Richard A Lempicki

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, SAIC Frederick, Inc, National Cancer Institute at Frederick, MD 21702, USA
    Nucleic Acids Res 35:W169-75. 2007
  2. pmc Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 37:1-13. 2009
  3. pmc Cytokine/chemokine patterns connect host and viral characteristics with clinics during chronic hepatitis C
    Antonios Katsounas
    Department of Gastroenterology and Hepatology, University Hospital of Essen, Germany
    Eur J Med Res 17:9. 2012
  4. pmc Retinoic acid and liver X receptor agonist synergistically inhibit HIV infection in CD4+ T cells by up-regulating ABCA1-mediated cholesterol efflux
    Hong Jiang
    Laboratory of Molecular Cell Biology, SAIC Frederick, Inc, Frederick National Laboratory, Frederick, MD 21702, USA
    Lipids Health Dis 11:69. 2012
  5. pmc The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Genome Biol 8:R183. 2007
  6. pmc Gene duplications in prokaryotes can be associated with environmental adaptation
    Marit S Bratlie
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    BMC Genomics 11:588. 2010
  7. pmc Pre-gastrula expression of zebrafish extraembryonic genes
    Sung Kook Hong
    Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Dev Biol 10:42. 2010
  8. pmc DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
    Brad T Sherman
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    BMC Bioinformatics 8:426. 2007
  9. doi request reprint Extracting biological meaning from large gene lists with DAVID
    Da Wei Huang
    National Cancer Institute at Frederick, Frederick, Maryland, USA
    Curr Protoc Bioinformatics . 2009
  10. pmc Identifying biological themes within lists of genes with EASE
    Douglas A Hosack
    Laboratory of Immunopathogenesis and Bioinformatics, PO Box B, SAIC Frederick, Inc, Frederick, MD 21702, USA
    Genome Biol 4:R70. 2003

Collaborators

Detail Information

Publications29

  1. pmc DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, SAIC Frederick, Inc, National Cancer Institute at Frederick, MD 21702, USA
    Nucleic Acids Res 35:W169-75. 2007
    ..With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists...
  2. pmc Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 37:1-13. 2009
    ....
  3. pmc Cytokine/chemokine patterns connect host and viral characteristics with clinics during chronic hepatitis C
    Antonios Katsounas
    Department of Gastroenterology and Hepatology, University Hospital of Essen, Germany
    Eur J Med Res 17:9. 2012
    ....
  4. pmc Retinoic acid and liver X receptor agonist synergistically inhibit HIV infection in CD4+ T cells by up-regulating ABCA1-mediated cholesterol efflux
    Hong Jiang
    Laboratory of Molecular Cell Biology, SAIC Frederick, Inc, Frederick National Laboratory, Frederick, MD 21702, USA
    Lipids Health Dis 11:69. 2012
    ..In the present study, we aim to test the effect of all trans retinoic acid (ATRA) on ABCA1 expression in human CD4+ T cells and the involvement of cholesterol in ATRA mediated anti-HIV effect...
  5. pmc The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Genome Biol 8:R183. 2007
    ..It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretation of gene lists in a network context...
  6. pmc Gene duplications in prokaryotes can be associated with environmental adaptation
    Marit S Bratlie
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    BMC Genomics 11:588. 2010
    ..The aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relating gene properties to life style of the corresponding prokaryotes...
  7. pmc Pre-gastrula expression of zebrafish extraembryonic genes
    Sung Kook Hong
    Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Dev Biol 10:42. 2010
    ..The yolk syncytial layer initially forms below the margin, in a domain called the external yolk syncytial layer (E-YSL)...
  8. pmc DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
    Brad T Sherman
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    BMC Bioinformatics 8:426. 2007
    ..Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis...
  9. doi request reprint Extracting biological meaning from large gene lists with DAVID
    Da Wei Huang
    National Cancer Institute at Frederick, Frederick, Maryland, USA
    Curr Protoc Bioinformatics . 2009
    ..This unit will describe step-by-step procedures to use DAVID tools, as well as a brief rationale and key parameters in the DAVID analysis...
  10. pmc Identifying biological themes within lists of genes with EASE
    Douglas A Hosack
    Laboratory of Immunopathogenesis and Bioinformatics, PO Box B, SAIC Frederick, Inc, Frederick, MD 21702, USA
    Genome Biol 4:R70. 2003
    ..EASE is a powerful tool for rapidly converting the results of functional genomics studies from 'genes' to 'themes'...
  11. doi request reprint Interleukin-27 induces interferon-inducible genes: analysis of gene expression profiles using Affymetrix microarray and DAVID
    Tomozumi Imamichi
    Laboratory of Human Retrovirology, Clinical Services Programs CSP, Applied Developmental Directorate ADD, Science Applications International Corporation SAIC Frederick, Inc, National Cancer Institute NCI Frederick, Frederick, MD 21702, USA
    Methods Mol Biol 820:25-53. 2012
    ..IL-27 significantly induces IFN-inducible genes including antiviral genes in macrophages as does IFN-α, suggesting that IL-27 inhibits HIV replication in macrophages via a mechanism similar to that of IFN-α...
  12. pmc Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties
    Sanjay Swaminathan
    Applied and Developmental Research Directorate, Science Application International Corporation SAIC Frederick, Inc, Frederick National Laboratory for Cancer Research FNLCR, Frederick, MD 21702, USA
    Biochem Biophys Res Commun 434:228-34. 2013
    ....
  13. pmc Interleukin-2 inhibits HIV-1 replication in some human T cell lymphotrophic virus-1-infected cell lines via the induction and incorporation of APOBEC3G into the virion
    Raphael M Oguariri
    Laboratory of Human Retrovirology, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
    J Biol Chem 288:17812-22. 2013
    ..These findings demonstrate a novel role for IL-2 in regulating production of infectious HIV-1 virions in HTLV-1-infected cells through the induction of APOBEC3G...
  14. pmc DAVID-WS: a stateful web service to facilitate gene/protein list analysis
    Xiaoli Jiao
    Laboratory of Immunopathogenesis and Bioinformatics, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Bioinformatics 28:1805-6. 2012
    ..DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions...
  15. pmc IL-27 inhibits HIV-1 infection in human macrophages by down-regulating host factor SPTBN1 during monocyte to macrophage differentiation
    Lue Dai
    Applied and Developmental Directorate, Science Applications International Corporation Frederick, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
    J Exp Med 210:517-34. 2013
    ....
  16. doi request reprint Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick Inc, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    Nat Protoc 4:44-57. 2009
    ..By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies...
  17. ncbi request reprint IL-27, a novel anti-HIV cytokine, activates multiple interferon-inducible genes in macrophages
    Tomozumi Imamichi
    Laboratory of Human Retrovirology, National Cancer Institute at Frederick, Frederick, Maryland, USA
    AIDS 22:39-45. 2008
    ..To elucidate the mechanism of the antiviral activity, we compared the activity and the gene expression profile of IL-27-treated cells with that of IFN-alpha-treated cells...
  18. pmc Interleukin-27 is a potent inhibitor of cis HIV-1 replication in monocyte-derived dendritic cells via a type I interferon-independent pathway
    Qian Chen
    Applied and Developmental Research Directorate ADD, Science Application International Corporation SAIC Frederick, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
    PLoS ONE 8:e59194. 2013
    ....
  19. pdf DAVID: Database for Annotation, Visualization, and Integrated Discovery
    Glynn Dennis
    Science Applications International Corporation Frederick, Clinical Services Program, Laboratory of Immunopathogenesis and Bioinformatics, National Cancer Institute at Frederick, MD 21702, USA
    Genome Biol 4:P3. 2003
    ..A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information...
  20. pmc LIM kinase 1 - dependent cofilin 1 pathway and actin dynamics mediate nuclear retinoid receptor function in T lymphocytes
    Mohammad Ishaq
    Laboratory of Molecular Cell Biology, SAIC Frederick, National Cancer Institute, Frederick, MD 21702, USA
    BMC Mol Biol 12:41. 2011
    ..Here we have investigated the role of actin dynamics and the effect of actin cytoskeleton modifying agents on retinoid receptor-mediated transactivation...
  21. pmc Gene expression patterns induced by HPV-16 L1 virus-like particles in leukocytes from vaccine recipients
    Alfonso J Garcia-Pineres
    HPV Immunology Laboratory, Science Applications International Corporation Frederick National Cancer Institute Frederick, Frederick, MD 21702, USA
    J Immunol 182:1706-29. 2009
    ..Further studies are needed to identify gene expression signatures of immunogenicity and long-term protection with potential utility in prediction of long-term HPV vaccination outcomes in clinical trials...
  22. pmc Cutting edge: Ku70 is a novel cytosolic DNA sensor that induces type III rather than type I IFN
    Xing Zhang
    Applied and Developmental Research Directorate, Science Applications International Corporation Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    J Immunol 186:4541-5. 2011
    ..Thus, to our knowledge, we show for the first time that Ku70 mediates type III IFN induction by DNA...
  23. pmc Differential effects of HIV viral load and CD4 count on proliferation of naive and memory CD4 and CD8 T lymphocytes
    Sharat Srinivasula
    Biostatistics Research Branch, SAIC Frederick Inc, NCI Frederick, Frederick, MD, USA
    Blood 118:262-70. 2011
    ..Microbial translocation does not appear to play an important role in this proliferation...
  24. pmc Differential gene and microRNA expression between etoposide resistant and etoposide sensitive MCF7 breast cancer cell lines
    Karobi Moitra
    Laboratory of Experimental Immunology, Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
    PLoS ONE 7:e45268. 2012
    ..In an exploratory study we have found several possible indicators of etoposide resistance operating in MCF7VP cells, including up-regulation of ABC transporter genes, modulation of miRNA, and alteration in copy numbers of genes...
  25. pmc Actinomycin D induces high-level resistance to thymidine analogs in replication of human immunodeficiency virus type 1 by interfering with host cell thymidine kinase expression
    Tomozumi Imamichi
    Laboratory of Molecular Retrovirology, Clinical Services Program, Science Applications International Corporation Frederick Inc, National Cancer Institute Frederick, Maryland 21702, USA
    J Virol 77:1011-20. 2003
    ..These results suggest that administration of combination drugs to HIV-1-infected patients may induce resistance to antiretroviral compounds via a modification of cellular factors...
  26. ncbi request reprint Zap70 signaling pathway mediates glucocorticoid receptor-dependent transcriptional activation: role in the regulation of annexin 1 expression in T cells
    Mohammad Ishaq
    Laboratory of Molecular Cell Biology, SAIC Frederick, National Cancer Institute, Frederick, MD 21702, USA
    J Immunol 179:3851-8. 2007
    ..To summarize, our data demonstrate an important role for Zap70 signaling in GR-mediated transactivation in T lymphocytes and also point out a crucial role of this kinase in maintaining normal ANXA1 levels in these cells...
  27. ncbi request reprint Retinoic acid-induced downmodulation of telomerase activity in human cancer cells
    Xiaodong Xiao
    Protein Interactions Group, Laboratory of Experimental and Computational Biology, NCI Frederick, NIH, Bldg 469, Rm 139, P O Box B, Miller Drive, Frederick, MD 21702 1201, USA
    Exp Mol Pathol 79:108-17. 2005
    ..The complex mechanism through which telomerase activity is controlled during differentiation and cancer transformation is also reflected...
  28. pmc Increased peripheral expansion of naive CD4+ T cells in vivo after IL-2 treatment of patients with HIV infection
    Ven Natarajan
    Science Applications International Corporation Frederick, Inc, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 99:10712-7. 2002
    ....