Research Topics
| I T PaulsenSummaryAffiliation: The Institute for Genomic Research Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristicDaniel H Haft
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville MD 20850, USA
BMC Biol 4:29. 2006..Detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families...
Microbial genome analyses: comparative transport capabilities in eighteen prokaryotesI T Paulsen
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
J Mol Biol 301:75-100. 2000..Archaea and spirochetes exhibit fewer proteins with multiple transmembrane segments and fewer net transporters than most bacteria. These results provide insight into the relevance of transport to the overall physiology of prokaryotes...- Multidrug efflux pumps and resistance: regulation and evolutionIan T Paulsen
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Curr Opin Microbiol 6:446-51. 2003..This structural data provides the context for understanding other questions about the evolution of multidrug transporters and their natural physiological roles... - Comparative genomics of microbial drug efflux systemsI T Paulsen
The Institute for Genomic Research, Rockville, MD 20850, USA
J Mol Microbiol Biotechnol 3:145-50. 2001..Microarray and gene knockout studies to date have suggested that predicted drug efflux genes often appear to be a) non-essential and b) expressed at detectable levels under standard laboratory growth conditions... - Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalisI T Paulsen
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 299:2071-4. 2003..The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci... - The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbiontsIan T Paulsen
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 99:13148-53. 2002..A limited repertoire of genes homologous to known bacterial virulence factors were identified... - Complete genome sequence of a virulent isolate of Streptococcus pneumoniaeH Tettelin
The Institute for Genomic Research (TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 293:498-506. 2001..Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity... - Genome of Geobacter sulfurreducens: metal reduction in subsurface environmentsB A Methé
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 302:1967-9. 2003..As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity... - Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the ChlamydiaceaeT D Read
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 31:2134-47. 2003..pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens... - Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elementsMartin Wu
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Biol 2:E69. 2004..With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections... - Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensisJohn F Heidelberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nat Biotechnol 20:1118-23. 2002.... - Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440K E Nelson
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Environ Microbiol 4:799-808. 2002..Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production... - Complete genome sequence of Caulobacter crescentusW C Nierman
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 98:4136-41. 2001.... - Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiaeHerve Tettelin
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 99:12391-6. 2002..agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms... - Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5Ian T Paulsen
The Institute for Genomic Research, Rockville, Maryland, USA
Nat Biotechnol 23:873-8. 2005..In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5... - Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strainSteven R Gill
Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
J Bacteriol 187:2426-38. 2005..Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis... - Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentusJonathan H Badger
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
J Bacteriol 188:6841-50. 2006..neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging... - Genome sequence of Aedes aegypti, a major arbovirus vectorVishvanath Nene
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 316:1718-23. 2007..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species... - Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomesRekha 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.... - The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris HildenboroughJohn F Heidelberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nat Biotechnol 22:554-9. 2004.... - Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this speciesKaren E Nelson
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 32:2386-95. 2004..Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs... - Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)Naomi Ward
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Biol 2:e303. 2004..We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential... - Large-scale comparative genomic analyses of cytoplasmic membrane transport systems in prokaryotesQinghu Ren
The Institute for Genomic Research, Rockville, MD 20850, USA
J Mol Microbiol Biotechnol 12:165-79. 2007..These findings strongly suggest the correlation of transporter profiles to both evolutionary history and the overall physiology and lifestyles of the organisms... - Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytesMalcolm J Gardner
Institute for Genomic Research TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 309:134-7. 2005..Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated... - Genome sequence of the human malaria parasite Plasmodium falciparumMalcolm J Gardner
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nature 419:498-511. 2002..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria... - The value of complete microbial genome sequencing (you get what you pay for)Claire M Fraser
The Institute for Genomic Research, Rockville, Maryland 20850, USA
J Bacteriol 184:6403-5; discusion 6405. 2002 - The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacteriumJonathan A Eisen
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 99:9509-14. 2002..tepidum and many Archaeal species... - The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteriaTimothy D Read
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nature 423:81-6. 2003..The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis... - Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83Karen E Nelson
The Institute for Genomic Research, Rockville, Maryland 20850, USA
J Bacteriol 185:5591-601. 2003..gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease... - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000C Robin Buell
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 100:10181-6. 2003..Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function... - TransportDB: a relational database of cellular membrane transport systemsQinghu Ren
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 32:D284-8. 2004..TransportDB will be regularly updated with data obtained from newly sequenced genomes... - TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channelsQinghu Ren
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 35:D274-9. 2007..TransportDB has now been in existence for over 10 years and continues to be regularly updated with new evidence and data from newly sequenced genomes, as well as having new features added periodically... - Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotesQinghu Ren
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Comput Biol 1:e27. 2005.... - Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosusGarry S A Myers
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nat Biotechnol 25:569-75. 2007..Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine... - Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringensGarry S A Myers
The Institute for Genomic Research, Rockville, Maryland 20850, USA
Genome Res 16:1031-40. 2006.... - Complete genome sequence of the Q-fever pathogen Coxiella burnetiiRekha Seshadri
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 100:5455-60. 2003..burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation... - Transport capabilities encoded within the Bacillus subtilis genomeMilton H Saier
Department of Biology University of California at San Diego La Jolla, 92093 0116, USA
J Mol Microbiol Biotechnol 4:37-67. 2002..The recognized transporters fall into 58 families including 4 channel types, 42 secondary carrier types, 3 primary carrier types, 4 PTS-types and 5 unknown types... - Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environmentBrian Palenik
Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA
Proc Natl Acad Sci U S A 103:13555-9. 2006..In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments... - Regulation of carbon utilization by sulfur availability in Escherichia coli and Salmonella typhimuriumJohn A Quan
Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
Microbiology 148:123-31. 2002..These observations may have physiological significance allowing carbon and sulfur regulon coordination during the growth of enteric bacteria in response to nutrient availability... - The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2Kathleen M Scott
Biology Department, University of South Florida, Tampa, Florida, United States of America
PLoS Biol 4:e383. 2006..The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome... - Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificansStefan M Sievert
Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA
Appl Environ Microbiol 74:1145-56. 2008..An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress... - Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoaKelly A Brayton
Program in Genomics, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
PLoS Pathog 3:1401-13. 2007..The genome sequence provides a greater understanding of B. bovis metabolism and potential avenues for drug therapies and vaccine development... - The Chlamydomonas genome reveals the evolution of key animal and plant functionsSabeeha S Merchant
Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
Science 318:245-50. 2007.... - The EcoCyc DatabasePeter D Karp
Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue EK207, Menlo Park, CA 94025, USA
Nucleic Acids Res 30:56-8. 2002..EcoCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc is available at http://ecocyc.org/... - Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteriaAlexis Dufresne
Université Paris 6 and CNRS, UMR 7144, Station Biologique, 29682 Roscoff, France
Genome Biol 9:R90. 2008..Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group... - Microbial drug efflux proteins of the major facilitator superfamilyMassoud Saidijam
Astbury Centre for Structural Molecular Biology, School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, UK
Curr Drug Targets 7:793-811. 2006..This strategy is an important step towards reproducible production of transport proteins for the screening of drug binding and for optimisation of crystallisation conditions to enable subsequent structure determination... - Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environmentMary Ann Moran
Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA
Nature 432:910-3. 2004..This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean... - EcoCyc: a comprehensive database resource for Escherichia coliIngrid M Keseler
SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
Nucleic Acids Res 33:D334-7. 2005.... - High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genesDaniel A Johnson
J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS Genet 4:e1000211. 2008..Thus, rapid phenotype identification assays are an invaluable tool for confirming and extending bioinformatic predictions... - Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondiiAsis Khan
Department of Molecular Microbiology, Center for Infectious Diseases, Washington University School of Medicine St Louis, MO 63110, USA
Nucleic Acids Res 33:2980-92. 2005..The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies... - Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102Zhengchang Su
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Nucleic Acids Res 34:1050-65. 2006..Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions... - Regulation of type IV fimbrial biogenesis in Dichelobacter nodosusDane Parker
Australian Research Council Centre of Excellence for Structrral and Functional Microbial Genomics and Victorian Bioinformatics Consortium, Department of Microbiology, Monash University, Victoria 3800, Australia
J Bacteriol 188:4801-11. 2006..nodosus to cause ovine footrot is regulated, as we have shown that the biogenesis of type IV fimbriae in D. nodosus is regulated by a sigma 54-dependent PilR/S system that also indirectly controls protease secretion... - ToxoDB: accessing the Toxoplasma gondii genomeJessica C Kissinger
Department of Genetics Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602 2606, USA
Nucleic Acids Res 31:234-6. 2003..the database will provide an integrated data analysis platform facilitating user-defined queries across the different data types... - A high efficiency cloning and expression system for proteomic analysisXuan Z Ding
Department of Bacterial Diseases, Division of Communicable Diseases and Immunology, Walter Reed Army Institute of Reseach, Silver Spring, MD 20910 7500, USA
Proteomics 6:4038-46. 2006..This method will allow selection of new reagents for diagnosis of brucellosis and development of vaccine against Brucella, an important zoonotic disease and biothreat agent... - Identification of a Dichelobacter nodosus ferric uptake regulator and determination of its regulatory targetsDane Parker
ARC Centre for Structural and Functional Microbial Genomics and Victorian Bioinformatics Consortium, Department of Microbiology, Monash University, Victoria, Australia
J Bacteriol 187:366-75. 2005..Down-regulated proteins included a putative manganese superoxide dismutase and ornithine decarboxylase. Based on these data, it is suggested that in D. nodosus the Fur protein functions as a regulator of iron and oxidative metabolism... - Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophageEric S Miller
Department of Microbiology, North Carolina State University, Raleigh, NC 27695 7615, USA
J Bacteriol 185:5220-33. 2003..Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved... - Cloning, expression, and purification of Brucella suis outer membrane proteinsXuan Z Ding
Division of CD and I, Department of Bacterial Diseases, Walter Reed Army Institute of Research, Washington, DC, USA
Protein Expr Purif 40:134-41. 2005..The results suggested that recombinant B. suis OMPs were successfully cloned, expressed and purified. Some of the expressed OMPs showed high binding activity with immunized rabbit antiserum...
Research Grants
- Genome Sequencing of Toxoplasma gondiiIan Paulsen; Fiscal Year: 2002..gondii research community is solidly behind this effort, and the history of this group (in supporting and successfully exploiting the T. gondii EST project, for example) bodes well for successful utilization of the genomic sequence...