P M Small

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. ncbi request reprint Tuberculosis in the 21st century: DOTS and SPOTS. Plenary lecture given at the 29th World Conference of the International Union Against Tuberculosis and Lung Disease, Bangkok, Thailand, 23-26 November 1998. Directly observed therapy
    P M Small
    Stanford Center for Tuberculosis Research, Stanford University, California, USA
    Int J Tuberc Lung Dis 3:949-55. 1999
  2. pmc Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data
    H Salamon
    Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California 94305, USA
    Genome Res 10:2044-54. 2000
  3. pmc Accommodating error analysis in comparison and clustering of molecular fingerprints
    H Salamon
    University of California, San Francisco, USA
    Emerg Infect Dis 4:159-68. 1998
  4. ncbi request reprint Use of multiple markers in population-based molecular epidemiologic studies of tuberculosis
    J T Rhee
    Department of Health Research and Policy, Stanford University School of Medicine, California, USA
    Int J Tuberc Lung Dis 4:1111-9. 2000
  5. pmc Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains
    S Raychaudhuri
    Department of Medicine, Stanford University, CA 94305 5479, USA
    Proc Int Conf Intell Syst Mol Biol 8:286-95. 2000
  6. pmc The dynamics of repeated elements: applications to the epidemiology of tuberculosis
    M M Tanaka
    Department of Biological Sciences, and Division of Infectious Diseases and Geographic Medicine, Stanford University, CA 94305, USA
    Proc Natl Acad Sci U S A 97:3532-7. 2000
  7. ncbi request reprint A historical and molecular phylogeny of BCG strains
    M A Behr
    Department of Medicine, Stanford University School of Medicine, CA, USA
    Vaccine 17:915-22. 1999
  8. ncbi request reprint Transmission of Mycobacterium tuberculosis from patients smear-negative for acid-fast bacilli
    M A Behr
    Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
    Lancet 353:444-9. 1999
  9. ncbi request reprint The private-public divide: impact of conflicting perceptions between the private and public health care sectors in India
    R M Vyas
    Department of Biological Sciences, Stanford University, Stanford, California, USA
    Int J Tuberc Lung Dis 7:543-9. 2003
  10. ncbi request reprint Clinical management of tuberculosis in the context of HIV infection
    Bouke C de Jong
    Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California 94305, USA
    Annu Rev Med 55:283-301. 2004

Collaborators

Detail Information

Publications40

  1. ncbi request reprint Tuberculosis in the 21st century: DOTS and SPOTS. Plenary lecture given at the 29th World Conference of the International Union Against Tuberculosis and Lung Disease, Bangkok, Thailand, 23-26 November 1998. Directly observed therapy
    P M Small
    Stanford Center for Tuberculosis Research, Stanford University, California, USA
    Int J Tuberc Lung Dis 3:949-55. 1999
    ..The synergy of a balanced portfolio incorporating a globalized public health commitment and creative basic research will provide us with the infrastructure and tools needed to eliminate tuberculosis before the close of the 21st century...
  2. pmc Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data
    H Salamon
    Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California 94305, USA
    Genome Res 10:2044-54. 2000
    ..Issues relating to the design of genome content screening experiments and the implications of these methods for studying population genomics and the evolution of genomes are discussed...
  3. pmc Accommodating error analysis in comparison and clustering of molecular fingerprints
    H Salamon
    University of California, San Francisco, USA
    Emerg Infect Dis 4:159-68. 1998
    ..tuberculosis fingerprints. Fully documented and validated methods of automated comparison and clustering will greatly expand the scope of molecular epidemiology...
  4. ncbi request reprint Use of multiple markers in population-based molecular epidemiologic studies of tuberculosis
    J T Rhee
    Department of Health Research and Policy, Stanford University School of Medicine, California, USA
    Int J Tuberc Lung Dis 4:1111-9. 2000
    ..Fingerprinting with a secondary marker in strains with fewer than six IS6110-hybridizing bands enhances the tracking of strains, but its impact on population-level inferences has not been well studied...
  5. pmc Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains
    S Raychaudhuri
    Department of Medicine, Stanford University, CA 94305 5479, USA
    Proc Int Conf Intell Syst Mol Biol 8:286-95. 2000
    ..The nonparametric approach outperforms all other methods tested in this study...
  6. pmc The dynamics of repeated elements: applications to the epidemiology of tuberculosis
    M M Tanaka
    Department of Biological Sciences, and Division of Infectious Diseases and Geographic Medicine, Stanford University, CA 94305, USA
    Proc Natl Acad Sci U S A 97:3532-7. 2000
    ..We find that the transposition parameters have a much stronger effect than the epidemic parameters on copy number distribution...
  7. ncbi request reprint A historical and molecular phylogeny of BCG strains
    M A Behr
    Department of Medicine, Stanford University School of Medicine, CA, USA
    Vaccine 17:915-22. 1999
    ....
  8. ncbi request reprint Transmission of Mycobacterium tuberculosis from patients smear-negative for acid-fast bacilli
    M A Behr
    Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
    Lancet 353:444-9. 1999
    ..We aimed to estimate the risk of transmission from smear-negative individuals...
  9. ncbi request reprint The private-public divide: impact of conflicting perceptions between the private and public health care sectors in India
    R M Vyas
    Department of Biological Sciences, Stanford University, Stanford, California, USA
    Int J Tuberc Lung Dis 7:543-9. 2003
    ..While several studies have demonstrated private physicians' dubious diagnosis and treatment styles and lack of cooperation with public physicians, very little is still known about the private sector...
  10. ncbi request reprint Clinical management of tuberculosis in the context of HIV infection
    Bouke C de Jong
    Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California 94305, USA
    Annu Rev Med 55:283-301. 2004
    ..However, given the disproportionate amount of TB/HIV in less-developed nations and the increasing availability of antiretroviral therapy in resource-limited settings, the issues presented will become increasingly relevant globally...
  11. ncbi request reprint Changes in the geographical distribution of tuberculosis patients in Veracruz, Mexico, after reinforcement of a tuberculosis control programme
    Lara M Jacobson
    Stanford University, Palo Alto, CA, USA
    Trop Med Int Health 10:305-11. 2005
    ....
  12. pmc Does resistance to pyrazinamide accurately indicate the presence of Mycobacterium bovis?
    Bouke C de Jong
    Division of Infectious Diseases, Stanford University, Stanford, California, USA
    J Clin Microbiol 43:3530-2. 2005
    ..The sensitivity for detection of M. bovis is lowered to 82% when only PZA-monoresistant isolates are screened...
  13. pmc Stable association between strains of Mycobacterium tuberculosis and their human host populations
    Aaron E Hirsh
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:4871-6. 2004
    ..tuberculosis suggests that these lineages diverged centuries ago. Thus, associations between host and pathogen populations appear to be highly stable...
  14. ncbi request reprint Effect of drug resistance on the generation of secondary cases of tuberculosis
    Marcos Burgos
    Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University Medical Center, Stanford, California, USA
    J Infect Dis 188:1878-84. 2003
    ..Here, we assess the relative pathogenicity of drug-resistant and drug-susceptible strains, in a human population...
  15. pmc High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography
    Ruth Hershberg
    Department of Biology, Stanford University, Stanford, California, USA
    PLoS Biol 6:e311. 2008
    ..tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis...
  16. pmc Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis
    Sebastian Gagneux
    Division of Infectious Diseases and Geographic Medicine, Stanford University Medical Center, Stanford, California, USA
    PLoS Pathog 2:e61. 2006
    ..tuberculosis lineages. Our results show that in addition to host and environmental factors, strain genetic diversity can influence the transmission dynamics of drug-resistant bacteria...
  17. ncbi request reprint Amplification dynamics: predicting the effect of HIV on tuberculosis outbreaks
    T C Porco
    San Francisco Department of Public Health, San Francisco, California, USA
    J Acquir Immune Defic Syndr 28:437-44. 2001
    ..tuberculosis can be expected to generate a large outbreak. We discuss the implications of these results in understanding the virulence of M. tuberculosis and in the planned elimination of tuberculosis in the United States...
  18. ncbi request reprint The competitive cost of antibiotic resistance in Mycobacterium tuberculosis
    Sebastien Gagneux
    Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
    Science 312:1944-6. 2006
    ..In contrast, we demonstrate that prolonged patient treatment can result in multidrug-resistant strains with no fitness defect and that strains with low- or no-cost resistance mutations are also the most frequent among clinical isolates...
  19. pmc High-throughput method for detecting genomic-deletion polymorphisms
    Yves Olivier Luc Goguet de la Salmonière
    Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University Medical Center, California, USA
    J Clin Microbiol 42:2913-8. 2004
    ..tuberculosis isolates for LSPs. This technique can be used to provide insights into the epidemiology, genomic evolution, and population structure of M. tuberculosis and can be adapted for the study of other organisms...
  20. pmc Determining the genomic locations of repetitive DNA sequences with a whole-genome microarray: IS6110 in Mycobacterium tuberculosis
    Marten Kivi
    Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California 94305, USA
    J Clin Microbiol 40:2192-8. 2002
    ..SiteMapping has general applicability and demonstrates an expansion in the applications of microarrays that complements conventional approaches in the study of genome architecture...
  21. pmc Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis
    Anthony G Tsolaki
    Division of Infectious Diseases and Geographic Medicine, Stanford University Medical Center, Stanford, California 94305, USA
    J Clin Microbiol 43:3185-91. 2005
    ..tuberculosis...
  22. ncbi request reprint Transmission of drug-resistant tuberculosis among treated patients in Shanghai, China
    Xia Li
    Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Shanghai, 200032, China
    J Infect Dis 195:864-9. 2007
    ..Our findings highlight the urgency of increasing efforts to interrupt the transmission of drug-resistant tuberculosis in communities and facilities in Shanghai, China...
  23. ncbi request reprint Rapid identification and susceptibility testing of Mycobacterium tuberculosis from MGIT cultures with luciferase reporter mycobacteriophages
    Niaz Banaiee
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
    J Med Microbiol 52:557-61. 2003
    ..LRPs offer an accurate and rapid approach for identification and susceptibility testing of M. tuberculosis from MGIT-960 cultures...
  24. ncbi request reprint Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development
    Sebastien Gagneux
    Institute for Systems Biology, Seattle, WA, USA
    Lancet Infect Dis 7:328-37. 2007
    ..We propose a strain selection framework, based on robust phylogenetic markers, which will allow for systematic and comprehensive evaluation of new tools for tuberculosis control...
  25. ncbi request reprint Genomic interrogation of ancestral Mycobacterium tuberculosis from south India
    Sujatha Narayanan
    Tuberculosis Research Centre, Mayor VR Ramanathan Road, Chetput, Chennai, India
    Infect Genet Evol 8:474-83. 2008
    ..2% belonged to the ancestral lineage of M. tuberculosis. Comparative whole-genome hybridization identified six new genomic regions within this lineage that were variably deleted...
  26. ncbi request reprint Public health. A National Tuberculosis Archive
    Damian Gessler
    National Center for Genome Resources, Santa Fe, NM 87505, USA
    Science 311:1245-6. 2006
  27. pmc Use of rapid genomic deletion typing to monitor a tuberculosis outbreak within an urban homeless population
    Robert Freeman
    Seattle Biomedical Research Institute, 307 Westlake Avenue N, Suite 500, Seattle, WA 98107 5219, USA
    J Clin Microbiol 43:5550-4. 2005
    ..This rapid turnaround facilitated public health efforts to prevent new outbreaks involving this strain...
  28. pmc The W-Beijing lineage of Mycobacterium tuberculosis overproduces triglycerides and has the DosR dormancy regulon constitutively upregulated
    Michael B Reed
    The Research Institute of the McGill University Health Centre, Montreal General Hospital, 1650 Cedar Ave, Montreal, Quebec, Canada H3G 1A4
    J Bacteriol 189:2583-9. 2007
    ....
  29. pmc Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains
    Anthony G Tsolaki
    Division of Infectious Diseases and Geographic Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:4865-70. 2004
    ..For some deletions, short-term evolutionary pressure due to the host immune system or antibiotics may favor the elimination of genes, whereas longer-term physiological requirements maintain the genes in the population...
  30. pmc Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia
    Bouke C de Jong
    Medical Research Council Laboratories, Banjul, The Gambia
    J Infect Dis 198:1037-43. 2008
    ..There is considerable variability in the outcome of Mycobacterium tuberculosis infection. We hypothesized that Mycobacterium africanum was less likely than M. tuberculosis to transmit and progress to tuberculosis disease...
  31. pmc Microevolution of the direct repeat locus of Mycobacterium tuberculosis in a strain prevalent in San Francisco
    Roxanne S Aga
    Division of Pulmonary and Critical Care Medicine, Department of Medicine SFGH, UCSF, 1001 Potrero Avenue, San Francisco General Hospital, Mail Box 0841, San Francisco, CA 94110, USA
    J Clin Microbiol 44:1558-60. 2006
    ..During the second outbreak, a direct variable repeat was lost. We discuss the mechanisms of this change and the implications of analyzing multiple genetic loci in this context...
  32. ncbi request reprint Mycobacterium africanum elicits an attenuated T cell response to early secreted antigenic target, 6 kDa, in patients with tuberculosis and their household contacts
    Bouke C de Jong
    Medical Research Council Laboratories, The Gambia
    J Infect Dis 193:1279-86. 2006
    ..Mycobacterium africanum, a member of the M. tuberculosis complex that is infrequently found outside of western Africa, is the cause of up to half of the tuberculosis cases there...
  33. pmc Variable host-pathogen compatibility in Mycobacterium tuberculosis
    Sebastien Gagneux
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 103:2869-73. 2006
    ..These observations suggest that mycobacterial lineages are adapted to particular human populations. If confirmed, our findings have important implications for tuberculosis control and vaccine development...
  34. ncbi request reprint Admitting defeat
    Mark D Perkins
    Int J Tuberc Lung Dis 10:1. 2006
  35. ncbi request reprint Mycobacterium africanum: a new opportunistic pathogen in HIV infection?
    Bouke C de Jong
    AIDS 19:1714-5. 2005
  36. ncbi request reprint Does DOTS work in populations with drug-resistant tuberculosis?
    Kathryn DeRiemer
    Division of Infectious Diseases and Geographic Medicine, Stanford University Medical Center, Stanford, CA, USA
    Lancet 365:1239-45. 2005
    ..Directly observed therapy (DOTS) is the main strategy for prevention and control of tuberculosis worldwide. However, its effect on tuberculosis transmission in populations with moderate rates of drug-resistant disease is not known...
  37. ncbi request reprint The in vitro evolution of BCG vaccines
    Serge Mostowy
    McGill University Health Centre, Montreal, Que, Canada H3G 1A4
    Vaccine 21:4270-4. 2003
    ..tuberculosis complex subspecies. The contrast between the two modes of evolution are discussed in its relevance towards TB pathogenicity...
  38. ncbi request reprint The control of copy number of IS6110 in Mycobacterium tuberculosis
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia
    Mol Biol Evol 21:2195-201. 2004
    ..Specifically, our analysis points to the interaction of separate copies of the element causing lethal effects. We discuss the implications of these findings for genome evolution and molecular epidemiology...
  39. ncbi request reprint Tuberculosis and diabetes in southern Mexico
    Alfredo Ponce-de-Leon
    National Institute of Medical Sciences and Nutrition, Salvador Zubiran, Distrito Federal, Mexico
    Diabetes Care 27:1584-90. 2004
    ..To determine the impact of diabetes on the rates of tuberculosis in a region where both diseases are prevalent...
  40. ncbi request reprint Gene expression diversity among Mycobacterium tuberculosis clinical isolates
    Qian Gao
    Department of Medicine, Division of Infectious Disease and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 5107, USA
    Microbiology 151:5-14. 2005
    ..This survey of mRNA expression among clinical isolates of M. tuberculosis demonstrates that genes with important functions can vary in their expression levels between strains grown under identical conditions...