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Items: 1 to 50 of 74

1.

In vivo delivery of synthetic DNA-encoded antibodies induces broad HIV-1-neutralizing activity.

Wise MC, Xu Z, Tello-Ruiz E, Beck C, Trautz A, Patel A, Elliott ST, Chokkalingam N, Kim S, Kerkau MG, Muthumani K, Jiang J, Fisher P, Ramos SJ, Smith TR, Mendoza J, Broderick KE, Montefiori DC, Ferrari G, Kulp DW, Humeau L, Weiner DB.

J Clin Invest. 2019 Nov 7. pii: 132779. doi: 10.1172/JCI132779. [Epub ahead of print]

2.

A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses.

Steichen JM, Lin YC, Havenar-Daughton C, Pecetta S, Ozorowski G, Willis JR, Toy L, Sok D, Liguori A, Kratochvil S, Torres JL, Kalyuzhniy O, Melzi E, Kulp DW, Raemisch S, Hu X, Bernard SM, Georgeson E, Phelps N, Adachi Y, Kubitz M, Landais E, Umotoy J, Robinson A, Briney B, Wilson IA, Burton DR, Ward AB, Crotty S, Batista FD, Schief WR.

Science. 2019 Oct 31. pii: eaax4380. doi: 10.1126/science.aax4380. [Epub ahead of print]

PMID:
31672916
3.

Enhancing humoral immunity via sustained-release implantable microneedle patch vaccination.

Boopathy AV, Mandal A, Kulp DW, Menis S, Bennett NR, Watkins HC, Wang W, Martin JT, Thai NT, He Y, Schief WR, Hammond PT, Irvine DJ.

Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16473-16478. doi: 10.1073/pnas.1902179116. Epub 2019 Jul 29.

PMID:
31358641
4.

Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance.

Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S.

Cell. 2019 May 16;177(5):1153-1171.e28. doi: 10.1016/j.cell.2019.04.012. Epub 2019 May 9.

PMID:
31080066
5.

Protein engineering and particulate display of B-cell epitopes to facilitate development of novel vaccines.

Xu Z, Kulp DW.

Curr Opin Immunol. 2019 Aug;59:49-56. doi: 10.1016/j.coi.2019.03.003. Epub 2019 Apr 28. Review.

PMID:
31029909
6.

Innate immune recognition of glycans targets HIV nanoparticle immunogens to germinal centers.

Tokatlian T, Read BJ, Jones CA, Kulp DW, Menis S, Chang JYH, Steichen JM, Kumari S, Allen JD, Dane EL, Liguori A, Sangesland M, Lingwood D, Crispin M, Schief WR, Irvine DJ.

Science. 2019 Feb 8;363(6427):649-654. doi: 10.1126/science.aat9120. Epub 2018 Dec 20.

7.

Vaccine-Induced Protection from Homologous Tier 2 SHIV Challenge in Nonhuman Primates Depends on Serum-Neutralizing Antibody Titers.

Pauthner MG, Nkolola JP, Havenar-Daughton C, Murrell B, Reiss SM, Bastidas R, Prévost J, Nedellec R, von Bredow B, Abbink P, Cottrell CA, Kulp DW, Tokatlian T, Nogal B, Bianchi M, Li H, Lee JH, Butera ST, Evans DT, Hangartner L, Finzi A, Wilson IA, Wyatt RT, Irvine DJ, Schief WR, Ward AB, Sanders RW, Crotty S, Shaw GM, Barouch DH, Burton DR.

Immunity. 2019 Jan 15;50(1):241-252.e6. doi: 10.1016/j.immuni.2018.11.011. Epub 2018 Dec 11.

8.

Enhancing Humoral Responses Against HIV Envelope Trimers via Nanoparticle Delivery with Stabilized Synthetic Liposomes.

Tokatlian T, Kulp DW, Mutafyan AA, Jones CA, Menis S, Georgeson E, Kubitz M, Zhang MH, Melo MB, Silva M, Yun DS, Schief WR, Irvine DJ.

Sci Rep. 2018 Nov 8;8(1):16527. doi: 10.1038/s41598-018-34853-2.

9.

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain.

Saunders A, Macosko EZ, Wysoker A, Goldman M, Krienen FM, de Rivera H, Bien E, Baum M, Bortolin L, Wang S, Goeva A, Nemesh J, Kamitaki N, Brumbaugh S, Kulp D, McCarroll SA.

Cell. 2018 Aug 9;174(4):1015-1030.e16. doi: 10.1016/j.cell.2018.07.028.

10.

The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen.

Havenar-Daughton C, Sarkar A, Kulp DW, Toy L, Hu X, Deresa I, Kalyuzhniy O, Kaushik K, Upadhyay AA, Menis S, Landais E, Cao L, Diedrich JK, Kumar S, Schiffner T, Reiss SM, Seumois G, Yates JR, Paulson JC, Bosinger SE, Wilson IA, Schief WR, Crotty S.

Sci Transl Med. 2018 Jul 4;10(448). pii: eaat0381. doi: 10.1126/scitranslmed.aat0381.

11.

Precursor Frequency and Affinity Determine B Cell Competitive Fitness in Germinal Centers, Tested with Germline-Targeting HIV Vaccine Immunogens.

Abbott RK, Lee JH, Menis S, Skog P, Rossi M, Ota T, Kulp DW, Bhullar D, Kalyuzhniy O, Havenar-Daughton C, Schief WR, Nemazee D, Crotty S.

Immunity. 2018 Jan 16;48(1):133-146.e6. doi: 10.1016/j.immuni.2017.11.023. Epub 2017 Dec 26.

12.

Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding.

Kulp DW, Steichen JM, Pauthner M, Hu X, Schiffner T, Liguori A, Cottrell CA, Havenar-Daughton C, Ozorowski G, Georgeson E, Kalyuzhniy O, Willis JR, Kubitz M, Adachi Y, Reiss SM, Shin M, de Val N, Ward AB, Crotty S, Burton DR, Schief WR.

Nat Commun. 2017 Nov 21;8(1):1655. doi: 10.1038/s41467-017-01549-6.

13.

Elicitation of Robust Tier 2 Neutralizing Antibody Responses in Nonhuman Primates by HIV Envelope Trimer Immunization Using Optimized Approaches.

Pauthner M, Havenar-Daughton C, Sok D, Nkolola JP, Bastidas R, Boopathy AV, Carnathan DG, Chandrashekar A, Cirelli KM, Cottrell CA, Eroshkin AM, Guenaga J, Kaushik K, Kulp DW, Liu J, McCoy LE, Oom AL, Ozorowski G, Post KW, Sharma SK, Steichen JM, de Taeye SW, Tokatlian T, Torrents de la Peña A, Butera ST, LaBranche CC, Montefiori DC, Silvestri G, Wilson IA, Irvine DJ, Sanders RW, Schief WR, Ward AB, Wyatt RT, Barouch DH, Crotty S, Burton DR.

Immunity. 2017 Jun 20;46(6):1073-1088.e6. doi: 10.1016/j.immuni.2017.05.007.

14.

Global site-specific N-glycosylation analysis of HIV envelope glycoprotein.

Cao L, Diedrich JK, Kulp DW, Pauthner M, He L, Park SR, Sok D, Su CY, Delahunty CM, Menis S, Andrabi R, Guenaga J, Georgeson E, Kubitz M, Adachi Y, Burton DR, Schief WR, Yates JR III, Paulson JC.

Nat Commun. 2017 Mar 28;8:14954. doi: 10.1038/ncomms14954.

15.

Effects of partially dismantling the CD4 binding site glycan fence of HIV-1 Envelope glycoprotein trimers on neutralizing antibody induction.

Crooks ET, Osawa K, Tong T, Grimley SL, Dai YD, Whalen RG, Kulp DW, Menis S, Schief WR, Binley JM.

Virology. 2017 May;505:193-209. doi: 10.1016/j.virol.2017.02.024. Epub 2017 Mar 6.

16.

Small Molecule Inhibition of Rab7 Impairs B Cell Class Switching and Plasma Cell Survival To Dampen the Autoantibody Response in Murine Lupus.

Lam T, Kulp DV, Wang R, Lou Z, Taylor J, Rivera CE, Yan H, Zhang Q, Wang Z, Zan H, Ivanov DN, Zhong G, Casali P, Xu Z.

J Immunol. 2016 Nov 15;197(10):3792-3805. Epub 2016 Oct 14.

17.

HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies.

Steichen JM, Kulp DW, Tokatlian T, Escolano A, Dosenovic P, Stanfield RL, McCoy LE, Ozorowski G, Hu X, Kalyuzhniy O, Briney B, Schiffner T, Garces F, Freund NT, Gitlin AD, Menis S, Georgeson E, Kubitz M, Adachi Y, Jones M, Mutafyan AA, Yun DS, Mayer CT, Ward AB, Burton DR, Wilson IA, Irvine DJ, Nussenzweig MC, Schief WR.

Immunity. 2016 Sep 20;45(3):483-496. doi: 10.1016/j.immuni.2016.08.016. Epub 2016 Sep 8.

18.

Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies.

Briney B, Sok D, Jardine JG, Kulp DW, Skog P, Menis S, Jacak R, Kalyuzhniy O, de Val N, Sesterhenn F, Le KM, Ramos A, Jones M, Saye-Francisco KL, Blane TR, Spencer S, Georgeson E, Hu X, Ozorowski G, Adachi Y, Kubitz M, Sarkar A, Wilson IA, Ward AB, Nemazee D, Burton DR, Schief WR.

Cell. 2016 Sep 8;166(6):1459-1470.e11. doi: 10.1016/j.cell.2016.08.005.

19.

Sequential Immunization Elicits Broadly Neutralizing Anti-HIV-1 Antibodies in Ig Knockin Mice.

Escolano A, Steichen JM, Dosenovic P, Kulp DW, Golijanin J, Sok D, Freund NT, Gitlin AD, Oliveira T, Araki T, Lowe S, Chen ST, Heinemann J, Yao KH, Georgeson E, Saye-Francisco KL, Gazumyan A, Adachi Y, Kubitz M, Burton DR, Schief WR, Nussenzweig MC.

Cell. 2016 Sep 8;166(6):1445-1458.e12. doi: 10.1016/j.cell.2016.07.030.

20.

Priming HIV-1 broadly neutralizing antibody precursors in human Ig loci transgenic mice.

Sok D, Briney B, Jardine JG, Kulp DW, Menis S, Pauthner M, Wood A, Lee EC, Le KM, Jones M, Ramos A, Kalyuzhniy O, Adachi Y, Kubitz M, MacPherson S, Bradley A, Friedrich GA, Schief WR, Burton DR.

Science. 2016 Sep 30;353(6307):1557-1560. Epub 2016 Sep 8.

21.

Holes in the Glycan Shield of the Native HIV Envelope Are a Target of Trimer-Elicited Neutralizing Antibodies.

McCoy LE, van Gils MJ, Ozorowski G, Messmer T, Briney B, Voss JE, Kulp DW, Macauley MS, Sok D, Pauthner M, Menis S, Cottrell CA, Torres JL, Hsueh J, Schief WR, Wilson IA, Ward AB, Sanders RW, Burton DR.

Cell Rep. 2016 Aug 30;16(9):2327-38. doi: 10.1016/j.celrep.2016.07.074. Epub 2016 Aug 18.

22.

HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen.

Jardine JG, Kulp DW, Havenar-Daughton C, Sarkar A, Briney B, Sok D, Sesterhenn F, Ereño-Orbea J, Kalyuzhniy O, Deresa I, Hu X, Spencer S, Jones M, Georgeson E, Adachi Y, Kubitz M, deCamp AC, Julien JP, Wilson IA, Burton DR, Crotty S, Schief WR.

Science. 2016 Mar 25;351(6280):1458-63. doi: 10.1126/science.aad9195.

23.

A guide to genome-wide association analysis and post-analytic interrogation.

Reed E, Nunez S, Kulp D, Qian J, Reilly MP, Foulkes AS.

Stat Med. 2015 Dec 10;34(28):3769-92. doi: 10.1002/sim.6605. Epub 2015 Sep 6.

24.

Glycan clustering stabilizes the mannose patch of HIV-1 and preserves vulnerability to broadly neutralizing antibodies.

Pritchard LK, Spencer DI, Royle L, Bonomelli C, Seabright GE, Behrens AJ, Kulp DW, Menis S, Krumm SA, Dunlop DC, Crispin DJ, Bowden TA, Scanlan CN, Ward AB, Schief WR, Doores KJ, Crispin M.

Nat Commun. 2015 Jun 24;6:7479. doi: 10.1038/ncomms8479.

25.

Immunization for HIV-1 Broadly Neutralizing Antibodies in Human Ig Knockin Mice.

Dosenovic P, von Boehmer L, Escolano A, Jardine J, Freund NT, Gitlin AD, McGuire AT, Kulp DW, Oliveira T, Scharf L, Pietzsch J, Gray MD, Cupo A, van Gils MJ, Yao KH, Liu C, Gazumyan A, Seaman MS, Björkman PJ, Sanders RW, Moore JP, Stamatatos L, Schief WR, Nussenzweig MC.

Cell. 2015 Jun 18;161(7):1505-15. doi: 10.1016/j.cell.2015.06.003.

26.

HIV-1 VACCINES. Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen.

Jardine JG, Ota T, Sok D, Pauthner M, Kulp DW, Kalyuzhniy O, Skog PD, Thinnes TC, Bhullar D, Briney B, Menis S, Jones M, Kubitz M, Spencer S, Adachi Y, Burton DR, Schief WR, Nemazee D.

Science. 2015 Jul 10;349(6244):156-61. doi: 10.1126/science.aac5894. Epub 2015 Jun 18.

27.

Vaccine-Elicited Tier 2 HIV-1 Neutralizing Antibodies Bind to Quaternary Epitopes Involving Glycan-Deficient Patches Proximal to the CD4 Binding Site.

Crooks ET, Tong T, Chakrabarti B, Narayan K, Georgiev IS, Menis S, Huang X, Kulp D, Osawa K, Muranaka J, Stewart-Jones G, Destefano J, O'Dell S, LaBranche C, Robinson JE, Montefiori DC, McKee K, Du SX, Doria-Rose N, Kwong PD, Mascola JR, Zhu P, Schief WR, Wyatt RT, Whalen RG, Binley JM.

PLoS Pathog. 2015 May 29;11(5):e1004932. doi: 10.1371/journal.ppat.1004932. eCollection 2015 May.

28.

The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

Zhang SQ, Kulp DW, Schramm CA, Mravic M, Samish I, DeGrado WF.

Structure. 2015 Mar 3;23(3):527-541. doi: 10.1016/j.str.2015.01.009. Epub 2015 Feb 19.

29.

Promiscuous glycan site recognition by antibodies to the high-mannose patch of gp120 broadens neutralization of HIV.

Sok D, Doores KJ, Briney B, Le KM, Saye-Francisco KL, Ramos A, Kulp DW, Julien JP, Menis S, Wickramasinghe L, Seaman MS, Schief WR, Wilson IA, Poignard P, Burton DR.

Sci Transl Med. 2014 May 14;6(236):236ra63. doi: 10.1126/scitranslmed.3008104.

30.

Escape from neutralization by the respiratory syncytial virus-specific neutralizing monoclonal antibody palivizumab is driven by changes in on-rate of binding to the fusion protein.

Bates JT, Keefer CJ, Slaughter JC, Kulp DW, Schief WR, Crowe JE Jr.

Virology. 2014 Apr;454-455:139-44. doi: 10.1016/j.virol.2014.02.010. Epub 2014 Mar 3.

31.

Nitric oxide synthase domain interfaces regulate electron transfer and calmodulin activation.

Smith BC, Underbakke ES, Kulp DW, Schief WR, Marletta MA.

Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):E3577-86. doi: 10.1073/pnas.1313331110. Epub 2013 Sep 3.

32.

Advances in structure-based vaccine design.

Kulp DW, Schief WR.

Curr Opin Virol. 2013 Jun;3(3):322-31. doi: 10.1016/j.coviro.2013.05.010. Epub 2013 Jun 25. Review.

33.

Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins.

Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Solomon EI, DeGrado WF.

Nat Chem. 2012 Nov;4(11):900-6. doi: 10.1038/nchem.1454. Epub 2012 Sep 23. Erratum in: Nat Chem. 2012 Dec;4(12):1050. Szyperski, Thomas G [corrected to Szyperski, Thomas].

34.

Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).

Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A.

J Comput Chem. 2012 Jul 30;33(20):1645-61. doi: 10.1002/jcc.22968. Epub 2012 May 8.

35.

Generalized fragment picking in Rosetta: design, protocols and applications.

Gront D, Kulp DW, Vernon RM, Strauss CE, Baker D.

PLoS One. 2011;6(8):e23294. doi: 10.1371/journal.pone.0023294. Epub 2011 Aug 24.

36.

Design of a switchable eliminase.

Korendovych IV, Kulp DW, Wu Y, Cheng H, Roder H, DeGrado WF.

Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):6823-7. doi: 10.1073/pnas.1018191108. Epub 2011 Apr 11.

37.

Salt bridges: geometrically specific, designable interactions.

Donald JE, Kulp DW, DeGrado WF.

Proteins. 2011 Mar;79(3):898-915. doi: 10.1002/prot.22927. Epub 2011 Jan 5.

38.

A novel multifunctional oligonucleotide microarray for Toxoplasma gondii.

Bahl A, Davis PH, Behnke M, Dzierszinski F, Jagalur M, Chen F, Shanmugam D, White MW, Kulp D, Roos DS.

BMC Genomics. 2010 Oct 25;11:603. doi: 10.1186/1471-2164-11-603.

39.

Consensus motif for integrin transmembrane helix association.

Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF.

Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):703-8. doi: 10.1073/pnas.0910873107. Epub 2009 Dec 18.

40.

Experimental and computational evaluation of forces directing the association of transmembrane helices.

Zhang Y, Kulp DW, Lear JD, DeGrado WF.

J Am Chem Soc. 2009 Aug 19;131(32):11341-3. doi: 10.1021/ja904625b.

PMID:
19722646
41.

Multiple approaches converge on the structure of the integrin alphaIIb/beta3 transmembrane heterodimer.

Metcalf DG, Kulp DW, Bennett JS, DeGrado WF.

J Mol Biol. 2009 Oct 2;392(4):1087-101. doi: 10.1016/j.jmb.2009.06.032. Epub 2009 Jun 13.

42.

Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2.

Kwan AL, Li L, Kulp DC, Dutcher SK, Stormo GD.

BMC Genomics. 2009 May 7;10:210. doi: 10.1186/1471-2164-10-210.

43.

Small-molecule inhibitors of integrin alpha2beta1 that prevent pathological thrombus formation via an allosteric mechanism.

Miller MW, Basra S, Kulp DW, Billings PC, Choi S, Beavers MP, McCarty OJ, Zou Z, Kahn ML, Bennett JS, DeGrado WF.

Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):719-24. doi: 10.1073/pnas.0811622106. Epub 2009 Jan 13.

44.

Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering.

Jagalur M, Pal C, Learned-Miller E, Zoeller RT, Kulp D.

BMC Bioinformatics. 2007;8 Suppl 10:S5. doi: 10.1186/1471-2105-8-S10-S5.

45.
46.

Genome sequence of Aedes aegypti, a major arbovirus vector.

Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW.

Science. 2007 Jun 22;316(5832):1718-23. Epub 2007 May 17.

47.
48.

Conformational and quantitative characterization of oritavancin-peptidoglycan complexes in whole cells of Staphylococcus aureus by in vivo 13C and 15N labeling.

Cegelski L, Steuber D, Mehta AK, Kulp DW, Axelsen PH, Schaefer J.

J Mol Biol. 2006 Apr 7;357(4):1253-62. Epub 2006 Jan 30.

PMID:
16483598
49.

Unusual intron conservation near tissue-regulated exons found by splicing microarrays.

Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M Jr.

PLoS Comput Biol. 2006 Jan;2(1):e4. Epub 2006 Jan 20.

50.

Model-P: a basecalling method for resequencing microarrays of diploid samples.

Zhan Y, Kulp D.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii182-9.

PMID:
16204100

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