David A. Relman
Publications
- The increasingly compelling moral responsibilities of life scientists. Hastings Cent Rep. 2013 Mar-Apr; (2): 34-5
- Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One. 2013; (1): e53838
- Microbiology. Undernutrition--looking within for answers. Science. 2013; (6119): 530-2
- Restoration of the gut microbial habitat as a disease therapy. Nat Biotechnol. 2013; (1): 35-7
- Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 2013; (1): 111-20
- Type I interferon suppresses type II interferon-triggered human anti-mycobacterial responses. Science. 2013; (6126): 1448-53
- Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ Microbiol. 2012; (9): 2564-76
- Comparisons of distance methods for combining covariates and abundances in microbiome studies. Pac Symp Biocomput. 2012: 213-24
- Creating a mammalian-transmissible A/H5N1 influenza virus: social contracts, prudence, and alternative perspectives. J Infect Dis. 2012; (11): 1636-8
- Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 2012; (5): 915-26
- Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012; (7): 1578-93
- Microbiology: Learning about who we are. Nature. 2012; (7402): 194-5
- Microbiota-targeted therapies: an ecological perspective. Sci Transl Med. 2012; (137): 137rv5
- Policy: Adaptations of avian flu virus are a cause for concern. Nature. 2012; (7384): 153-4
- Public health and biosecurity. Adaptations of avian flu virus are a cause for concern. Science. 2012; (6069): 660-1
- Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Res. 2012; (6): 1107-19
- Temporal dynamics of the transcriptional response to dengue virus infection in Nicaraguan children. PLoS Negl Trop Dis. 2012; (12): e1966
- The application of ecological theory toward an understanding of the human microbiome. Science. 2012; (6086): 1255-62
- The human microbiome: ecosystem resilience and health. Nutr Rev. 2012: S2-9
- Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res. 2011; (1): 126-36
- Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011: 4554-61
- Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A. 2011: 4547-53
- Microbial genomics and infectious diseases. N Engl J Med. 2011; (4): 347-57
- Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011; (5): 415-20
- Modulation of the host interferon response and ISGylation pathway by B. pertussis filamentous hemagglutinin. PLoS One. 2011; (11): e27535
- Myocardial depressant effects of interleukin 6 in meningococcal sepsis are regulated by p38 mitogen-activated protein kinase. Crit Care Med. 2011; (7): 1692-711
- Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A. 2011; (3): 1128-33
- Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus. PLoS One. 2011; (1): e15615
- Transcriptional profiling of the iron starvation response in Bordetella pertussis provides new insights into siderophore utilization and virulence gene expression. J Bacteriol. 2011; (18): 4798-812
- Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011; (1): 16-25
- Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 2010; (8): 962-74
- Dissecting interferon-induced transcriptional programs in human peripheral blood cells. PLoS One. 2010; (3): e9753
- Genetic technologies. Synthetic "life," ethics, national security, and public discourse. Science. 2010; (5987): 38-9
- Microbial invasion of the amniotic cavity in preeclampsia as assessed by cultivation and sequence-based methods. J Perinat Med. 2010; (5): 503-13
- Microbial invasion of the amniotic cavity in pregnancies with small-for-gestational-age fetuses. J Perinat Med. 2010; (5): 495-502
- Microbial threat lists: obstacles in the quest for biosecurity? Nat Rev Microbiol. 2010; (2): 149-54
- Prevalence and diversity of microbes in the amniotic fluid, the fetal inflammatory response, and pregnancy outcome in women with preterm pre-labor rupture of membranes. Am J Reprod Immunol. 2010; (1): 38-57
- SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Bioinformatics. 2010; (23): 2979-80
- The biological century: coming to terms with risk in the life sciences. Nat Immunol. 2010; (4): 275-8
- Cross-talk in the gut. Genome Biol. 2009; (1): 203
- Gene transcript abundance profiles distinguish Kawasaki disease from adenovirus infection. J Infect Dis. 2009; (4): 657-66
- Majority rules? Tallying the microbial census in an abscess by means of molecular methods. Clin Infect Dis. 2009; (9): 1179-81
- Natural-host animal models indicate functional interchangeability between the filamentous haemagglutinins of Bordetella pertussis and Bordetella bronchiseptica and reveal a role for the mature C-terminal domain, but not the RGD motif, during infection. Mol Microbiol. 2009; (6): 1574-90
- 'Til death do us part': coming to terms with symbiotic relationships. Forward. Nat Rev Microbiol. 2008; (10): 721-4
- Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes. PLoS One. 2008; (7): e2628
- Erratum. PLoS Genet. 2008; (11)
- Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 2008; (11): e1000255
- Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota. Infect Immun. 2008; (1): 403-16
- Learning to appreciate our differences. J Infect Dis. 2008; (1): 4-5
- Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl Environ Microbiol. 2008; (10): 3143-50
- Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS One. 2008; (8): e3056
- Microbiology in the post-genomic era. Nat Rev Microbiol. 2008; (6): 419-30
- Modulation of the NF-kappaB pathway by Bordetella pertussis filamentous hemagglutinin. PLoS One. 2008; (11): e3825
- The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008; (11): e280
- An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007; (7164): 811-8
- Building a better virus trap. Trends Biotechnol. 2007; (12): 535-8
- Development of the human infant intestinal microbiota. PLoS Biol. 2007; (7): e177
- Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A. 2007; (29): 11889-94
- Gene-expression patterns reveal underlying biological processes in Kawasaki disease. Genome Biol. 2007; (12): R261
- Patterns of host genome-wide gene transcript abundance in the peripheral blood of patients with acute dengue hemorrhagic fever. J Infect Dis. 2007; (8): 1097-107
- Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis. BMC Genomics. 2007: 122
- The importance of individuals and scale: moving towards single cell microbiology. Environ Microbiol. 2007; (1): 8-10
- The role of microbes in Crohn's disease. Clin Infect Dis. 2007; (2): 256-62
- The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever. Genome Biol. 2007; (8): R174
- Assembly of the human intestinal microbiota. Trends Ecol Evol. 2006; (9): 517-23
- Bioterrorism--preparing to fight the next war. N Engl J Med. 2006; (2): 113-5
- Characterization of a highly conserved island in the otherwise divergent Bordetella holmesii and Bordetella pertussis genomes. J Bacteriol. 2006; (24): 8385-94
- Early days: genomics and human responses to infection. Curr Opin Microbiol. 2006; (3): 312-9
- Genomic features of Bordetella parapertussis clades with distinct host species specificity. Genome Biol. 2006; (9): R81
- Growth phase- and nutrient limitation-associated transcript abundance regulation in Bordetella pertussis. Infect Immun. 2006; (10): 5537-48
- How bacterial communities expand functional repertoires. PLoS Biol. 2006; (12): e430
- In search of biosecurity. Science. 2006; (5769): 1835
- Metagenomic analysis of the human distal gut microbiome. Science. 2006; (5778): 1355-9
- Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A. 2006; (3): 732-7
- Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 2006; (1): e5
- Significant gene order and expression differences in Bordetella pertussis despite limited gene content variation. J Bacteriol. 2006; (7): 2375-82
- Species- and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. J Bacteriol. 2006; (5): 1775-85
- Acquired predisposition to mycobacterial disease due to autoantibodies to IFN-gamma. J Clin Invest. 2005; (9): 2480-8
- Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica. PLoS Pathog. 2005; (4): e45
- Diversity of the human intestinal microbial flora. Science. 2005; (5728): 1635-8
- Genomewide analysis of the host response to malaria in Kenyan children. J Infect Dis. 2005; (10): 1599-611
- VCAM-1 expression on CD8+ cells correlates with enhanced anti-HIV suppressing activity. J Immunol. 2005; (3): 1574-9
- Bordetella pertussis infection of primary human monocytes alters HLA-DR expression. Infect Immun. 2004; (3): 1450-62
- Bordetella species are distinguished by patterns of substantial gene loss and host adaptation. J Bacteriol. 2004; (5): 1484-92
- Exploring the potential of variola virus infection of cynomolgus macaques as a model for human smallpox. Proc Natl Acad Sci U S A. 2004; (42): 15196-200
- Methanogenic Archaea and human periodontal disease. Proc Natl Acad Sci U S A. 2004; (16): 6176-81
- Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock. Lancet. 2004; (9404): 203-9
- The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate model. Proc Natl Acad Sci U S A. 2004; (42): 15190-5
- Analysis of conserved non-rRNA genes of Tropheryma whipplei. Syst Appl Microbiol. 2003; (1): 3-12
- Archaea and their potential role in human disease. Infect Immun. 2003; (2): 591-6
- Cultivation of Tropheryma whipplei from cerebrospinal fluid. J Infect Dis. 2003; (6): 801-8
- Images in clinical medicine. Progression of the lesion at the site of inoculation after smallpox vaccination. N Engl J Med. 2003; (5): 414
- Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci (USA). 2003; (100): 1896-1901
- Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci U S A. 2003; (4): 1896-901
- Lethal invasive cestodiasis in immunosuppressed patients. J Infect Dis. 2003; (12): 1962-6
- Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease. Appl Environ Microbiol. 2003; (3): 1687-94
- Public health. Understanding threats to scientific openness. Science. 2003; (5652): 1898
- Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet. 2003; (9358): 637-44
- Shedding light on microbial detection. N Engl J Med. 2003; (22): 2162-3
- Single-cell enumeration of an uncultivated TM7 subgroup in the human subgingival crevice. Appl Environ Microbiol. 2003; (10): 6294-8
- Broad-range bacterial detection and the analysis of unexplained death and critical illness. Emerg Infect Dis. 2002; (2): 188-94
- Genome-wide responses of a pathogenic bacterium to its host. J Clin Invest. 2002; (8): 1071-3
- Genomics and microbiology. Microbial forensics--"cross-examining pathogens". Science. 2002; (5575): 1976-9
- Human herpesvirus 8 and sarcoidosis. Clin Infect Dis. 2002; (4): 559-60
- Identification of Cardiobacterium hominis by broad-range bacterial polymerase chain reaction analysis in a case of culture-negative endocarditis. Arch Intern Med. 2002; (4): 477-9
- Mining the natural world for new pathogens. Am J Trop Med Hyg. 2002; (2): 133-4
- Molecular identification of cyanobacteria associated with stromatolites from distinct geographical locations. Astrobiology. 2002; (3): 271-80
- New technologies, human-microbe interactions, and the search for previously unrecognized pathogens. J Infect Dis. 2002: S254-8
- Role of phosphatidylinositol 3-kinase in the binding of Bordetella pertussis to human monocytes. Cell Microbiol. 2002; (12): 825-33
- Smallpox research activities: U.S. interagency collaboration, 2001. Emerg Infect Dis. 2002; (7): 743-5
- Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A. 2002; (2): 972-7
- Surveillance for unexplained deaths and critical illnesses due to possibly infectious causes, United States, 1995-1998. Emerg Infect Dis. 2002; (2): 145-53
- The human body as microbial observatory. Nat Genet. 2002; (2): 131-3
- Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions. Curr Opin Microbiol. 2001; (1): 95-101
- Does blood of healthy subjects contain bacterial ribosomal DNA? J Clin Microbiol. 2001; (5): 1956-9
- Invasion of human respiratory epithelial cells by Bordetella pertussis: possible role for a filamentous hemagglutinin Arg-Gly-Asp sequence and alpha5beta1 integrin. Microb Pathog. 2001; (5): 279-88
- Localization of Tropheryma whippelii rRNA in tissues from patients with Whipple's disease. J Infect Dis. 2001; (8): 1229-37
- Proinflammatory and proapoptotic activities associated with Bordetella pertussis filamentous hemagglutinin. Infect Immun. 2001; (4): 2650-8
- Sequence variability in the first internal transcribed spacer region within and among Cyclospora species is consistent with polyparasitism. Int J Parasitol. 2001; (13): 1475-87
- The meaning and impact of the human genome sequence for microbiology. Trends Microbiol. 2001; (5): 206-8
- Tropheryma whippelii DNA is rare in the intestinal mucosa of patients without other evidence of Whipple disease. Ann Intern Med. 2001; (2): 115-9
- Whipple's disease and Tropheryma whippelii: secrets slowly revealed. Clin Infect Dis. 2001; (3): 457-63
- Using DNA microarrays to study host-microbe interactions. Emerg Infect Dis. 2000 Sep-Oct; (5): 513-25
- Rhinosporidium seeberi: a human pathogen from a novel group of aquatic protistan parasites. Emerg Infect Dis. 2000 May-Jun; (3): 273-82
- Collaborative multidisciplinary workshop report: detection, culture, serology, and antimicrobial susceptibility testing of Chlamydia pneumoniae. J Infect Dis. 2000: S460-1
- How the host 'sees' pathogens: global gene expression responses to infection. Curr Opin Immunol. 2000; (2): 215-8
- Molecular characterization of Bordetella bronchiseptica filamentous haemagglutinin and its secretion machinery. Microbiology. 2000: 1211-21
- Organization, structure, and variability of the rRNA operon of the Whipple's disease bacterium (Tropheryma whippelii). J Bacteriol. 2000; (11): 3292-7
- The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proc Natl Acad Sci U S A. 2000; (25): 13847-52
- Absence of Kaposi's sarcoma-associated herpesvirus DNA in bacillary angiomatosis-peliosis lesions. J Infect Dis. 1999; (4): 1386-9
- Application of polymerase chain reaction to the diagnosis of infectious diseases. Clin Infect Dis. 1999; (3): 475-86; quiz 487-8
- Bacterial diversity within the human subgingival crevice. Proc Natl Acad Sci U S A. 1999; (25): 14547-52
- Molecular approaches for identification of infectious agents in Wegener's granulomatosis and other vasculitides. Curr Opin Rheumatol. 1999; (1): 11-6
- Molecular characterization of Cyclospora-like organisms from baboons. J Infect Dis. 1999; (3): 670-6
- Paraffin removal from tissue sections for digestion and PCR analysis. Biotechniques. 1999; (2): 198-200
- The search for unrecognized pathogens. Science. 1999; (5418): 1308-10
- Detection and identification of previously unrecognized microbial pathogens. Emerg Infect Dis. 1998 Jul-Sep; (3): 382-9
- Explaining the unexplained in clinical infectious diseases: looking forward. Emerg Infect Dis. 1998 Jul-Sep; (3): 395-7
- Are all Bartonella henselae strains created equal? Clin Infect Dis. 1998; (6): 1300-1
- Culture-negative endocarditis caused by Bartonella henselae. J Pediatr. 1998; (6): 1051-4
- Cyclospora. Infect Dis Clin North Am. 1998; (1): 1-12
- Diagnostic utility of the polymerase chain reaction in 2 cases of suspected Whipple disease. Arch Intern Med. 1998; (7): 801-3
- Filamentous hemagglutinin of Bordetella bronchiseptica is required for efficient establishment of tracheal colonization. Infect Immun. 1998; (12): 5921-9
- Improved amplification of microbial DNA from blood cultures by removal of the PCR inhibitor sodium polyanetholesulfonate. J Clin Microbiol. 1998; (10): 2810-6
- Infectious agents and the etiology of chronic idiopathic diseases. Curr Clin Top Infect Dis. 1998: 180-200
- Molecular and cellular microbiology: new tools of the trade. Curr Opin Microbiol. 1998; (3): 337-339
- PCR analysis of T. whippelii DNA in a case of Whipple's disease: effect of antibiotics and correlation with histology. Am J Gastroenterol. 1998; (9): 1579-82
- Radiologic features of a fatal platyhelminth (tapeworm) infection in an AIDS patient. AJR Am J Roentgenol. 1998; (1): 136-8
- The 'emergence' of Bartonella and the development of molecular discovery methods for microbial pathogens. Neth J Med. 1998; (6): 249-55
- Bordetella bronchiseptica expresses the fimbrial structural subunit gene fimA. J Bacteriol. 1997; (24): 7882-5
- Bordetella pertussis infection of human monocytes inhibits antigen-dependent CD4 T cell proliferation. J Infect Dis. 1997; (3): 678-86
- Cultivation of Whipple bacillus: the irony and the ecstasy. Lancet. 1997; (9087): 1262-3
- Diagnosis and monitoring of Whipple disease by polymerase chain reaction. Ann Intern Med. 1997; (7): 520-7
- Emerging infections and newly-recognised pathogens. Neth J Med. 1997; (5): 216-20
- Polymerase chain reaction-based detection of Tropheryma whippelii in central nervous system Whipple's disease. Ann Neurol. 1997; (1): 120-4
- The Whipple bacillus lives (ex vivo)! J Infect Dis. 1997; (3): 752-4
- Lethal infection by a previously unrecognised metazoan parasite. Lancet. 1996; (9018): 1797-801
- Limited role for PCR-based diagnosis of Whipple's disease from peripheral blood mononuclear cells. Lancet. 1996; (9019): 66-7
- Molecular phylogenetic analysis of Cyclospora, the human intestinal pathogen, suggests that it is closely related to Eimeria species. J Infect Dis. 1996; (2): 440-5
- Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates. Clin Microbiol Rev. 1996; (1): 18-33
- Brief report: uveitis caused by Tropheryma whippelii (Whipple's bacillus) N Engl J Med. 1995; (6): 363-6
- Has trench fever returned? N Engl J Med. 1995; (7): 463-4
- Bacillary angiomatosis and Rochalimaea species. Curr Clin Top Infect Dis. 1994: 205-19
- Bordetella pertussis filamentous hemagglutinin interacts with a leukocyte signal transduction complex and stimulates bacterial adherence to monocyte CR3 (CD11b/CD18). J Exp Med. 1994; (4): 1225-33
- Haemophilus parainfluenzae endocarditis: application of a molecular approach for identification of pathogenic bacterial species. Clin Infect Dis. 1994; (4): 677-83
- Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods Enzymol. 1994: 205-22
- Search for highly conserved viral and bacterial nucleic acid sequences corresponding to an etiologic agent of Kawasaki disease. Pediatr Res. 1994; (5): 567-71
- Isolation of Rochalimaea species. N Engl J Med. 1993; (19): 1422-3
- The identification of uncultured microbial pathogens. J Infect Dis. 1993; (1): 1-8
- Identification of the uncultured bacillus of Whipple's disease. N Engl J Med. 1992; (5): 293-301
- Identification of uncultured microorganisms: expanding the spectrum of characterized microbial pathogens. Infect Agents Dis. 1992; (5): 245-53
- Localization of Mycobacterium avium-intracellulare within a skin lesion of bacillary angiomatosis in a patient with AIDS. Diagn Mol Pathol. 1992; (3): 212-6
- Phylogenetic relationships among the agent of bacillary angiomatosis, Bartonella bacilliformis, and other alpha-proteobacteria. Mol Microbiol. 1992; (13): 1801-7
- The organism causing bacillary angiomatosis, peliosis hepatis, and fever and bacteremia in immunocompromised patients. N Engl J Med. 1991; (21): 1514
- Bordetella pertussis filamentous hemagglutinin: evaluation as a protective antigen and colonization factor in a mouse respiratory infection model. Infect Immun. 1990; (1): 7-16
- Genetic characterization of Bordetella pertussis filamentous haemagglutinin: a protein processed from an unusually large precursor. Mol Microbiol. 1990; (5): 787-800
- Recognition of a bacterial adhesion by an integrin: macrophage CR3 (alpha M beta 2, CD11b/CD18) binds filamentous hemagglutinin of Bordetella pertussis. Cell. 1990; (7): 1375-82
- The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N Engl J Med. 1990; (23): 1573-80
- Filamentous hemagglutinin of Bordetella pertussis: nucleotide sequence and crucial role in adherence. Proc Natl Acad Sci U S A. 1989; (8): 2637-41
- Stomatococcus mucilaginosus endocarditis in an intravenous drug abuser. J Infect Dis. 1987; (5): 1080-2
- Mechanical instability of the oxy-form of sickle haemoglobin. Nature. 1973; (5416): 437-8
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