Division of Infection and Immunity



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  1. Roe JK, Thomas N, Gil E, Best K, Tsaliki E, Morris-Jones S, Stafford S, Simpson N, Witt KD, Chain B, Miller RF, Martineau A, Noursadeghi M. Blood transcriptomic diagnosis of pulmonary and extrapulmonary tuberculosis. JCI Insight. 2016 Oct 6;1(16):e87238. PubMed PMID: 27734027; PubMed Central PMCID:PMC5053151.
  2. Kundu R, Theodoraki A, Haas CT, Zhang Y, Chain B, Kriston-Vizi J, Noursadeghi M, Khoo B. Cell-type-specific modulation of innate immune signalling by vitamin D in human mononuclear phagocytes. Immunology. 2017 Jan;150(1):55-63. doi:10.1111/imm.12669. Epub 2016 Oct 3. PubMed PMID: 27608289; PubMed Central PMCID: PMC5167305.
  3. Inkeles MS, Teles RM, Pouldar D, Andrade PR, Madigan CA, Lopez D, Ambrose M, Noursadeghi M, Sarno EN, Rea TH, Ochoa MT, Iruela-Arispe ML, Swindell WR, Ottenhoff TH, Geluk A, Bloom BR, Pellegrini M, Modlin RL. Cell-type deconvolution with immune pathways identifies gene networks of host defense and immunopathology in leprosy. JCI Insight. 2016 Sep 22;1(15):e88843. PubMed PMID: 27699251; PubMed Central PMCID: PMC5033757.
  4. Bell LC, Pollara G, Pascoe M, Tomlinson GS, Lehloenya RJ, Roe J, Meldau R, Miller RF, Ramsay A, Chain BM, Dheda K, Noursadeghi M. In Vivo Molecular Dissection of the Effects of HIV-1 in Active Tuberculosis. PLoS Pathog. 2016 Mar 17;12(3):e1005469. doi: 10.1371/journal.ppat.1005469. eCollection 2016 Mar. PubMed PMID: 26986567; PubMed Central PMCID: PMC4795555.
  5. Tomlinson GS, Thomas N, Chain BM, Best K, Simpson N, Hardavella G, Brown J, Bhowmik A, Navani N, Janes SM, Miller RF, Noursadeghi M. Transcriptional Profiling of Endobronchial Ultrasound-Guided Lymph Node Samples Aids Diagnosis of Mediastinal Lymphadenopathy. Chest. 2016 Feb;149(2):535-544. doi:10.1378/chest.15-0647. Epub 2016 Jan 12. PubMed PMID: 26270185; PubMed Central PMCID: PMC4740456.
  6. Heather JM, Best K, Oakes T, Gray ER, Roe JK, Thomas N, Friedman N, Noursadeghi M, Chain B. Dynamic Perturbations of the T-Cell Receptor Repertoire in Chronic HIV Infection and following Antiretroviral Therapy. Front Immunol. 2016 Jan 11;6:644. doi: 10.3389/fimmu.2015.00644. eCollection 2015. PubMed PMID: 26793190; PubMed Central PMCID: PMC4707277.
  7. Best K, Oakes T, Heather JM, Shawe-Taylor J, Chain B. Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding. Sci Rep. 2015 Oct 13;5:14629. doi: 10.1038/srep14629. PubMed PMID: 26459131; PubMed Central PMCID: PMC4602216.
  8. Lapp T, Zaher SS, Haas CT, Becker DL, Thrasivoulou C, Chain BM, Larkin DF, Noursadeghi M. Identification of Therapeutic Targets of Inflammatory Monocyte Recruitment to Modulate the Allogeneic Injury to Donor Cornea. Invest Ophthalmol Vis Sci. 2015 Nov;56(12):7250-9. doi: 10.1167/iovs.15-16941. PubMed PMID: 26544793.
  9. Best K, Chain B, Watkins C. Immune Tolerance Maintained by Cooperative Interactions between T Cells and Antigen Presenting Cells Shapes a Diverse TCR Repertoire. Front Immunol. 2015 Aug 7;6:360. doi: 10.3389/fimmu.2015.00360. eCollection 2015. PubMed PMID: 26300880; PubMed Central PMCID: PMC4528093.
  10. Chain B, Arnold J, Akthar S, Brandt M, Davis D, Noursadeghi M, Lapp T, Ji C, Sankuratri S, Zhang Y, Govada L, Saridakis E, Chayen N. A Linear Epitope in the N-Terminal Domain of CCR5 and Its Interaction with Antibody. PLoS One. 2015 Jun 1;10(6):e0128381. doi: 10.1371/journal.pone.0128381. eCollection 2015. PubMed PMID: 26030924; PubMed Central PMCID: PMC4451072.
  11. Zhang C, Zhou S, Miller JC, Cox IJ, Chain BM. Optimizing hybrid spreading in metapopulations. Sci Rep. 2015 Apr 29;5:9924. doi: 10.1038/srep09924. PubMed PMID: 25923411; PubMed Central PMCID: PMC4413882.
  12. Jarvis JN, Meintjes G, Bicanic T, Buffa V, Hogan L, Mo S, Tomlinson G, Kropf P, Noursadeghi M, Harrison TS. Cerebrospinal fluid cytokine profiles predict risk of early mortality and immune reconstitution inflammatory syndrome in HIV-associated cryptococcal meningitis. PLoS Pathog. 2015 Apr 8;11(4):e1004754.doi: 10.1371/journal.ppat.1004754. eCollection 2015 Apr. PubMed PMID: 25853653; PubMed Central PMCID: PMC4390200.
  13. Zhang C, Zhou S, Groppelli E, Pellegrino P, Williams I, Borrow P, Chain BM, Jolly C. Hybrid spreading mechanisms and T cell activation shape the dynamics of HIV-1 infection. PLoS Comput Biol. 2015 Apr 2;11(4):e1004179. doi:10.1371/journal.pcbi.1004179. eCollection 2015 Apr. PubMed PMID: 25837979; PubMed Central PMCID: PMC4383537.
  14. Camberlein E, Cohen JM, José R, Hyams CJ, Callard R, Chimalapati S, Yuste J, Edwards LA, Marshall H, van Rooijen N, Noursadeghi M, Brown JS. Importance of bacterial replication and alveolar macrophage-independent clearance mechanisms during early lung infection with Streptococcus pneumoniae. Infect Immun. 2015 Mar;83(3):1181-9. doi: 10.1128/IAI.02788-14. Epub 2015 Jan 12. PubMed PMID: 25583525; PubMed Central PMCID: PMC4333471.
  15. Kim S, Becker J, Bechheim M, Kaiser V, Noursadeghi M, Fricker N, Beier E, Klaschik S, Boor P, Hess T, Hofmann A, Holdenrieder S, Wendland JR, Fröhlich H, Hartmann G, Nöthen MM, Müller-Myhsok B, Pütz B, Hornung V, Schumacher J. Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes. Nat Commun. 2014 Oct 20;5:5236. doi: 10.1038/ncomms6236. PubMed PMID: 25327457.
  16. Tomlinson G, Chimalapati S, Pollard T, Lapp T, Cohen J, Camberlein E, Stafford S, Periselneris J, Aldridge C, Vollmer W, Picard C, Casanova JL, Noursadeghi M, Brown J. TLR-mediated inflammatory responses to Streptococcus pneumoniae are highly dependent on surface expression of bacterial lipoproteins. J Immunol. 2014 Oct 1;193(7):3736-45. doi: 10.4049/jimmunol.1401413. Epub 2014 Aug 29. PubMed PMID: 25172490; PubMed Central PMCID: PMC4170674.
  17. Thomas N, Best K, Cinelli M, Reich-Zeliger S, Gal H, Shifrut E, Madi A, Friedman N, Shawe-Taylor J, Chain B. Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. Bioinformatics. 2014 Nov 15;30(22):3181-8. doi: 10.1093/bioinformatics/btu523. Epub 2014 Aug 5. PubMed PMID: 25095879; PubMed Central PMCID: PMC4221123.
  18. Madi A, Shifrut E, Reich-Zeliger S, Gal H, Best K, Ndifon W, Chain B, Cohen IR, Friedman N. T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity. Genome Res. 2014 Oct;24(10):1603-12. doi: 10.1101/gr.170753.113. Epub 2014 Jul 14. PubMed PMID: 25024161; PubMed Central PMCID: PMC4199372.
  19. Towers GJ, Noursadeghi M. Interactions between HIV-1 and the cell-autonomous innate immune system. Cell Host Microbe. 2014 Jul 9;16(1):10-8. doi:10.1016/j.chom.2014.06.009. Review. PubMed PMID: 25011104; PubMed Central PMCID: PMC4096382.
  20. Mlcochova P, Watters SA, Towers GJ, Noursadeghi M, Gupta RK. Vpx complementation of 'non-macrophage tropic' R5 viruses reveals robust entry of infectious HIV-1 cores into macrophages. Retrovirology. 2014 Mar 21;11:25. doi:10.1186/1742-4690-11-25. PubMed PMID: 24656066; PubMed Central PMCID: PMC3997928.
  21. Kundu R, Chain BM, Coussens AK, Khoo B, Noursadeghi M. Regulation of CYP27B1 and CYP24A1 hydroxylases limits cell-autonomous activation of vitamin D in dendritic cells. Eur J Immunol. 2014 Jun;44(6):1781-90. doi:10.1002/eji.201344157. Epub 2014 Apr 10. PubMed PMID: 24643654.
  22. Thomas N, Heather J, Pollara G, Simpson N, Matjeka T, Shawe-Taylor J, Noursadeghi M, Chain B. The immune system as a biomonitor: explorations in innate and adaptive immunity. Interface Focus. 2013 Apr 6;3(2):20120099. doi:10.1098/rsfs.2012.0099. PubMed PMID: 24427535; PubMed Central PMCID: PMC3638490.
  23. Tomlinson GS, Bell LC, Walker NF, Tsang J, Brown JS, Breen R, Lipman M, Katz DR, Miller RF, Chain BM, Elkington PT, Noursadeghi M. HIV-1 infection of macrophages dysregulates innate immune responses to Mycobacterium tuberculosis by inhibition of interleukin-10. J Infect Dis. 2014 Apr 1;209(7):1055-65. doi:10.1093/infdis/jit621. Epub 2013 Nov 21. PubMed PMID: 24265436; PubMed Central PMCID: PMC3952672.
  24. Waysbort N, Russ D, Chain BM, Friedman N. Coupled IL-2-dependent extracellular feedbacks govern two distinct consecutive phases of CD4 T cell activation. J Immunol. 2013 Dec 15;191(12):5822-30. doi: 10.4049/jimmunol.1301575. Epub 2013 Nov 15. PubMed PMID: 24244020.
  25. Rasaiyaah J, Tan CP, Fletcher AJ, Price AJ, Blondeau C, Hilditch L, Jacques DA, Selwood DL, James LC, Noursadeghi M, Towers GJ. HIV-1 evades innate immune recognition through specific cofactor recruitment. Nature. 2013 Nov 21;503(7476):402-405. doi: 10.1038/nature12769. Epub 2013 Nov 6. PubMed PMID:24196705; PubMed Central PMCID: PMC3928559.
  26. Hyams C, Trzcinski K, Camberlein E, Weinberger DM, Chimalapati S, Noursadeghi M, Lipsitch M, Brown JS. Streptococcus pneumoniae capsular serotype invasiveness correlates with the degree of factor H binding and opsonization with C3b/iC3b.Infect Immun. 2013 Jan;81(1):354-63. doi: 10.1128/IAI.00862-12. Epub 2012 Nov 12.PubMed PMID: 23147038; PubMed Central PMCID: PMC3536142.
  27. Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B. Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics. 2013 Mar 1;29(5):542-50. doi:10.1093/bioinformatics/btt004. Epub 2013 Jan 9. PubMed PMID: 23303508.
  28. Dhanoya A, Wang T, Keshavarz-Moore E, Fassati A, Chain BM. Importin-7 mediates nuclear trafficking of DNA in mammalian cells. Traffic. 2013 Feb;14(2):165-75. doi: 10.1111/tra.12021. Epub 2012 Nov 7. PubMed PMID: 23067392; PubMed Central PMCID: PMC3672689.
  29. Thomas N, Matejovicova L, Srikusalanukul W, Shawe-Taylor J, Chain B. Directional migration of recirculating lymphocytes through lymph nodes via random walks. PLoS One. 2012;7(9):e45262. doi: 10.1371/journal.pone.0045262. Epub 2012 Sep 20. PubMed PMID: 23028891; PubMed Central PMCID: PMC3447944.