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Items: 34

1.

Response to Comment on "Development of Asthma in Inner-City Children: Possible Roles of MAIT Cells and Variation in the Home Environment".

Chandra S, Wingender G, Greenbaum JA, Kronenberg M.

J Immunol. 2018 May 15;200(10):3317-3318. doi: 10.4049/jimmunol.1800397. No abstract available.

PMID:
29735642
2.

Transcriptomic Analysis of CD4+ T Cells Reveals Novel Immune Signatures of Latent Tuberculosis.

Burel JG, Lindestam Arlehamn CS, Khan N, Seumois G, Greenbaum JA, Taplitz R, Gilman RH, Saito M, Vijayanand P, Sette A, Peters B.

J Immunol. 2018 May 1;200(9):3283-3290. doi: 10.4049/jimmunol.1800118. Epub 2018 Mar 30.

PMID:
29602771
3.

Development of Asthma in Inner-City Children: Possible Roles of MAIT Cells and Variation in the Home Environment.

Chandra S, Wingender G, Greenbaum JA, Khurana A, Gholami AM, Ganesan AP, Rosenbach M, Jaffee K, Gern JE, Wood R, O'Connor G, Sandel M, Kattan M, Bacharier L, Togias A, Horner AA, Kronenberg M.

J Immunol. 2018 Mar 15;200(6):1995-2003. doi: 10.4049/jimmunol.1701525. Epub 2018 Feb 5.

PMID:
29431692
4.

Improved methods for predicting peptide binding affinity to MHC class II molecules.

Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M.

Immunology. 2018 Jul;154(3):394-406. doi: 10.1111/imm.12889. Epub 2018 Feb 6.

PMID:
29315598
5.

An automated benchmarking platform for MHC class II binding prediction methods.

Andreatta M, Trolle T, Yan Z, Greenbaum JA, Peters B, Nielsen M.

Bioinformatics. 2018 May 1;34(9):1522-1528. doi: 10.1093/bioinformatics/btx820.

PMID:
29281002
6.

Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA.

Tian Y, Babor M, Lane J, Schulten V, Patil VS, Seumois G, Rosales SL, Fu Z, Picarda G, Burel J, Zapardiel-Gonzalo J, Tennekoon RN, De Silva AD, Premawansa S, Premawansa G, Wijewickrama A, Greenbaum JA, Vijayanand P, Weiskopf D, Sette A, Peters B.

Nat Commun. 2017 Nov 13;8(1):1473. doi: 10.1038/s41467-017-01728-5.

7.

Immunodominance in allergic T-cell reactivity to Japanese cedar in different geographic cohorts.

Oseroff C, Pham J, Frazier A, Hinz D, Sidney J, Paul S, Greenbaum JA, Vita R, Peters B, Schulten V, Sette A.

Ann Allergy Asthma Immunol. 2016 Dec;117(6):680-689.e1. doi: 10.1016/j.anai.2016.10.014. Erratum in: Ann Allergy Asthma Immunol. 2017 Mar;118(3):384.

8.

T-cell epitope conservation across allergen species is a major determinant of immunogenicity.

Westernberg L, Schulten V, Greenbaum JA, Natali S, Tripple V, McKinney DM, Frazier A, Hofer H, Wallner M, Sallusto F, Sette A, Peters B.

J Allergy Clin Immunol. 2016 Aug;138(2):571-578.e7. doi: 10.1016/j.jaci.2015.11.034. Epub 2016 Feb 13.

9.

Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with the allergen-specific modulation of immune reactivity.

Hinz D, Seumois G, Gholami AM, Greenbaum JA, Lane J, White B, Broide DH, Schulten V, Sidney J, Bakhru P, Oseroff C, Wambre E, James EA, Kwok WW, Peters B, Vijayanand P, Sette A.

Clin Exp Allergy. 2016 May;46(5):705-19. doi: 10.1111/cea.12692.

10.

Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing.

McKinney DM, Fu Z, Le L, Greenbaum JA, Peters B, Sette A.

Hum Immunol. 2015 Dec;76(12):917-22. doi: 10.1016/j.humimm.2015.04.007. Epub 2015 May 28.

11.

IL-10-producing intestinal macrophages prevent excessive antibacterial innate immunity by limiting IL-23 synthesis.

Krause P, Morris V, Greenbaum JA, Park Y, Bjoerheden U, Mikulski Z, Muffley T, Shui JW, Kim G, Cheroutre H, Liu YC, Peters B, Kronenberg M, Murai M.

Nat Commun. 2015 May 11;6:7055. doi: 10.1038/ncomms8055.

12.

Dengue Virus Evolution under a Host-Targeted Antiviral.

Plummer E, Buck MD, Sanchez M, Greenbaum JA, Turner J, Grewal R, Klose B, Sampath A, Warfield KL, Peters B, Ramstedt U, Shresta S.

J Virol. 2015 May;89(10):5592-601. doi: 10.1128/JVI.00028-15. Epub 2015 Mar 11.

13.

Automated benchmarking of peptide-MHC class I binding predictions.

Trolle T, Metushi IG, Greenbaum JA, Kim Y, Sidney J, Lund O, Sette A, Peters B, Nielsen M.

Bioinformatics. 2015 Jul 1;31(13):2174-81. doi: 10.1093/bioinformatics/btv123. Epub 2015 Feb 25.

14.

Immunological consequences of intragenus conservation of Mycobacterium tuberculosis T-cell epitopes.

Lindestam Arlehamn CS, Paul S, Mele F, Huang C, Greenbaum JA, Vita R, Sidney J, Peters B, Sallusto F, Sette A.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):E147-55. doi: 10.1073/pnas.1416537112. Epub 2014 Dec 29.

15.

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.

16.

Properties of MHC class I presented peptides that enhance immunogenicity.

Calis JJ, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Keşmir C, Peters B.

PLoS Comput Biol. 2013 Oct;9(10):e1003266. doi: 10.1371/journal.pcbi.1003266. Epub 2013 Oct 24.

17.

Query enhancement through the practical application of ontology: the IEDB and OBI.

Vita R, Overton JA, Greenbaum JA, Sette A; OBI consortium, Peters B.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S6. doi: 10.1186/2041-1480-4-S1-S6. Epub 2013 Apr 15.

18.

Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells.

Weiskopf D, Angelo MA, de Azeredo EL, Sidney J, Greenbaum JA, Fernando AN, Broadwater A, Kolla RV, De Silva AD, de Silva AM, Mattia KA, Doranz BJ, Grey HM, Shresta S, Peters B, Sette A.

Proc Natl Acad Sci U S A. 2013 May 28;110(22):E2046-53. doi: 10.1073/pnas.1305227110. Epub 2013 Apr 11.

19.

Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals.

Schulten V, Greenbaum JA, Hauser M, McKinney DM, Sidney J, Kolla R, Lindestam Arlehamn CS, Oseroff C, Alam R, Broide DH, Ferreira F, Grey HM, Sette A, Peters B.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3459-64. doi: 10.1073/pnas.1300512110. Epub 2013 Feb 11. Erratum in: Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):5269. Ferreira-Briza, Fatima [corrected to Ferreira, Fatima]. Proc Natl Acad Sci U S A. 2013 May 21;110(21):8750.

20.

Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset.

Lindestam Arlehamn CS, Gerasimova A, Mele F, Henderson R, Swann J, Greenbaum JA, Kim Y, Sidney J, James EA, Taplitz R, McKinney DM, Kwok WW, Grey H, Sallusto F, Peters B, Sette A.

PLoS Pathog. 2013 Jan;9(1):e1003130. doi: 10.1371/journal.ppat.1003130. Epub 2013 Jan 24.

21.

Selective inhibition of CD4+ T-cell cytokine production and autoimmunity by BET protein and c-Myc inhibitors.

Bandukwala HS, Gagnon J, Togher S, Greenbaum JA, Lamperti ED, Parr NJ, Molesworth AM, Smithers N, Lee K, Witherington J, Tough DF, Prinjha RK, Peters B, Rao A.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14532-7. doi: 10.1073/pnas.1212264109. Epub 2012 Aug 21.

22.

T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts.

Oseroff C, Sidney J, Vita R, Tripple V, McKinney DM, Southwood S, Brodie TM, Sallusto F, Grey H, Alam R, Broide D, Greenbaum JA, Kolla R, Peters B, Sette A.

J Immunol. 2012 Aug 15;189(4):1800-11. doi: 10.4049/jimmunol.1200850. Epub 2012 Jul 11.

23.

Dissecting mechanisms of immunodominance to the common tuberculosis antigens ESAT-6, CFP10, Rv2031c (hspX), Rv2654c (TB7.7), and Rv1038c (EsxJ).

Arlehamn CS, Sidney J, Henderson R, Greenbaum JA, James EA, Moutaftsi M, Coler R, McKinney DM, Park D, Taplitz R, Kwok WW, Grey H, Peters B, Sette A.

J Immunol. 2012 May 15;188(10):5020-31. doi: 10.4049/jimmunol.1103556. Epub 2012 Apr 13.

24.

Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design.

Weiskopf D, Yauch LE, Angelo MA, John DV, Greenbaum JA, Sidney J, Kolla RV, De Silva AD, de Silva AM, Grey H, Peters B, Shresta S, Sette A.

J Immunol. 2011 Oct 15;187(8):4268-79. doi: 10.4049/jimmunol.1101970. Epub 2011 Sep 14.

25.

TiArA: a virtual appliance for the analysis of Tiling Array data.

Greenbaum JA, Assarsson E, Chung JL, Head S, Sette A, Peters B.

PLoS One. 2010 Apr 1;5(4):e9993. doi: 10.1371/journal.pone.0009993.

26.

A multivalent and cross-protective vaccine strategy against arenaviruses associated with human disease.

Kotturi MF, Botten J, Sidney J, Bui HH, Giancola L, Maybeno M, Babin J, Oseroff C, Pasquetto V, Greenbaum JA, Peters B, Ting J, Do D, Vang L, Alexander J, Grey H, Buchmeier MJ, Sette A.

PLoS Pathog. 2009 Dec;5(12):e1000695. doi: 10.1371/journal.ppat.1000695. Epub 2009 Dec 18.

27.

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.

28.

The immune epitope database 2.0.

Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B.

Nucleic Acids Res. 2010 Jan;38(Database issue):D854-62. doi: 10.1093/nar/gkp1004. Epub 2009 Nov 11.

29.

Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes.

Assarsson E, Greenbaum JA, Sundström M, Schaffer L, Hammond JA, Pasquetto V, Oseroff C, Hendrickson RC, Lefkowitz EJ, Tscharke DC, Sidney J, Grey HM, Head SR, Peters B, Sette A.

Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2140-5. doi: 10.1073/pnas.0711573105. Epub 2008 Feb 1. Erratum in: Proc Natl Acad Sci U S A. 2008 May 6;105(18):6787.

30.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

31.

Construction of a genome-scale structural map at single-nucleotide resolution.

Greenbaum JA, Pang B, Tullius TD.

Genome Res. 2007 Jun;17(6):947-53.

32.

Detection of DNA structural motifs in functional genomic elements.

Greenbaum JA, Parker SC, Tullius TD.

Genome Res. 2007 Jun;17(6):940-6.

33.

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools.

Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B.

J Mol Recognit. 2007 Mar-Apr;20(2):75-82. Review.

PMID:
17205610
34.

Mapping nucleic acid structure by hydroxyl radical cleavage.

Tullius TD, Greenbaum JA.

Curr Opin Chem Biol. 2005 Apr;9(2):127-34. Review.

PMID:
15811796

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