollander, Petra, Miller, Christopher A., Delgado, David A., Li, Jian, Coarfa, Cristian, ...
By applying a method that combines end-sequence profiling and massively parallel sequencing, we obtained a sequence-level map of chromosomal aberrations in the genome of the MCF-7 breast cancer cell...
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...
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...
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...
A second generation human haplotype map of over 3.1 million SNPs (2007)
Frazer, Kelly A., Ballinger, Dennis G., Cox, David R., Hinds, David A., Stuve, Laura L., Gibbs, Richard A., ...
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and...
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...
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...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Robinson, Gene E, Gibbs, Richard A, Worley, Kim C, Evans, Jay D, Maleszka, Ryszard, ...
Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes,...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
Recurrent duplication-driven transposition of DNA during hominoid evolution. (2006)
Johnson, Matthew E., Cheng, Ze, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., ...
The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes, we show that a particular...
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....
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection (2005)
Jinghui Zhang, David A. Wheeler, Imtiaz Yakub, Sharon Wei, Raman Sood, William Rowe, ...
Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de...
Positive Selection of a Pre-expansion CAG Repeat of the Human SCA2 Gene (2005)
Fuli Yu, Pardis Christine Sabeti, Paul Hardenbol, Qing Fu, Ben Fry, Xiuhua Lu, ...
A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium (LD) in Americans with ancestry from northern and western Europe. This strikingly large LD block...
Positive Selection of a Pre-Expansion CAG Repeat of the Human SCA2 Gene (2005)
Fuli Yu, Pardis C. Sabeti, Paul Hardenbol, Qing Fu, Ben Fry, Xiuhua Lu, ...
A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium in Utah residents with ancestry from northern and western Europe. This strikingly large linkage...
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...
Hardenbol, Paul, Yu, Fuli, Belmont, John, MacKenzie, Jennifer, Bruckner, Carsten, Brundage, Tiffany, ...
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color,...
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...
Genome sequence of the Brown Norway rat yields insights into mammalian evolution (2004)
Gibbs,Richard A. ..., Himmelbauer,Heinz, Lehrach,Hans ..., Collins,Francis
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome...
Genome sequence of the Brown Norway rat yields insights into mammalian evolution (2004)
Gibbs, Richard A. ..., Himmelbauer, Heinz, Lehrach, Hans ..., Collins, Francis
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome...
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...
Zhang, Zhengdong, Burch, Paula E., Cooney, Austin J., Lanz, Rainer B., Pereira, Fred A., Wu, Jiaqian, ...
Completion of the Rattus norvegicus genome sequence enabled a global inventory and analysis of the nuclear receptors (NRs) in three mammalian species. Forty-nine NR members were found in mouse, 48 in...
Identification of Rat Genes by TWINSCAN Gene Prediction, RT-PCR, and Direct Sequencing (2004)
Wu, Jia Qian, Shteynberg, David, Arumugam, Manimozhiyan, Gibbs, Richard A., Brent, Michael R.
The publication of a draft sequence of a third mammalian genome—that of the rat—suggests a need to rethink genome annotation. New mammalian sequences will not receive the kind of labor-intensive...
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...
Celniker, Susan E, Wheeler, David A, Kronmiller, Brent, Carlson, Joseph W, Halpern, Aaron, Patel, Sandeep, ...
Abstract Background The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were...
Maheshwari, Manjula, Christian, SL, Liu, C, Badner, JA, Detera-Wadleigh, S, Gershon, ES, ...
Abstract Background Multiple candidate regions as sites for Schizophrenia and Bipolar susceptibility genes have been reported, suggesting heterogeneity of susceptibility genes or oligogenic...
Shah, Gopi, Brugada, Ramon, Gonzalez, Oscar, Czernuszewicz, Grazyna, Gibbs, Richard A, Bachinski, Linda, ...
No abstract available.
The cloning, genomic organization and tissue expression profile of the human DLG5 gene (2002)
Shah, Gopi, Brugada, Ramon, Gonzalez, Oscar, Czernuszewicz, Grazyna, Gibbs, Richard A, Bachinski, Linda, ...
Abstract Background Familial atrial fibrillation, an autosomal dominant disease, was previously mapped to chromosome 10q22. One of the genes mapped to the 10q22 region is DLG5, a member of the MAGUKs...
Dederich, Debra A., Okwuonu, Geoffrey, Garner, Toni, Denn, Amanda, Sutton, Angelica, Escotto, Michael, ...
To meet the new challenge of generating the draft sequences of mammalian genomes, we describe the development of a novel high throughput 96-well method for the purification of plasmid DNA template...
Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome (2001)
Chen, Rui, Bouck, John B., Weinstock, George M., Gibbs, Richard A.
The Human Transcript Database: a catalogue of full length cDNA inserts (2000)
Bouck, John, McLeod, Michael P., Worley, Kim, Gibbs, Richard A.
Summary: Full length cDNA sequences are an important resource for the research community but are currently intermingled with other sequences. We have identified the human full length insert cDNA...
Signal Transduction Targets for Pharmacological Intervention in Type I Neurofibromatosis (1998)
Mattingly, Raymond R., Gibbs, Richard A., Tainsky, Michael A.
This New Investigator Award has the objective of the identification of new pharmacological approaches to NF1 treatment. We will proceed through the following aims and hypotheses: 1. Role of the...
Analysis of the Quality and Utility of Random Shotgun Sequencing at Low Redundancies (1998)
Bouck, John, Miller, Webb, Gorrell, James H., Muzny, Donna, Gibbs, Richard A.
Ansari-Lari, M. Ali, Oeltjen, John C., Schwartz, Scott, Zhang, Zheng, Muzny, Donna M., Lu, Jing, ...
Oeltjen, John C., Malley, Tracy M., Muzny, Donna M., Miller, Webb, Gibbs, Richard A., Belmont, John W.
Large-Scale Concatenation cDNA Sequencing (1997)
Yu, Wei, Andersson, Björn, Worley, Kim C., Muzny, Donna M., Ding, Yan, Liu, Wen, ...
Evan E. Eichler, Fei Lu, Ying Shen, Rachele Antonacci, Vesna Jurecic, Norman A. Doggett, ...
mechanism for paralogous genome evolution
Accurate determination of DNA in agarose gels using the novel algorithm GelScann(1.0) (1995)
Metzker, Michael L., Allain, Kyle M., Gibbs, Richard A.
GelScann(1.0) is a user-friendly program that accurately quantitates DNA from CCD imaged agarose gels. The algorithm automatically locates lanes, locates bands within a given lane, and quantitates...
Fine structure of the human FMR1 gene (1993)
Eichler, Evan E., Richards, Stephen, Gibbs, Richard A., Nelson, David L.
The fragile X syndrome is due to a CGG triplet expansion in the first exon of FMR1, resulting in hypermethylation and extinction of gene expression. To further our understanding of the gene's...
Gordon, Ross B., Dawson, Paul A., Sculley, Donna G., Emmerson, Bryan T., Caskey, C.Thomas, Gibbs, Richard A.
A complete deficiency of the purine salvage enzyme, hypoxanthine phosphoribosyltransferase (HPRT; EC 2.4.2.8), in man results in the Lesch-Nyhan (LN) syndrome. Two unrelated patients with the full LN...
Detection of single DNA base differences by competitive oligonucleotide priming (1989)
Gibbs, Richard A., Nguyen, Phi-Nga, Caskey, C. Thomas
Synthetic DNA oligonucleotides can serve as efficient primers for DNA synthesis even when there is a single base mismatch between the primers and the corresponding DNA template. However, when the...
Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification (1988)
Chamberlain, Jeffrey S., Gibbs, Richard A., Rainer, Joel E., Nguyen, Phi Nga, Thomas, C.
The application of recombinant DNA technology to prenatal diagnosis of many recessively inherited X-linked diseases is complicated by a high frequency of heterogenous, new mutations (1). Partial gene...
Mutagenesis by X-rays and [125I] iododeoxyuridine in mammalian cells (1985)
Typescript (photocopy) Bibliography: leaves 168-181.
The cloning, genomic organization and tissue expression profile of the human DLG5 gene
Shah, Gopi, Brugada, Ramon, Gonzalez, Oscar, Czernuszewicz, Grazyna, Gibbs, Richard A, Bachinski, Linda, ...
Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes
Dederich, Debra A., Okwuonu, Geoffrey, Garner, Toni, Denn, Amanda, Sutton, Angelica, Escotto, Michael, ...
To meet the new challenge of generating the draft sequences of mammalian genomes, we describe the development of a novel high throughput 96-well method for the purification of plasmid DNA template...
The cloning, genomic organization and tissue expression profile of the human DLG5 gene: Correction
Shah, Gopi, Brugada, Ramon, Gonzalez, Oscar, Czernuszewicz, Grazyna, Gibbs, Richard A, Bachinski, Linda, ...
Molecular evidence of HIV-1 transmission in a criminal case
Metzker, Michael L., Mindell, David P., Liu, Xiao-Mei, Ptak, Roger G., Gibbs, Richard A., Hillis, David M.
A gastroenterologist was convicted of attempted second-degree murder by injecting his former girlfriend with blood or blood-products obtained from an HIV type 1 (HIV-1)-infected patient under his...
Large-Scale Concatenation cDNA Sequencing
Yu, Wei, Andersson, Björn, Worley, Kim C., Muzny, Donna M., Ding, Yan, Liu, Wen, ...
A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are...
Celniker, Susan E, Wheeler, David A, Kronmiller, Brent, Carlson, Joseph W, Halpern, Aaron, Patel, Sandeep, ...
The Drosophila melanogaster genome was the first metazoan genome to be sequenced by whole-genome shotgun. Now, the sequence has been finished in a process designed to close gaps, improve sequence...
Sutcliffe, James S., Nakao, Mitsuyoshi, Shen, Ying, Gibbs, Richard A., Beaudet, Arthur L.
The gene encoding the small nuclear ribonucleoprotein-associated polypeptide N (SNRPN) maps to the Prader–Willi syndrome critical region on chromosome 15 and is expressed preferentially from the...
Analysis of the Quality and Utility of Random Shotgun Sequencing at Low Redundancies
Bouck, John, Miller, Webb, Gorrell, James H., Muzny, Donna, Gibbs, Richard A.
The currently favored approach for sequencing the human genome involves selecting representative large-insert clones (100–200 kb), randomly shearing this DNA to construct shotgun libraries, and...
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....
Zhang, Zhengdong, Burch, Paula E., Cooney, Austin J., Lanz, Rainer B., Pereira, Fred A., Wu, Jiaqian, ...
Completion of the Rattus norvegicus genome sequence enabled a global inventory and analysis of the nuclear receptors (NRs) in three mammalian species. Forty-nine NR members were found in mouse, 48 in...
Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing
Wu, Jia Qian, Shteynberg, David, Arumugam, Manimozhiyan, Gibbs, Richard A., Brent, Michael R.
The publication of a draft sequence of a third mammalian genome—that of the rat—suggests a need to rethink genome annotation. New mammalian sequences will not receive the kind of labor-intensive...
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...
Variation in GRM3 affects cognition, prefrontal glutamate, and risk for schizophrenia
Egan, Michael F., Straub, Richard E., Goldberg, Terry E., Yakub, Imtiaz, Callicott, Joseph H., Hariri, Ahmad R., ...
GRM3, a metabotropic glutamate receptor-modulating synaptic glutamate, is a promising schizophrenia candidate gene. In a family-based association study, a common GRM3 haplotype was strongly...
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...
Hardenbol, Paul, Yu, Fuli, Belmont, John, MacKenzie, Jennifer, Bruckner, Carsten, Brundage, Tiffany, ...
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color,...
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...
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...
Positive Selection of a Pre-Expansion CAG Repeat of the Human SCA2 Gene
Yu, Fuli, Sabeti, Pardis C, Hardenbol, Paul, Fu, Qing, Fry, Ben, Lu, Xiuhua, ...
A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium in Utah residents with ancestry from northern and western Europe. This strikingly large linkage...
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection
Zhang, Jinghui, Wheeler, David A, Yakub, Imtiaz, Wei, Sharon, Sood, Raman, Rowe, William, ...
Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de...
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...
Lalani, Seema R., Safiullah, Arsalan M., Fernbach, Susan D., Harutyunyan, Karine G., Thaller, Christina, Peterson, Leif E., ...
CHARGE syndrome is a well-established multiple-malformation syndrome with distinctive consensus diagnostic criteria. Characteristic associated anomalies include ocular coloboma, choanal atresia,...
The cloning, genomic organization and tissue expression profile of the human DLG5 gene
Shah, Gopi, Brugada, Ramon, Gonzalez, Oscar, Czernuszewicz, Grazyna, Gibbs, Richard A, Bachinski, Linda, ...
Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes
Dederich, Debra A., Okwuonu, Geoffrey, Garner, Toni, Denn, Amanda, Sutton, Angelica, Escotto, Michael, ...
To meet the new challenge of generating the draft sequences of mammalian genomes, we describe the development of a novel high throughput 96-well method for the purification of plasmid DNA template...
The cloning, genomic organization and tissue expression profile of the human DLG5 gene: Correction
Shah, Gopi, Brugada, Ramon, Gonzalez, Oscar, Czernuszewicz, Grazyna, Gibbs, Richard A, Bachinski, Linda, ...
Molecular evidence of HIV-1 transmission in a criminal case
Metzker, Michael L., Mindell, David P., Liu, Xiao-Mei, Ptak, Roger G., Gibbs, Richard A., Hillis, David M.
A gastroenterologist was convicted of attempted second-degree murder by injecting his former girlfriend with blood or blood-products obtained from an HIV type 1 (HIV-1)-infected patient under his...
Large-Scale Concatenation cDNA Sequencing
Yu, Wei, Andersson, Björn, Worley, Kim C., Muzny, Donna M., Ding, Yan, Liu, Wen, ...
A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are...
Celniker, Susan E, Wheeler, David A, Kronmiller, Brent, Carlson, Joseph W, Halpern, Aaron, Patel, Sandeep, ...
The Drosophila melanogaster genome was the first metazoan genome to be sequenced by whole-genome shotgun. Now, the sequence has been finished in a process designed to close gaps, improve sequence...
Sutcliffe, James S., Nakao, Mitsuyoshi, Shen, Ying, Gibbs, Richard A., Beaudet, Arthur L.
The gene encoding the small nuclear ribonucleoprotein-associated polypeptide N (SNRPN) maps to the Prader–Willi syndrome critical region on chromosome 15 and is expressed preferentially from the...
Analysis of the Quality and Utility of Random Shotgun Sequencing at Low Redundancies
Bouck, John, Miller, Webb, Gorrell, James H., Muzny, Donna, Gibbs, Richard A.
The currently favored approach for sequencing the human genome involves selecting representative large-insert clones (100–200 kb), randomly shearing this DNA to construct shotgun libraries, and...
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....
Zhang, Zhengdong, Burch, Paula E., Cooney, Austin J., Lanz, Rainer B., Pereira, Fred A., Wu, Jiaqian, ...
Completion of the Rattus norvegicus genome sequence enabled a global inventory and analysis of the nuclear receptors (NRs) in three mammalian species. Forty-nine NR members were found in mouse, 48 in...
Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing
Wu, Jia Qian, Shteynberg, David, Arumugam, Manimozhiyan, Gibbs, Richard A., Brent, Michael R.
The publication of a draft sequence of a third mammalian genome—that of the rat—suggests a need to rethink genome annotation. New mammalian sequences will not receive the kind of labor-intensive...
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...
Variation in GRM3 affects cognition, prefrontal glutamate, and risk for schizophrenia
Egan, Michael F., Straub, Richard E., Goldberg, Terry E., Yakub, Imtiaz, Callicott, Joseph H., Hariri, Ahmad R., ...
GRM3, a metabotropic glutamate receptor-modulating synaptic glutamate, is a promising schizophrenia candidate gene. In a family-based association study, a common GRM3 haplotype was strongly...
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...
Hardenbol, Paul, Yu, Fuli, Belmont, John, MacKenzie, Jennifer, Bruckner, Carsten, Brundage, Tiffany, ...
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color,...
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...
Hattori, Eiji, Liu, Chunyu, Badner, Judith A., Bonner, Tom I., Christian, Susan L., Maheshwari, Manjula, ...
Linkage evidence suggests that chromosome 13 (13q32-33) contains susceptibility genes for both bipolar disorder and schizophrenia. Recently, genes called “G72” and “G30” were identified, and...
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...
Positive Selection of a Pre-Expansion CAG Repeat of the Human SCA2 Gene
Yu, Fuli, Sabeti, Pardis C, Hardenbol, Paul, Fu, Qing, Fry, Ben, Lu, Xiuhua, ...
A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium in Utah residents with ancestry from northern and western Europe. This strikingly large linkage...
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection
Zhang, Jinghui, Wheeler, David A, Yakub, Imtiaz, Wei, Sharon, Sood, Raman, Rowe, William, ...
Identification of single nucleotide polymorphisms (SNPs) and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de...
Lalani, Seema R., Safiullah, Arsalan M., Fernbach, Susan D., Harutyunyan, Karine G., Thaller, Christina, Peterson, Leif E., ...
CHARGE syndrome is a well-established multiple-malformation syndrome with distinctive consensus diagnostic criteria. Characteristic associated anomalies include ocular coloboma, choanal atresia,...
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...
Recurrent duplication-driven transposition of DNA during hominoid evolution
Johnson, Matthew E., Cheng, Ze, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., ...
The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes, we show that a particular...
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,...
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...
Novel MicroRNA Candidates and miRNA-mRNA Pairs in Embryonic Stem (ES) Cells
Gu, Peili, Reid, Jeffrey G., Gao, Xiaolian, Shaw, Chad A., Creighton, Chad, Tran, Peter L., ...
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...
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
Reid, Jeffrey G., Nagaraja, Ankur K., Lynn, Francis C., Drabek, Rafal B., Muzny, Donna M., Shaw, Chad A., ...
Massively parallel sequencing of millions of
Martinez-Moczygemba, Margarita, Doan, Minh L., Elidemir, Okan, Fan, Leland L., Cheung, Sau Wai, Lei, Jonathan T., ...
Pulmonary alveolar proteinosis (PAP) is a rare lung disorder in which surfactant-derived lipoproteins accumulate excessively within pulmonary alveoli, causing severe respiratory distress. The...
Hampton, Oliver A., Den Hollander, Petra, Miller, Christopher A., Delgado, David A., Li, Jian, Coarfa, Cristian, ...
By applying a method that combines end-sequence profiling and massively parallel sequencing, we obtained a sequence-level map of chromosomal aberrations in the genome of the MCF-7 breast cancer cell...