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Analysis of Human RSV Immunity at the Molecular Level: Learning from the Past and Present.

Vaughan K, Ponomarenko J, Peters B, Sette A.

PLoS One. 2015 May 22;10(5):e0127108. doi: 10.1371/journal.pone.0127108. eCollection 2015. Review.


Conservancy of mAb Epitopes in Ebolavirus Glycoproteins of Previous and 2014 Outbreaks.

Ponomarenko J, Vaughan K, Sette A, Maurer-Stroh S.

PLoS Curr. 2014 Nov 3;6. pii: ecurrents.outbreaks.f1a7028a13ce1c5f0bdbb4b0cc0b919b. doi: 10.1371/currents.outbreaks.f1a7028a13ce1c5f0bdbb4b0cc0b919b.


The immune epitope database (IEDB) 3.0.

Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B.

Nucleic Acids Res. 2015 Jan;43(Database issue):D405-12. doi: 10.1093/nar/gku938. Epub 2014 Oct 9.


Elucidation of antioxidant properties of wood bark derived saturated diarylheptanoids: a comprehensive (DFT-supported) understanding.

Ponomarenko J, Trouillas P, Martin N, Dizhbite T, Krasilnikova J, Telysheva G.

Phytochemistry. 2014 Jul;103:178-87. doi: 10.1016/j.phytochem.2014.03.010. Epub 2014 Apr 3.


IκBε is a key regulator of B cell expansion by providing negative feedback on cRel and RelA in a stimulus-specific manner.

Alves BN, Tsui R, Almaden J, Shokhirev MN, Davis-Turak J, Fujimoto J, Birnbaum H, Ponomarenko J, Hoffmann A.

J Immunol. 2014 Apr 1;192(7):3121-32. doi: 10.4049/jimmunol.1302351. Epub 2014 Mar 3.


An integrative approach to inferring gene regulatory module networks.

Baitaluk M, Kozhenkov S, Ponomarenko J.

PLoS One. 2012;7(12):e52836. doi: 10.1371/journal.pone.0052836. Epub 2012 Dec 20.


Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways.

Shih VF, Davis-Turak J, Macal M, Huang JQ, Ponomarenko J, Kearns JD, Yu T, Fagerlund R, Asagiri M, Zuniga EI, Hoffmann A.

Nat Immunol. 2012 Dec;13(12):1162-70. doi: 10.1038/ni.2446. Epub 2012 Oct 21.


Immune epitope database analysis resource.

Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W525-30. doi: 10.1093/nar/gks438. Epub 2012 May 18.


IntegromeDB: an integrated system and biological search engine.

Baitaluk M, Kozhenkov S, Dubinina Y, Ponomarenko J.

BMC Genomics. 2012 Jan 19;13:35. doi: 10.1186/1471-2164-13-35.


The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50.

Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A.

Sci Signal. 2011 Feb 22;4(161):ra11. doi: 10.1126/scisignal.2001501.


BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies.

Kozhenkov S, Sedova M, Dubinina Y, Gupta A, Ray A, Ponomarenko J, Baitaluk M.

BMC Syst Biol. 2011 Jan 14;5:7. doi: 10.1186/1752-0509-5-7.


BiologicalNetworks 2.0--an integrative view of genome biology data.

Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M.

BMC Bioinformatics. 2010 Dec 29;11:610. doi: 10.1186/1471-2105-11-610.


IEDB-3D: structural data within the immune epitope database.

Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1164-70. doi: 10.1093/nar/gkq888. Epub 2010 Oct 28.


Semantic integration of data on transcriptional regulation.

Baitaluk M, Ponomarenko J.

Bioinformatics. 2010 Jul 1;26(13):1651-61. doi: 10.1093/bioinformatics/btq231. Epub 2010 Apr 28.


Limitations of Ab initio predictions of peptide binding to MHC class II molecules.

Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B.

PLoS One. 2010 Feb 17;5(2):e9272. doi: 10.1371/journal.pone.0009272.


Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population.

Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B.

Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20365-70. doi: 10.1073/pnas.0911580106. Epub 2009 Nov 16.


ElliPro: a new structure-based tool for the prediction of antibody epitopes.

Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B.

BMC Bioinformatics. 2008 Dec 2;9:514. doi: 10.1186/1471-2105-9-514.


Immune epitope database analysis resource (IEDB-AR).

Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W513-8. doi: 10.1093/nar/gkn254. Epub 2008 May 31.

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