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The Innate Immune Database (IIDB).
Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H. Korb M, et al. Among authors: johnson c. BMC Immunol. 2008 Mar 5;9:7. doi: 10.1186/1471-2172-9-7. BMC Immunol. 2008. PMID: 18321385 Free PMC article.
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.
Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I. Ramsey SA, et al. Among authors: johnson cd. PLoS Comput Biol. 2008 Mar 21;4(3):e1000021. doi: 10.1371/journal.pcbi.1000021. PLoS Comput Biol. 2008. PMID: 18369420 Free PMC article.
Systems analysis identifies an essential role for SHANK-associated RH domain-interacting protein (SHARPIN) in macrophage Toll-like receptor 2 (TLR2) responses.
Zak DE, Schmitz F, Gold ES, Diercks AH, Peschon JJ, Valvo JS, Niemistö A, Podolsky I, Fallen SG, Suen R, Stolyar T, Johnson CD, Kennedy KA, Hamilton MK, Siggs OM, Beutler B, Aderem A. Zak DE, et al. Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11536-41. doi: 10.1073/pnas.1107577108. Epub 2011 Jun 27. Proc Natl Acad Sci U S A. 2011. PMID: 21709223 Free PMC article.
Innate transcriptional effects by adjuvants on the magnitude, quality, and durability of HIV envelope responses in NHPs.
Francica JR, Zak DE, Linde C, Siena E, Johnson C, Juraska M, Yates NL, Gunn B, De Gregorio E, Flynn BJ, Valiante NM, Malyala P, Barnett SW, Sarkar P, Singh M, Jain S, Ackerman M, Alam M, Ferrari G, Salazar A, Tomaras GD, O'Hagan DT, Aderem A, Alter G, Seder RA. Francica JR, et al. Among authors: johnson c. Blood Adv. 2017 Nov 17;1(25):2329-2342. doi: 10.1182/bloodadvances.2017011411. eCollection 2017 Nov 28. Blood Adv. 2017. PMID: 29296883 Free PMC article.
Decoding the blueprint of receptor binding by filoviruses through large-scale binding assays and machine learning.
Lasso G, Grodus M, Valencia E, DeJesus V, Liang E, Delwel I, Bortz RH 3rd, Lupyan D, Ehrlich HY, Castellanos AA, Gazzo A, Wells HL, Wacharapluesadee S, Tremeau-Bravard A, Seetahal JFR, Hughes T, Lee J, Lee MH, Sjodin AR, Geldenhuys M, Mortlock M, Navarrete-Macias I, Gilardi K, Willig MR, Nava AFD, Loh EH, Asrat M, Smiley-Evans T, Magesa WS, Zikankuba S, Wolking D, Suzán G, Ojeda-Flores R, Carrington CVF, Islam A, Esptein JH, Markotter W, Johnson CK, Goldstein T, Han BA, Mazet JAK, Jangra RK, Chandran K, Anthony SJ. Lasso G, et al. Among authors: johnson ck. Cell Host Microbe. 2025 Jan 8:S1931-3128(24)00483-9. doi: 10.1016/j.chom.2024.12.016. Online ahead of print. Cell Host Microbe. 2025. PMID: 39818205
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