Difference between revisions of "Shreffler:Resources"

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(R analysis)
(Scripts)
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*[[Image:jax_pcr.R]]
 
*[[Image:jax_pcr.R]]
 
** for analysis of pbmc pcr data in the JAX project -- good use of %in% and grep as well as loops to mash data together from two sources
 
** for analysis of pbmc pcr data in the JAX project -- good use of %in% and grep as well as loops to mash data together from two sources
[[Image:milk_mash_script.R]]
+
*[[Image:milk_mash_script.R]]
 
** script used by Wayne and Lara to do interim analysis of milk basophil data
 
** script used by Wayne and Lara to do interim analysis of milk basophil data
 
+
*[[Image:AAAAI_rCode.R]]
 +
** Lara's analysis script for her abstract
 
===Shell===
 
===Shell===
  

Revision as of 06:54, 5 September 2009

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Protocols

Reading List

  1. Steinfelder S, Andersen JF, Cannons JL, Feng CG, Joshi M, Dwyer D, Caspar P, Schwartzberg PL, Sher A, and Jankovic D. The major component in schistosome eggs responsible for conditioning dendritic cells for Th2 polarization is a T2 ribonuclease (omega-1). J Exp Med. 2009 Aug 3;206(8):1681-90. DOI:10.1084/jem.20082462 | PubMed ID:19635859 | HubMed [Steinfelder]
  2. Everts B, Perona-Wright G, Smits HH, Hokke CH, van der Ham AJ, Fitzsimmons CM, Doenhoff MJ, van der Bosch J, Mohrs K, Haas H, Mohrs M, Yazdanbakhsh M, and Schramm G. Omega-1, a glycoprotein secreted by Schistosoma mansoni eggs, drives Th2 responses. J Exp Med. 2009 Aug 3;206(8):1673-80. DOI:10.1084/jem.20082460 | PubMed ID:19635864 | HubMed [Everts]
    two significant papers on SEA as Th2 adjuvants
  3. Suzuki K, Grigorova I, Phan TG, Kelly LM, and Cyster JG. Visualizing B cell capture of cognate antigen from follicular dendritic cells. J Exp Med. 2009 Jul 6;206(7):1485-93. DOI:10.1084/jem.20090209 | PubMed ID:19506051 | HubMed [Susuki]
    interesting for methods related to baso confocal project
  4. Geiger R, Duhen T, Lanzavecchia A, and Sallusto F. Human naive and memory CD4+ T cell repertoires specific for naturally processed antigens analyzed using libraries of amplified T cells. J Exp Med. 2009 Jul 6;206(7):1525-34. DOI:10.1084/jem.20090504 | PubMed ID:19564353 | HubMed [Geiger]
    another methodology paper perhaps for frequency of allergen-specific T cells
  5. Campbell JD, Buckland KF, McMillan SJ, Kearley J, Oldfield WL, Stern LJ, Grönlund H, van Hage M, Reynolds CJ, Boyton RJ, Cobbold SP, Kay AB, Altmann DM, Lloyd CM, and Larché M. Peptide immunotherapy in allergic asthma generates IL-10-dependent immunological tolerance associated with linked epitope suppression. J Exp Med. 2009 Jul 6;206(7):1535-47. DOI:10.1084/jem.20082901 | PubMed ID:19528258 | HubMed [Campbell]
    madhan's project
  6. la Sala A, He J, Laricchia-Robbio L, Gorini S, Iwasaki A, Braun M, Yap GS, Sher A, Ozato K, and Kelsall B. Cholera toxin inhibits IL-12 production and CD8alpha+ dendritic cell differentiation by cAMP-mediated inhibition of IRF8 function. J Exp Med. 2009 Jun 8;206(6):1227-35. DOI:10.1084/jem.20080912 | PubMed ID:19487420 | HubMed [la_Sala]
    mechanisms of CT
  7. Duhen T, Geiger R, Jarrossay D, Lanzavecchia A, and Sallusto F. Production of interleukin 22 but not interleukin 17 by a subset of human skin-homing memory T cells. Nat Immunol. 2009 Aug;10(8):857-63. DOI:10.1038/ni.1767 | PubMed ID:19578369 | HubMed [Duhen]
    characterization of a distinct Th subset producing IL-22; relevance to PN adjuvant?, second independent paper also published back-to-back
  8. Okamoto M, Van Stry M, Chung L, Koyanagi M, Sun X, Suzuki Y, Ohara O, Kitamura H, Hijikata A, Kubo M, and Bix M. Mina, an Il4 repressor, controls T helper type 2 bias. Nat Immunol. 2009 Aug;10(8):872-9. DOI:10.1038/ni.1747 | PubMed ID:19561615 | HubMed [Okamoto]
    new transcriptional regulator for Th2 described, could be useful for Th2 phenotyping
All Medline abstracts: PubMed | HubMed

Scripts

R analysis

  • File:Array flinterman.R
    • script used for Flinterman paper -- one of the first 'BATCH' functions for analysis of multiple data files
  • File:Jax pcr.R
    • for analysis of pbmc pcr data in the JAX project -- good use of %in% and grep as well as loops to mash data together from two sources
  • File:Milk mash script.R
    • script used by Wayne and Lara to do interim analysis of milk basophil data
  • File:AAAAI rCode.R
    • Lara's analysis script for her abstract

Shell

Perl

Courses