George M Weinstock

Summary

Affiliation: Texas Medical Center
Country: USA

Publications

  1. pmc Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032
    Jason Gioia
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
    PLoS ONE 2:e928. 2007
  2. pmc Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis
    X Qin
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
    Insect Mol Biol 15:715-8. 2006
  3. pmc Creating a honey bee consensus gene set
    Christine G Elsik
    Department of Animal Science, Texas A and M University, TAMU, College Station, Texas 77843, USA
    Genome Biol 8:R13. 2007
  4. pmc Expression capable library for studies of Neisseria gonorrhoeae, version 1.0
    Thomas Brettin
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Microbiol 5:50. 2005
  5. ncbi request reprint ENCODE: more genomic empowerment
    George M Weinstock
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 17:667-8. 2007
  6. pmc Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium
    Sandor E Karpathy
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America
    PLoS ONE 2:e659. 2007
  7. pmc Identification and phenotypic characterization of a second collagen adhesin, Scm, and genome-based identification and analysis of 13 other predicted MSCRAMMs, including four distinct pilus loci, in Enterococcus faecium
    Jouko Sillanpaa
    Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School, Houston, TX, USA
    Microbiology 154:3199-211. 2008
  8. pmc Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays
    Petra Matejková
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1619, Houston, TX 77030, USA
    BMC Microbiol 8:76. 2008
  9. pmc The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny
    Jason Gioia
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
    J Bacteriol 188:7257-66. 2006
  10. pmc A novel Treponema pallidum antigen, TP0136, is an outer membrane protein that binds human fibronectin
    Mary Beth Brinkman
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Infect Immun 76:1848-57. 2008

Research Grants

  1. Bacillus anthracis clone set
    George Weinstock; Fiscal Year: 2002
  2. Francisella Genomics
    George Weinstock; Fiscal Year: 2004
  3. Genomic Comparison of Infectious Strains E. Faecalis
    George Weinstock; Fiscal Year: 2006
  4. Comparative Genomics of Francisella
    George Weinstock; Fiscal Year: 2006

Collaborators

Detail Information

Publications69

  1. pmc Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032
    Jason Gioia
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
    PLoS ONE 2:e928. 2007
    ....
  2. pmc Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis
    X Qin
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
    Insect Mol Biol 15:715-8. 2006
    ..Ongoing efforts to characterize the genomes of these species can be used to understand and mitigate the effects of two important pathogens, and will provide a contrast with pathogenic, benign and freeliving relatives...
  3. pmc Creating a honey bee consensus gene set
    Christine G Elsik
    Department of Animal Science, Texas A and M University, TAMU, College Station, Texas 77843, USA
    Genome Biol 8:R13. 2007
    ..Second, we wished to provide a single official gene list that the research community could further utilize for consistent and comparable analyses and functional annotation...
  4. pmc Expression capable library for studies of Neisseria gonorrhoeae, version 1.0
    Thomas Brettin
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Microbiol 5:50. 2005
    ..Here, we describe the initial phases of the construction of an expression-capable clone set representing the protein-coding ORFs of the gonococcal genome using a recombination-based cloning system...
  5. ncbi request reprint ENCODE: more genomic empowerment
    George M Weinstock
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 17:667-8. 2007
  6. pmc Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium
    Sandor E Karpathy
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America
    PLoS ONE 2:e659. 2007
    ..These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common...
  7. pmc Identification and phenotypic characterization of a second collagen adhesin, Scm, and genome-based identification and analysis of 13 other predicted MSCRAMMs, including four distinct pilus loci, in Enterococcus faecium
    Jouko Sillanpaa
    Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School, Houston, TX, USA
    Microbiology 154:3199-211. 2008
    ..faecium isolates tested. The common occurrence of MSCRAMM- and pilus-encoding genes and the presence of a second collagen-binding protein may have important implications for our understanding of this emerging pathogen...
  8. pmc Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays
    Petra Matejková
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1619, Houston, TX 77030, USA
    BMC Microbiol 8:76. 2008
    ..pallidum remains the enigmatic pathogen, since no virulence factors have been identified and the pathogenesis of the disease is poorly understood. Increasing rates of new syphilis cases per year have been observed recently...
  9. pmc The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny
    Jason Gioia
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
    J Bacteriol 188:7257-66. 2006
    ..haemolytica, Actinobacillus pleuropneumoniae, and Haemophilus ducreyi form a lineage distinct from other Pasteurellaceae. This observation was supported by a phylogenetic analysis using sequences of predicted housekeeping genes...
  10. pmc A novel Treponema pallidum antigen, TP0136, is an outer membrane protein that binds human fibronectin
    Mary Beth Brinkman
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Infect Immun 76:1848-57. 2008
    ..These results demonstrate that TP0136 is expressed on the outer membrane of the treponeme during infection and may be involved in attachment to host extracellular matrix components...
  11. pmc Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence
    Joseph F Petrosino
    Department of Molecular Virology and Microbiology, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, BCM280, Houston, TX 77030, USA
    J Bacteriol 188:6977-85. 2006
    ..Nonconservative differences between the two strains likely include the LVS attenuating mutation(s)...
  12. pmc Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF
    Agathe Bourgogne
    Division of Infectious Diseases, Department of Medicine, University of Texas Medical School, Houston, Texas 77030, USA
    Genome Biol 9:R110. 2008
    ..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 and virulence studies...
  13. pmc Reactivity of antibodies from syphilis patients to a protein array representing the Treponema pallidum proteome
    Mary Beth Brinkman
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    J Clin Microbiol 44:888-91. 2006
    ..pallidum proteins develops at different rates during the time course of infection...
  14. pmc Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae
    Michael P McLeod
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030 7783, USA
    J Bacteriol 186:5842-55. 2004
    ..conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae...
  15. pmc A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis Group, biotype I)
    Jouko Sillanpaa
    Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, Texas 77030, USA
    J Bacteriol 191:6643-53. 2009
    ..gallolyticus subsp. gallolyticus isolates may play an important role in the predominance of this subspecies in S. bovis endocarditis...
  16. pmc A SNP discovery method to assess variant allele probability from next-generation resequencing data
    Yufeng Shen
    The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 20:273-80. 2010
    ..Validation results show that Atlas-SNP2 achieves a false-positive rate of lower than 10%, with an approximately 5% or lower false-negative rate...
  17. pmc Systematic cloning of Treponema pallidum open reading frames for protein expression and antigen discovery
    Matthew McKevitt
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 13:1665-74. 2003
    ..pallidum antigens, and the remaining five represent novel antigens. These results demonstrate the potential of the T. pallidum clone set for antigen discovery and, more generally, for advancing the biology of this enigmatic spirochete...
  18. pmc Bos taurus genome assembly
    Yue Liu
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    BMC Genomics 10:180. 2009
    ..The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque...
  19. pmc Conservation of Ebp-type pilus genes among Enterococci and demonstration of their role in adherence of Enterococcus faecalis to human platelets
    Sreedhar R Nallapareddy
    Division of Infectious Diseases, Department of Internal Medicine, Center for the Study of Emerging and Re Emerging Pathogens, University of Texas Medical School, Houston, Texas 77030, USA
    Infect Immun 79:2911-20. 2011
    ....
  20. pmc An Enterococcus faecium secreted antigen, SagA, exhibits broad-spectrum binding to extracellular matrix proteins and appears essential for E. faecium growth
    Fang Teng
    Division of Infectious Disease, Department of Internal Medicine and Center for the Study of Emerging and Reemerging Pathogens, University of Texas Houston Medical School, Houston, Texas 77030, USA
    Infect Immun 71:5033-41. 2003
    ..In conclusion, the extracelluar E. faecium SagA protein is apparently essential for growth, shows broad-spectrum binding to ECM proteins, forms oligomers, and is antigenic during infection...
  21. pmc Genome scale identification of Treponema pallidum antigens
    Matthew McKevitt
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Infect Immun 73:4445-50. 2005
    ..Additionally, sera collected from rabbits throughout the course of infection demonstrated a progression in the breadth and intensity of humoral immunoreactivity against a representative panel of T. pallidum antigens...
  22. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  23. pmc Identification of novel and cross-species seroreactive proteins from Bacillus anthracis using a ligation-independent cloning-based, SOS-inducible expression system
    Brian D McWilliams
    Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Microb Pathog 53:250-8. 2012
    ..These results will contribute to the future selection of targets in antigenicity and protection studies as one or more of these proteins may prove to be worthy of inclusion in future vaccine preparations...
  24. ncbi request reprint The genome of the model beetle and pest Tribolium castaneum
    Stephen Richards
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 452:949-55. 2008
    ..Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control...
  25. pmc Transcriptome of Treponema pallidum: gene expression profile during experimental rabbit infection
    David Smajs
    Human Genome Sequencing Center, University of Texas Houston Medical School, Houston, Texas, USA
    J Bacteriol 187:1866-74. 2005
    ..This characterization of the T. pallidum transcriptome during experimental infection provides further insight into the importance of gene expression levels for the survival and pathogenesis of this bacterium...
  26. pmc A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery
    Xiaohu Wang
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
    Nucleic Acids Res 36:4863-71. 2008
    ....
  27. doi request reprint The complete genome of an individual by massively parallel DNA sequencing
    David A Wheeler
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 452:872-6. 2008
    ..This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'...
  28. pmc A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement
    Sara J Bowne
    Human Genetics Center, The University of Texas Health Science Center, Houston, TX, USA
    Eur J Hum Genet 19:1074-81. 2011
    ..Gene therapy for LCA patients with RPE65 mutations has shown great promise, raising the possibility of related therapies for dominant-acting mutations in this gene...
  29. pmc Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus
    Sarah K Highlander
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
    BMC Microbiol 7:99. 2007
    ..Epidemiological studies suggest that USA300 is more virulent than other CA-MRSA. The genetic determinants that render virulence and dominance to USA300 remain unclear...
  30. pmc Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy
    Truc T Tran
    Department of Internal Medicine, Division of Infectious Diseases, University of Houston College of Pharmacy, Houston, Texas, USA
    Antimicrob Agents Chemother 57:261-8. 2013
    ..Our results suggest that, apart from the LiaFSR system, the essential YycFG system is likely to be an important mediator of DAP resistance in some E. faecium strains...
  31. pmc Molecular characterization of a widespread, pathogenic, and antibiotic resistance-receptive Enterococcus faecalis lineage and dissemination of its putative pathogenicity island
    Sreedhar R Nallapareddy
    Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, 6431 Fannin Street, MSB 2 112, Houston, TX 77030, USA
    J Bacteriol 187:5709-18. 2005
    ..faecalis with different members resistant to the primary therapies of choice, ampicillin and vancomycin, has important implications for the evolution of virulence and successful lineages and for public health monitoring and control...
  32. pmc Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes
    Xiang Qin
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
    BMC Microbiol 12:135. 2012
    ..faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references...
  33. pmc Translocation of Enterococcus faecalis strains across a monolayer of polarized human enterocyte-like T84 cells
    Jing Zeng
    Division of Infectious Diseases, Department of Medicine, Center for the Study of Emerging and Re Emerging Pathogens, University of Texas, Houston, Texas 77030, USA
    J Clin Microbiol 42:1149-54. 2004
    ..These results suggest that this model may be a useful in vitro system for studying the process of translocation from the intestinal tract...
  34. pmc Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
    Stephen Richards
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA
    Genome Res 15:1-18. 2005
    ..Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila...
  35. pmc Candidate genes that may be responsible for the unusual resistances exhibited by Bacillus pumilus SAFR-032 spores
    Madhan R Tirumalai
    Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
    PLoS ONE 8:e66012. 2013
    ..This cluster of five genes is considered to be an especially promising target for future experimental work. ..
  36. pmc Application of next-generation sequencing to identify genes and mutations causing autosomal dominant retinitis pigmentosa (adRP)
    Stephen P Daiger
    Human Genetics Center, School of Public Health, Univ of Texas HSC, 1200 Herman Pressler Dr, 77030, Houston, TX, USA
    Adv Exp Med Biol 801:123-9. 2014
    ..We detected mutations in 11 of these families (31 %) bringing the total detected in the adRP cohort to 70 %. Several large families have also been tested for linkage using Afymetrix single nucleotide polymorphism (SNP) arrays. ..
  37. pmc Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing
    Sara J Bowne
    Human Genetics Center, The University of Texas Health Science Center, Houston, Texas 77030, USA
    Invest Ophthalmol Vis Sci 52:494-503. 2011
    ..RP has multiple patterns of inheritance, with mutations in many genes for each inheritance pattern and numerous, distinct, disease-causing mutations at each locus; further, many RP genes have not been identified yet...
  38. pmc The Atlas genome assembly system
    Paul Havlak
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:721-32. 2004
    ..Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects...
  39. ncbi request reprint Clinical isolates of Enterococcus faecium exhibit strain-specific collagen binding mediated by Acm, a new member of the MSCRAMM family
    Sreedhar R Nallapareddy
    Division of Infectious Diseases, Department of Internal Medicine and Center for the Study of Emerging and Re emerging Pathogens, University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
    Mol Microbiol 47:1733-47. 2003
    ..faecium, and suggest that Acm is the primary adhesin responsible for the ability of E. faecium to bind collagen...
  40. pmc Pooled genomic indexing of rhesus macaque
    Aleksandar Milosavljevic
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 15:292-301. 2005
    ..A further innovation, short-tag pooled genomic indexing (ST-PGI), was also introduced to further improve the economy of mapping by sequencing multiple, short, mapable tags within a single sequencing reaction...
  41. ncbi request reprint Shedding genomic light on Aristotle's lantern
    Erica Sodergren
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1519, Houston, TX 77030, USA
    Dev Biol 300:2-8. 2006
    ..Analysis of the basic deuterostome genetic complement supports the sea urchin's role as a model system for deuterostome and, by extension, chordate development...
  42. pmc Evidence that the enterococcal polysaccharide antigen gene (epa) cluster is widespread in Enterococcus faecalis and influences resistance to phagocytic killing of E. faecalis
    Fang Teng
    Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas 77030, USA
    Infect Immun 70:2010-5. 2002
    ..faecalis endocarditis all reacted with polysaccharide extracts of OG1RF. These results indicate that the epa gene cluster is widespread among E. faecalis and confers some protection against human host defenses...
  43. pmc Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project
    Rui Chen
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:679-84. 2004
    ..Combined with the assembled BAC fingerprint map, a set of BAC clones that covered >97% of the genome was identified and used in the RGSP...
  44. pmc Involvement of PhoP-PhoS homologs in Enterococcus faecalis virulence
    Fang Teng
    Department of Microbiology and Molecular Genetics, University of Texas Houston Medical School, Houston, Texas 77030, USA
    Infect Immun 70:1991-6. 2002
    ..In conclusion, many potential two-component systems are identified for E. faecalis, one of which, EtaRS, was shown to be involved in stress response and virulence...
  45. ncbi request reprint Colicins produced by the Escherichia fergusonii strains closely resemble colicins encoded by Escherichia coli
    David Smajs
    Department of Microbiology and Molecular Genetics, University of Texas Houston Medical School, Houston, TX, USA
    FEMS Microbiol Lett 208:259-62. 2002
    ..fergusonii strain EF36 (pColE1-EF36) was found to be only partially immune to E1 colicins produced by two other E. fergusonii strains suggesting that pColE1-EF36 may represent an ancestor ColE1 plasmid...
  46. ncbi request reprint Complete nucleotide sequence of a P2 family lysogenic bacteriophage, varphiMhaA1-PHL101, from Mannheimia haemolytica serotype A1
    Sarah K Highlander
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Virology 350:79-89. 2006
    ..Southern blot analysis revealed phiMhaA1-PHL101 sequences in other A1 isolates as well as in serotype A5, A6, A9, and A12 strains of M. haemolytica, but not in the related organisms, Mannheimia glucosida or Pasteurella trehalosi...
  47. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  48. pmc Targeted high-throughput DNA sequencing for gene discovery in retinitis pigmentosa
    Stephen P Daiger
    Department of Ophthalmology and Visual Science, University of Texas Health Science Center, Houston, TX, USA
    Adv Exp Med Biol 664:325-31. 2010
    ..After validation studies, the first DNA's tested will be from 89 unrelated adRP families in which the prevalent RP genes have been excluded. This approach should identify new RP genes and will substantially reduce the cost per patient...
  49. pmc Genetic basis for in vivo daptomycin resistance in enterococci
    Cesar A Arias
    Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical School at Houston, Houston, TX 77030, USA
    N Engl J Med 365:892-900. 2011
    ..However, the emergence of resistance to daptomycin during therapy threatens its usefulness...
  50. pmc BAC library of T. pallidum DNA in E. coli
    David Smajs
    Department of Microbiology and Molecular Genetics, University of Texas Houston Medical School, Houston, TX 77030, USA
    Genome Res 12:515-22. 2002
    ..Using this minimal set of clones, at least 12 T. pallidum proteins were shown to react with pooled sera from rabbits immunized with T. pallidum, indicating that at least some T. pallidum genes are transcribed and expressed in E. coli...
  51. ncbi request reprint Construction of small genome BAC library for functional and genomic applications
    David Smajs
    Department of Microbiology and Molecular Genetics, University of Texas Houston Medical School, USA
    Methods Mol Biol 255:47-56. 2004
  52. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
    ..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization...
  53. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  54. pmc An Enterococcus faecalis ABC homologue (Lsa) is required for the resistance of this species to clindamycin and quinupristin-dalfopristin
    Kavindra V Singh
    Center for the Study of Emerging and Reemerging Pathogens, Division of Infectious Diseases, Department of Internal Medicine, The University of Texas Medical School at Houston, 77030, USA
    Antimicrob Agents Chemother 46:1845-50. 2002
    ..In conclusion, lsa appears to be an intrinsic gene of E. faecalis that explains the characteristic resistance of this species to CLI and Q-D...
  55. pmc Genome differences between Treponema pallidum subsp. pallidum strain Nichols and T. paraluiscuniculi strain Cuniculi A
    Michal Strouhal
    Department of Biology, Building A6, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
    Infect Immun 75:5859-66. 2007
    ..6 to 99.3%. These results are consistent with a close genetic relationship among the T. pallidum strains and subspecies and a strong, but relatively divergent connection between the human and rabbit pathogens...
  56. pmc Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
    ..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure...
  57. pmc The genome of the sea urchin Strongylocentrotus purpuratus
    Erica Sodergren
    Science 314:941-52. 2006
    ..This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes...
  58. pmc Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:5646-51. 2004
    ....
  59. ncbi request reprint Direct selection of human genomic loci by microarray hybridization
    Thomas J Albert
    NimbleGen Systems Inc, 1 Science Court, Madison, Wisconsin 53711, USA
    Nat Methods 4:903-5. 2007
    ..These direct selection methods supersede multiplex PCR for the large-scale analysis of genomic regions...
  60. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  61. pmc Characterizing the cancer genome in lung adenocarcinoma
    Barbara A Weir
    Department of Medical Oncology and Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Nature 450:893-8. 2007
    ..More generally, our results indicate that many of the genes that are involved in lung adenocarcinoma remain to be discovered...
  62. pmc 28-way vertebrate alignment and conservation track in the UCSC Genome Browser
    Webb Miller
    Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA
    Genome Res 17:1797-808. 2007
    ..Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions...
  63. pmc Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects
    Joel Savard
    Abteilung für Evolutionsgenetik, Institut fur Genetik, Universitat zu Koln, Köln 50674, Germany
    Genome Res 16:1334-8. 2006
    ..We validate our results by meticulous examination of potential confounding factors. Phylogenomic approaches are thus able to resolve long-standing questions about the phylogeny of insects...
  64. ncbi request reprint Preparation of BAC libraries from bacterial genomes by in vitro packaging
    Sangita Pal
    Department of Microbiology and Molecular Genetics, University of Texas Houston Medical School, USA
    Methods Mol Biol 255:57-68. 2004
  65. pmc The genome of Apis mellifera: dialog between linkage mapping and sequence assembly
    Michel Solignac
    Genome Biol 8:403. 2007
    ..Each construct was used to control the quality of the other. The co-linearity of markers in the sequence and the map is almost perfect and argues in favor of the high quality of both...
  66. pmc The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse
    Tim Durfee
    DNASTAR, Inc, Madison, Wisconsin 53705, USA
    J Bacteriol 190:2597-606. 2008
    ..Finally, while the sequence confirms most of the reported alleles, the sequence of deoR is wild type, necessitating reexamination of the assumed basis for the high transformability of DH10B...
  67. ncbi request reprint Community annotation: procedures, protocols, and supporting tools
    Christine G Elsik
    Department of Animal Science, Texas A and M University, College Station, Texas 77843, USA
    Genome Res 16:1329-33. 2006
    ..We present annotation procedures, standard protocols, and tools used for sequence analysis, data submission, and data management. We also report lessons learned from this dispersed community annotation effort for a metazoan genome...
  68. ncbi request reprint Recognition of pore-forming colicin Y by its cognate immunity protein
    David Smajs
    Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
    FEMS Microbiol Lett 258:108-13. 2006
    ..Mutations in cui, which converted Cui sequence to Cyi sequence in positions 104, 107, 110, 112 and 159, resulted in an immunity gene that also conferred (besides immunity to colicin U) a high degree of immunity to colicin Y...

Research Grants4

  1. Bacillus anthracis clone set
    George Weinstock; Fiscal Year: 2002
    ..During Phase I of this project, covered by the present application, genes from the two virulence plasmids and a limited number of chromosomal genes will be cloned and expressed and probed with immunological reagents. ..
  2. Francisella Genomics
    George Weinstock; Fiscal Year: 2004
    ..tularensis contains a high proportion of unique genes compared to other bacterial genomes. Therefore, knowledge of the complete genome sequences of F. tularensis strains is needed for the understanding of the virulence mechanisms. ..
  3. Genomic Comparison of Infectious Strains E. Faecalis
    George Weinstock; Fiscal Year: 2006
    ..The introduction of the novel methods will reduce costs and increase throughput, both of which are important for future scale-up to larger numbers of strains. ..
  4. Comparative Genomics of Francisella
    George Weinstock; Fiscal Year: 2006
    ..abstract_text> ..