Research Topics
| DAVID ARNOLD RELMANSummaryAffiliation: Stanford University Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Development of the human infant intestinal microbiotaChana Palmer
Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
PLoS Biol 5:e177. 2007..By the end of the first year of life, the idiosyncratic microbial ecosystems in each baby, although still distinct, had converged toward a profile characteristic of the adult gastrointestinal tract...- Microbiology in the post-genomic eraDuccio Medini
Novartis Vaccines and Diagnostics, 53100 Siena, Italy
Nat Rev Microbiol 6:419-30. 2008.... - Cross-talk in the gutJennifer E Dinalo
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 5124, USA
Genome Biol 10:203. 2009..Modulation of host signaling by the products of microbial activity in the gut may affect weight gain and fat formation... - Gene-expression patterns reveal underlying biological processes in Kawasaki diseaseStephen J Popper
Departments of Microbiology and Immunology, and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
Genome Biol 8:R261. 2007..No etiologic agent(s) has been identified, and the processes that mediate formation of coronary artery aneurysms and abatement of fever following treatment with intravenous immunoglobulin (IVIG) remain poorly understood... - The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic feverKathleen H Rubins
Department of Microbiology and Immunology, 299 Campus Dr, Stanford University School of Medicine, Stanford, California 94305, USA
Genome Biol 8:R174. 2007..Infection with Ebola virus (EBOV) causes a fulminant and often fatal hemorrhagic fever. In order to improve our understanding of EBOV pathogenesis and EBOV-host interactions, we examined the molecular features of EBOV infection in vivo... - Phase variation and microevolution at homopolymeric tracts in Bordetella pertussisEmily B Gogol
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
BMC Genomics 8:122. 2007..This limitation might be overcome by phase variation, as observed for other mucosal pathogens. One of the most common mechanisms of phase variation is reversible expansion or contraction of homopolymeric tracts (HPTs)... - New technologies, human-microbe interactions, and the search for previously unrecognized pathogensDavid A Relman
Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
J Infect Dis 186:S254-8. 2002..These challenges and the goal of understanding microbial contributions to inflammatory disease may be addressed effectively through the thoughtful integration of modern technologies and clinical insight... - Genome-wide responses of a pathogenic bacterium to its hostDavid A Relman
Departments of Microbiology and Immunology and Medicine, Stanford University School of Medicine, Stanford, California 94304, USA
J Clin Invest 110:1071-3. 2002 - 'Til death do us part': coming to terms with symbiotic relationships. ForwardDavid A Relman
Stanford University, and VA Palo Alto Health Care System, Building 101, Room B4 185, 3801 Miranda Avenue 154T, Palo Alto, California 94304, USA
Nat Rev Microbiol 6:721-4. 2008..Here, David Relman discusses the selection of articles in this Focus issue, which reflects the exciting advances in our understanding of intimate partnerships between organisms and their environments... - Stereotyped and specific gene expression programs in human innate immune responses to bacteriaJennifer C Boldrick
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 99:972-7. 2002..Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria... - Rapid quantitative profiling of complex microbial populationsChana Palmer
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Nucleic Acids Res 34:e5. 2006..This simple, rapid microarray procedure can be used to explore and systematically characterize complex microbial communities, such as those found within the human body... - Genomics and microbiology. Microbial forensics--"cross-examining pathogens"Craig A Cummings
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
Science 296:1976-9. 2002 - Analysis of conserved non-rRNA genes of Tropheryma whippleiMatthias Maiwald
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
Syst Appl Microbiol 26:3-12. 2003..These data provide the basis for a more discriminatory typing method for T. whipplei... - Genomic features of Bordetella parapertussis clades with distinct host species specificityMary M Brinig
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
Genome Biol 7:R81. 2006..The disease process in sheep is not well understood, nor are the genetic and transcriptional differences that might provide the basis for host specificity among ovine and human strains... - Methanogenic Archaea and human periodontal diseasePaul W Lepp
Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 101:6176-81. 2004..Because they are potential alternative syntrophic partners, our finding of larger Treponema populations sites without archaea provides further support for this hypothesis... - Assembly of the human intestinal microbiotaLes Dethlefsen
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
Trends Ecol Evol 21:517-23. 2006..We argue here that the unique history of each community and intrinsic temporal dynamics also influence the structure of human intestinal communities... - Diversity of the human intestinal microbial floraPaul B Eckburg
Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
Science 308:1635-8. 2005..We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease... - Genomewide analysis of the host response to malaria in Kenyan childrenMichael J Griffiths
Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK
J Infect Dis 191:1599-611. 2005..The delineation of subjects on the basis of patterns of gene expression provides a molecular perspective of the host response to malaria and further functional insight into the underlying processes of pathogenesis... - Molecular analysis of the bacterial microbiota in the human stomachElisabeth M Bik
Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild Science Building, 299 Campus Drive, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 103:732-7. 2006..The gastric microbiota may play important, as-yet-undiscovered roles in human health and disease... - Growth phase- and nutrient limitation-associated transcript abundance regulation in Bordetella pertussisMari M Nakamura
Department of Pediatrics/Infectious Diseases, Stanford University, Stanford, California, USA
Infect Immun 74:5537-48. 2006..Growth phase and nutrient availability may serve as cues by which B. pertussis regulates virulence according to the stage of infection or the location within the human airway... - Shedding light on microbial detectionDavid A Relman
Stanford University Medical Center, Stanford University, Stanford, Calif, USA
N Engl J Med 349:2162-3. 2003 - SmashCell: a software framework for the analysis of single-cell amplified genome sequencesEoghan D Harrington
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
Bioinformatics 26:2979-80. 2010..It also manages the data created by these analyses and provides visualization methods for rapid analysis of the results... - Gene transcript abundance profiles distinguish Kawasaki disease from adenovirus infectionStephen J Popper
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
J Infect Dis 200:657-66. 2009..As a result, diagnosis and critical therapies may be delayed... - Prevalence of bacteria of division TM7 in human subgingival plaque and their association with diseaseMary M Brinig
Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
Appl Environ Microbiol 69:1687-94. 2003..These data suggest that this phylotype, and the TM7 bacterial division in general, may play a role in the multifactorial process leading to periodontitis... - Bacterial diversity in the oral cavity of 10 healthy individualsElisabeth M Bik
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
ISME J 4:962-74. 2010.... - The role of microbes in Crohn's diseasePaul B Eckburg
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
Clin Infect Dis 44:256-62. 2007..We review how microbes may participate in the pathogenesis of CD and how they may inappropriately activate the mucosal immune system in genetically predisposed individuals... - Single-cell enumeration of an uncultivated TM7 subgroup in the human subgingival creviceCleber C Ouverney
Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
Appl Environ Microbiol 69:6294-8. 2003..In addition, IO25 bacterial cells from periodontitis site samples were more abundant and fourfold longer than IO25 cells from healthy site samples... - Significant gene order and expression differences in Bordetella pertussis despite limited gene content variationMary M Brinig
Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305, USA
J Bacteriol 188:2375-82. 2006..These findings have broad implications for host adaptation by microbial pathogens... - The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencingLes Dethlefsen
Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
PLoS Biol 6:e280. 2008..The rapid return to the pretreatment community composition is indicative of factors promoting community resilience, the nature of which deserves future investigation... - Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigationDaniel B Digiulio
Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
PLoS ONE 3:e3056. 2008..However, molecular studies that define the diversity and abundance of microbes invading the amniotic cavity, and evaluate their clinical significance within a causal framework, are lacking... - Individuality and variation in gene expression patterns in human bloodAdeline R Whitney
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 100:1896-901. 2003..These data help to define human individuality and provide a database with which disease-associated gene expression patterns can be compared... - Broad-range bacterial detection and the analysis of unexplained death and critical illnessSimo Nikkari
Stanford University School of Medicine, California, USA
Emerg Infect Dis 8:188-94. 2002..In conclusion, known bacterial pathogens cause some critical illnesses and deaths that fail to be explained with traditional diagnostic methods... - Molecular identification of cyanobacteria associated with stromatolites from distinct geographical locationsBrett A Neilan
Departments of Geological and Environmental Sciences and Microbiology and Immunology, Stanford University, Stanford, California, USA
Astrobiology 2:271-80. 2002..The data indicate that internal core samples of a stromatolite at least 10 years old can be successfully analyzed by DNA-based methods to identify preserved cyanobacteria... - The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate modelKathleen H Rubins
Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 101:15190-5. 2004..These results provide a detailed picture of the host transcriptional response during smallpox infection, and may help guide the development of diagnostic, therapeutic, and prophylactic strategies... - Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouthYann Marcy
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 104:11889-94. 2007..This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community... - Cultivation of Tropheryma whipplei from cerebrospinal fluidMatthias Maiwald
Department of Microbiology, Stanford University School of Medicine, Stanford, California, USA
J Infect Dis 188:801-8. 2003..This first isolation of T. whipplei from CSF provides clear evidence of viable bacteria in the central nervous system in individuals with WD, even after prolonged antibiotic therapy... - Early days: genomics and human responses to infectionMinghsun Liu
Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Grant S-169, Stanford, CA 94305, USA
Curr Opin Microbiol 9:312-9. 2006..The resolution of these problems should lead to a better understanding of the dialogue between the host and pathogen... - Building a better virus trapClara Davis Long
Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA 94305, USA
Trends Biotechnol 25:535-8. 2007..Although there will be technical hurdles to overcome, this concept might lead to benefits for both health and industry... - Bordetella pertussis infection of primary human monocytes alters HLA-DR expressionJennifer A Shumilla
Department of Pediatrics. Departments of Microbiology and Immunology and Medicine, Stanford University School of Medicine, Stanford, California, USA
Infect Immun 72:1450-62. 2004..These data demonstrate that B. pertussis utilizes several mechanisms to modulate HLA-DR expression... - Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiotaTrevor D Lawley
Department of Microbiology and Immunology, 299 Campus Drive, Stanford University, Stanford, CA 94305, USA
Infect Immun 76:403-16. 2008..This novel model should facilitate the study of host, pathogen, and intestinal microbiota factors that contribute to infectious disease transmission... - Archaea and their potential role in human diseasePaul B Eckburg
Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305, USA
Infect Immun 71:591-6. 2003 - Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomesKathleen H Rubins
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
PLoS ONE 3:e2628. 2008..Poxviruses engage in a complex and intricate dialogue with host cells as part of their strategy for replication. However, relatively little molecular detail is available with which to understand the mechanisms behind this dialogue... - Microbial threat lists: obstacles in the quest for biosecurity?Arturo Casadevall
Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York 10461, USA
Nat Rev Microbiol 8:149-54. 2010.... - Prevalence and diversity of microbes in the amniotic fluid, the fetal inflammatory response, and pregnancy outcome in women with preterm pre-labor rupture of membranesDaniel B Digiulio
Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
Am J Reprod Immunol 64:38-57. 2010..The role played by microbial invasion of the amniotic cavity (MIAC) in preterm pre-labor rupture of membranes (pPROM) is inadequately characterized, in part because of reliance on cultivation-based methods... - 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 NanoSIMSSebastian Behrens
Department of Chemical Engineering and of Civil, Stanford University, Stanford, California 94305 5429, USA
Appl Environ Microbiol 74:3143-50. 2008..Our novel approach will facilitate further studies of the ecophysiology of known and uncultured microorganisms in complex environments and communities... - The importance of individuals and scale: moving towards single cell microbiologyLes Dethlefsen
Department of Microbiology, Stanford University, Stanford, CA, USA
Environ Microbiol 9:8-10. 2007 - An ecological and evolutionary perspective on human-microbe mutualism and diseaseLes Dethlefsen
Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
Nature 449:811-8. 2007..In this way, looking to ecological and evolutionary principles might provide new strategies for restoring and maintaining human health... - Metagenomic analysis of the human distal gut microbiomeSteven R Gill
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 312:1355-9. 2006..Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes... - Patterns of host genome-wide gene transcript abundance in the peripheral blood of patients with acute dengue hemorrhagic feverCameron P Simmons
Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
J Infect Dis 195:1097-107. 2007..To our knowledge, these data provide the first snapshot of gene-expression patterns in peripheral blood during acute dengue and suggest that DSS is associated with attenuation of selected aspects of the innate host response... - Mining the natural world for new pathogensDavid A Relman
Am J Trop Med Hyg 67:133-4. 2002 - Identification of Cardiobacterium hominis by broad-range bacterial polymerase chain reaction analysis in a case of culture-negative endocarditisSimo Nikkari
Palo Alto Vetrans Affairs Health Care System, Calif, USA
Arch Intern Med 162:477-9. 2002..This case demonstrates the usefulness of both the Steiner stain and broad-range direct molecular amplification as supplemental diagnostic tools in identification of otherwise unexplained infections... - Exploring the potential of variola virus infection of cynomolgus macaques as a model for human smallpoxPeter B Jahrling
Headquarters, U S Army Research Institute of Infectious Diseases, Frederick, MD 21702, USA
Proc Natl Acad Sci U S A 101:15196-200. 2004..quot; A more precise understanding of disease pathogenesis should provide targets for therapeutic intervention, to be used alone or in combination with inhibitors of variola virus replication... - Lethal invasive cestodiasis in immunosuppressed patientsPeter D Olson
Parasitic Worms Division, Department of Zoology, Natural History Museum, London, United Kingdom
J Infect Dis 187:1962-6. 2003..A prior report of this case nearly 30 years ago, based on tissue examination, had suggested that the parasite was a sparganum... - Role of phosphatidylinositol 3-kinase in the binding of Bordetella pertussis to human monocytesYoshio Ishibashi
Department of Immunobiology, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo 204 8588, Japan
Cell Microbiol 4:825-33. 2002..These results suggest that PI3-K and a tyrosine phosphorylated 60 kDa protein may be involved in this biologically important integrin signalling pathway... - Human herpesvirus 8 and sarcoidosisDavid N Fredricks
Clin Infect Dis 34:559-60. 2002 - Role of interleukin 6 in myocardial dysfunction of meningococcal septic shockNazima Pathan
Department of Paediatrics, Imperial College of Science, Technology and Medicine, W2 1PG, London, UK
Lancet 363:203-9. 2004..During the sepsis-induced inflammatory process, specific factors are released that depress myocardial contractile function. We aimed to identify these mediators of myocardial depression in meningococcal septic shock... - Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whippleiStephen D Bentley
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Lancet 361:637-44. 2003.... - Learning to appreciate our differencesDavid A Relman
J Infect Dis 198:4-5. 2008
Research Grants
- Optimization of a microfluidic device for single bacterial cell genomicsDavid Relman; Fiscal Year: 2009....
- Crohn's Disease: Microflora Analysis and Host ResponseDavid Relman; Fiscal Year: 2005..This combination of approaches offers opportunities for characterizing Crohn?s disease, and for examining the complex interactions of human host and microbial flora during states of health and disease. ..
- Host responses to smallpox and monkeypoxDavid Relman; Fiscal Year: 2006....
- Analytical Tools for Comparative Microbial GenomicsDavid Relman; Fiscal Year: 2006..In addition, the classification and phylogeny program will be offered as an on-line tool, and a Bordetella genome and CGH database will be built, maintained, and served to the community on-line. ..
- APPLIED GENOMICS IN INFECTIOUS DISEASESDavid Relman; Fiscal Year: 2007..Trainees are expected to graduate to academic faculty appointments or to research-oriented positions in federal government, public health or the biotechnology commercial sector. ..
- Optimization of a microfluidic device for single bacterial cell genomicsDAVID ARNOLD RELMAN; Fiscal Year: 2010....
- Bordetella Response to Host Cues and Cell SignalsDavid Relman; Fiscal Year: 2004..pertussis virulence mechanisms and physiological adaptations, as well as the complex interplay between this pathogen and the human host, which could, in turn, lead to the development of novel pertussis vaccines and therapeutics. ..
- MOLECULAR ANALYSIS OF SUBGINGIVAL MICROBIAL DIVERSITYDavid Relman; Fiscal Year: 2003....
- BORDETELLA PERTUSSIS AND MONOCYTE INTEGRIN RECEPTORSDavid Relman; Fiscal Year: 2001..3) To examine the effect of B. pertussis binding on the topological distribution of monocyte integrin receptors and associated signaling molecules. 4) To examine B. pertussis inhibition of antigen-dependent T- cell proliferation. ..
- Optimization of a microfluidic device for single bacterial cell genomicsDavid Relman; Fiscal Year: 2009....