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• VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

  Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG. Toby IT, et al. BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333. doi: 10.1186/s12859-016-1214-3. BMC Bioinformatics. 2016. PMID: 27766961 Free PMC article.
• Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination.

  Rogers LRK, de Los Campos G, Mias GI. Rogers LRK, et al. Front Immunol. 2019 Nov 7;10:2616. doi: 10.3389/fimmu.2019.02616. eCollection 2019. Front Immunol. 2019. PMID: 31787983 Free PMC article.
• Single cell immune profiling of dengue virus patients reveals intact immune responses to Zika virus with enrichment of innate immune signatures.

  Zhao Y, Amodio M, Vander Wyk B, Gerritsen B, Kumar MM, van Dijk D, Moon K, Wang X, Malawista A, Richards MM, Cahill ME, Desai A, Sivadasan J, Venkataswamy MM, Ravi V, Fikrig E, Kumar P, Kleinstein SH, Krishnaswamy S, Montgomery RR. Zhao Y, et al. PLoS Negl Trop Dis. 2020 Mar 9;14(3):e0008112. doi: 10.1371/journal.pntd.0008112. eCollection 2020 Mar. PLoS Negl Trop Dis. 2020. PMID: 32150565 Free PMC article.
• A review of quantitative modeling of B cell responses to antigenic challenge.

  Hickling TP, Chen X, Vicini P, Nayak S. Hickling TP, et al. J Pharmacokinet Pharmacodyn. 2014 Oct;41(5):445-59. doi: 10.1007/s10928-014-9388-7. Epub 2014 Oct 19. J Pharmacokinet Pharmacodyn. 2014. PMID: 25326873 Review.
• VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.

  Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, Pogorelyy MV, Nazarov VI, Zvyagin IV, Kirgizova VI, Kirgizov KI, Skorobogatova EV, Chudakov DM. Shugay M, et al. PLoS Comput Biol. 2015 Nov 25;11(11):e1004503. doi: 10.1371/journal.pcbi.1004503. eCollection 2015 Nov. PLoS Comput Biol. 2015. PMID: 26606115 Free PMC article.