Difference between revisions of "Shreffler:Resources"

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*[[Image:format_bib_file.pl]]
 
*[[Image:format_bib_file.pl]]
 
** Perl script for reformating BiBTeX files exported from Papers so that they have double braces around the Title field in order to preserve capitalization.
 
** Perl script for reformating BiBTeX files exported from Papers so that they have double braces around the Title field in order to preserve capitalization.
*: Usage Note: format_bib_file.pl ''file_in.bib'' ''file_out.bib''
+
*: Usage Syntax: format_bib_file.pl ''file_in.bib'' ''file_out.bib''
  
 
==Courses==
 
==Courses==

Revision as of 08:13, 18 August 2010

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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 using data file, 20080818_BaselineBasoDataWithClinicalGroups.csv. Example of 2-way ANOVA.
  • File:Duke extract script.R
    • Wayne's analysis of duke peanut mucosal IT data that extracts text files from FlowJo analysis data directory tree and also mashes up baso data with clinical data file and produces time series data with multiple plots using layout for peanut, controls, egg by treatment or placebo

Shell

  • File:Rmquote
    • Shell script for reformatting data files from Array scanner to be more easily analyzed in R; removes empty spaces, quotation markes, etc. Also eliminates white space from file names. Requires directory containing data files as input.

Perl

  • File:Format bib file.pl
    • Perl script for reformating BiBTeX files exported from Papers so that they have double braces around the Title field in order to preserve capitalization.
    Usage Syntax: format_bib_file.pl file_in.bib file_out.bib

Courses

  1. Antonicelli L, Micucci C, Mistrello G, Roncarolo D, Zanotta S, Cinti B, Garritani MS, and Bonifazi F. Improving latex-allergy diagnosis: the clinical role of Hev b8-specific IgE. Allergy. 2008 May;63(5):620-1. DOI:10.1111/j.1398-9995.2008.01651.x | PubMed ID:18394137 | HubMed [Antonicelli]
  2. Hamilton RG, MacGlashan DW Jr, and Saini SS. IgE antibody-specific activity in human allergic disease. Immunol Res. 2010 Jul;47(1-3):273-84. DOI:10.1007/s12026-009-8160-3 | PubMed ID:20066506 | HubMed [Bauermeister]
  3. Giavina-Bianchi P, Oliveira E, and Kalil J. Specific IgE against recombinant allergens in allergic bronchopulmonary aspergillosis. Am J Respir Crit Care Med. 2007 May 1;175(9):967; author reply 967-8. DOI:10.1164/ajrccm.175.9.967a | PubMed ID:17446345 | HubMed [Flinterman]
  4. Quercia O, Stefanini GF, Scardovi A, and Asero R. Patients monosensitised to Hev b 8 (Hevea brasiliensis latex profilin) may safely undergo major surgery in a normal (non-latex safe) environment. Eur Ann Allergy Clin Immunol. 2009 Aug;41(4):112-6. PubMed ID:19877563 | HubMed [Giavina-Bianchi]
  5. Bauermeister K, Ballmer-Weber BK, Bublin M, Fritsche P, Hanschmann KM, Hoffmann-Sommergruber K, Lidholm J, Oberhuber C, Randow S, Holzhauser T, and Vieths S. Assessment of component-resolved in vitro diagnosis of celeriac allergy. J Allergy Clin Immunol. 2009 Dec;124(6):1273-1281.e2. DOI:10.1016/j.jaci.2009.07.033 | PubMed ID:19800675 | HubMed [Hamilton]
  6. Nicolaou N, Poorafshar M, Murray C, Simpson A, Winell H, Kerry G, Härlin A, Woodcock A, Ahlstedt S, and Custovic A. Allergy or tolerance in children sensitized to peanut: prevalence and differentiation using component-resolved diagnostics. J Allergy Clin Immunol. 2010 Jan;125(1):191-7.e1-13. DOI:10.1016/j.jaci.2009.10.008 | PubMed ID:20109746 | HubMed [Mittermann]
  7. Mittermann I, Zidarn M, Silar M, Markovic-Housley Z, Aberer W, Korosec P, Kosnik M, and Valenta R. Recombinant allergen-based IgE testing to distinguish bee and wasp allergy. J Allergy Clin Immunol. 2010 Jun;125(6):1300-1307.e3. DOI:10.1016/j.jaci.2010.03.017 | PubMed ID:20466415 | HubMed [Nicolaou]
  8. Pittner G, Vrtala S, Thomas WR, Weghofer M, Kundi M, Horak F, Kraft D, and Valenta R. Component-resolved diagnosis of house-dust mite allergy with purified natural and recombinant mite allergens. Clin Exp Allergy. 2004 Apr;34(4):597-603. DOI:10.1111/j.1365-2222.2004.1930.x | PubMed ID:15080813 | HubMed [Pittner]
  9. Shreffler WG, Beyer K, Chu TH, Burks AW, and Sampson HA. Microarray immunoassay: association of clinical history, in vitro IgE function, and heterogeneity of allergenic peanut epitopes. J Allergy Clin Immunol. 2004 Apr;113(4):776-82. DOI:10.1016/j.jaci.2003.12.588 | PubMed ID:15100687 | HubMed [Quercia]
  10. Flinterman AE, Knol EF, Lencer DA, Bardina L, den Hartog Jager CF, Lin J, Pasmans SG, Bruijnzeel-Koomen CA, Sampson HA, van Hoffen E, and Shreffler WG. Peanut epitopes for IgE and IgG4 in peanut-sensitized children in relation to severity of peanut allergy. J Allergy Clin Immunol. 2008 Mar;121(3):737-743.e10. DOI:10.1016/j.jaci.2007.11.039 | PubMed ID:18234310 | HubMed [Shreffler]
All Medline abstracts: PubMed | HubMed