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Items: 40

1.

Linear mixed model for heritability estimation that explicitly addresses environmental variation.

Heckerman D, Gurdasani D, Kadie C, Pomilla C, Carstensen T, Martin H, Ekoru K, Nsubuga RN, Ssenyomo G, Kamali A, Kaleebu P, Widmer C, Sandhu MS.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7377-82. doi: 10.1073/pnas.1510497113.

2.

Further improvements to linear mixed models for genome-wide association studies.

Widmer C, Lippert C, Weissbrod O, Fusi N, Kadie C, Davidson R, Listgarten J, Heckerman D.

Sci Rep. 2014 Nov 12;4:6874. doi: 10.1038/srep06874.

3.

HIV control is mediated in part by CD8+ T-cell targeting of specific epitopes.

Pereyra F, Heckerman D, Carlson JM, Kadie C, Soghoian DZ, Karel D, Goldenthal A, Davis OB, DeZiel CE, Lin T, Peng J, Piechocka A, Carrington M, Walker BD.

J Virol. 2014 Nov;88(22):12937-48. doi: 10.1128/JVI.01004-14. Epub 2014 Aug 27.

4.

Greater power and computational efficiency for kernel-based association testing of sets of genetic variants.

Lippert C, Xiang J, Horta D, Widmer C, Kadie C, Heckerman D, Listgarten J.

Bioinformatics. 2014 Nov 15;30(22):3206-14. doi: 10.1093/bioinformatics/btu504. Epub 2014 Jul 29.

5.

The benefits of selecting phenotype-specific variants for applications of mixed models in genomics.

Lippert C, Quon G, Kang EY, Kadie CM, Listgarten J, Heckerman D.

Sci Rep. 2013;3:1815. doi: 10.1038/srep01815.

6.

A powerful and efficient set test for genetic markers that handles confounders.

Listgarten J, Lippert C, Kang EY, Xiang J, Kadie CM, Heckerman D.

Bioinformatics. 2013 Jun 15;29(12):1526-33. doi: 10.1093/bioinformatics/btt177. Epub 2013 Apr 18.

7.

An exhaustive epistatic SNP association analysis on expanded Wellcome Trust data.

Lippert C, Listgarten J, Davidson RI, Baxter S, Poon H, Kadie CM, Heckerman D.

Sci Rep. 2013;3:1099. doi: 10.1038/srep01099. Epub 2013 Jan 22. Erratum in: Sci Rep. 2013 Feb 18;3:1321. Poong, Hoifung [corrected to Poon, Hoifung].

8.

High-dimensional immunomonitoring models of HIV-1-specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control.

Ndhlovu ZM, Chibnik LB, Proudfoot J, Vine S, McMullen A, Cesa K, Porichis F, Jones RB, Alvino DM, Hart MG, Stampouloglou E, Piechocka-Trocha A, Kadie C, Pereyra F, Heckerman D, De Jager PL, Walker BD, Kaufmann DE.

Blood. 2013 Jan 31;121(5):801-11. doi: 10.1182/blood-2012-06-436295. Epub 2012 Dec 11.

9.

Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans.

McLaren PJ, Ripke S, Pelak K, Weintrob AC, Patsopoulos NA, Jia X, Erlich RL, Lennon NJ, Kadie CM, Heckerman D, Gupta N, Haas DW, Deeks SG, Pereyra F, Walker BD, de Bakker PI; International HIV Controllers Study.

Hum Mol Genet. 2012 Oct 1;21(19):4334-47. doi: 10.1093/hmg/dds226. Epub 2012 Jun 19.

10.

Improved linear mixed models for genome-wide association studies.

Listgarten J, Lippert C, Kadie CM, Davidson RI, Eskin E, Heckerman D.

Nat Methods. 2012 May 30;9(6):525-6. doi: 10.1038/nmeth.2037. No abstract available.

11.

Learning transcriptional regulatory relationships using sparse graphical models.

Zhang X, Cheng W, Listgarten J, Kadie C, Huang S, Wang W, Heckerman D.

PLoS One. 2012;7(5):e35762. doi: 10.1371/journal.pone.0035762. Epub 2012 May 7.

12.

Widespread impact of HLA restriction on immune control and escape pathways of HIV-1.

Carlson JM, Listgarten J, Pfeifer N, Tan V, Kadie C, Walker BD, Ndung'u T, Shapiro R, Frater J, Brumme ZL, Goulder PJ, Heckerman D.

J Virol. 2012 May;86(9):5230-43. doi: 10.1128/JVI.06728-11. Epub 2012 Feb 29.

13.

FaST linear mixed models for genome-wide association studies.

Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D.

Nat Methods. 2011 Sep 4;8(10):833-5. doi: 10.1038/nmeth.1681.

PMID:
21892150
14.

Translation of HLA-HIV associations to the cellular level: HIV adapts to inflate CD8 T cell responses against Nef and HLA-adapted variant epitopes.

Almeida CA, Bronke C, Roberts SG, McKinnon E, Keane NM, Chopra A, Kadie C, Carlson J, Haas DW, Riddler SA, Haubrich R, Heckerman D, Mallal S, John M.

J Immunol. 2011 Sep 1;187(5):2502-13. doi: 10.4049/jimmunol.1100691. Epub 2011 Aug 5.

15.

HIV-1 adaptation to NK-cell-mediated immune pressure.

Alter G, Heckerman D, Schneidewind A, Fadda L, Kadie CM, Carlson JM, Oniangue-Ndza C, Martin M, Li B, Khakoo SI, Carrington M, Allen TM, Altfeld M.

Nature. 2011 Aug 3;476(7358):96-100. doi: 10.1038/nature10237.

16.

Conditional random fields for fast, large-scale genome-wide association studies.

Huang JC, Meek C, Kadie C, Heckerman D.

PLoS One. 2011;6(7):e21591. doi: 10.1371/journal.pone.0021591. Epub 2011 Jul 12.

17.

Variable HIV peptide stability in human cytosol is critical to epitope presentation and immune escape.

Lazaro E, Kadie C, Stamegna P, Zhang SC, Gourdain P, Lai NY, Zhang M, Martinez SA, Heckerman D, Le Gall S.

J Clin Invest. 2011 Jun;121(6):2480-92. doi: 10.1172/JCI44932. Epub 2011 May 9.

18.

Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers.

Brumme ZL, Li C, Miura T, Sela J, Rosato PC, Brumme CJ, Markle TJ, Martin E, Block BL, Trocha A, Kadie CM, Allen TM, Pereyra F, Heckerman D, Walker BD, Brockman MA.

J Acquir Immune Defic Syndr. 2011 Feb 1;56(2):100-8. doi: 10.1097/QAI.0b013e3181fe9450.

19.

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation.

International HIV Controllers Study, Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Ripke S, Brumme CJ, Pulit SL, Carrington M, Kadie CM, Carlson JM, Heckerman D, Graham RR, Plenge RM, Deeks SG, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Gao X, Qi Y, Yuki Y, Piechocka-Trocha A, Cutrell E, Rosenberg R, Moss KL, Lemay P, O'Leary J, Schaefer T, Verma P, Toth I, Block B, Baker B, Rothchild A, Lian J, Proudfoot J, Alvino DM, Vine S, Addo MM, Allen TM, Altfeld M, Henn MR, Le Gall S, Streeck H, Haas DW, Kuritzkes DR, Robbins GK, Shafer RW, Gulick RM, Shikuma CM, Haubrich R, Riddler S, Sax PE, Daar ES, Ribaudo HJ, Agan B, Agarwal S, Ahern RL, Allen BL, Altidor S, Altschuler EL, Ambardar S, Anastos K, Anderson B, Anderson V, Andrady U, Antoniskis D, Bangsberg D, Barbaro D, Barrie W, Bartczak J, Barton S, Basden P, Basgoz N, Bazner S, Bellos NC, Benson AM, Berger J, Bernard NF, Bernard AM, Birch C, Bodner SJ, Bolan RK, Boudreaux ET, Bradley M, Braun JF, Brndjar JE, Brown SJ, Brown K, Brown ST, Burack J, Bush LM, Cafaro V, Campbell O, Campbell J, Carlson RH, Carmichael JK, Casey KK, Cavacuiti C, Celestin G, Chambers ST, Chez N, Chirch LM, Cimoch PJ, Cohen D, Cohn LE, Conway B, Cooper DA, Cornelson B, Cox DT, Cristofano MV, Cuchural G Jr, Czartoski JL, Dahman JM, Daly JS, Davis BT, Davis K, Davod SM, DeJesus E, Dietz CA, Dunham E, Dunn ME, Ellerin TB, Eron JJ, Fangman JJ, Farel CE, Ferlazzo H, Fidler S, Fleenor-Ford A, Frankel R, Freedberg KA, French NK, Fuchs JD, Fuller JD, Gaberman J, Gallant JE, Gandhi RT, Garcia E, Garmon D, Gathe JC Jr, Gaultier CR, Gebre W, Gilman FD, Gilson I, Goepfert PA, Gottlieb MS, Goulston C, Groger RK, Gurley TD, Haber S, Hardwicke R, Hardy WD, Harrigan PR, Hawkins TN, Heath S, Hecht FM, Henry WK, Hladek M, Hoffman RP, Horton JM, Hsu RK, Huhn GD, Hunt P, Hupert MJ, Illeman ML, Jaeger H, Jellinger RM, John M, Johnson JA, Johnson KL, Johnson H, Johnson K, Joly J, Jordan WC, Kauffman CA, Khanlou H, Killian RK, Kim AY, Kim DD, Kinder CA, Kirchner JT, Kogelman L, Kojic EM, Korthuis PT, Kurisu W, Kwon DS, LaMar M, Lampiris H, Lanzafame M, Lederman MM, Lee DM, Lee JM, Lee MJ, Lee ET, Lemoine J, Levy JA, Llibre JM, Liguori MA, Little SJ, Liu AY, Lopez AJ, Loutfy MR, Loy D, Mohammed DY, Man A, Mansour MK, Marconi VC, Markowitz M, Marques R, Martin JN, Martin HL Jr, Mayer KH, McElrath MJ, McGhee TA, McGovern BH, McGowan K, McIntyre D, Mcleod GX, Menezes P, Mesa G, Metroka CE, Meyer-Olson D, Miller AO, Montgomery K, Mounzer KC, Nagami EH, Nagin I, Nahass RG, Nelson MO, Nielsen C, Norene DL, O'Connor DH, Ojikutu BO, Okulicz J, Oladehin OO, Oldfield EC 3rd, Olender SA, Ostrowski M, Owen WF Jr, Pae E, Parsonnet J, Pavlatos AM, Perlmutter AM, Pierce MN, Pincus JM, Pisani L, Price LJ, Proia L, Prokesch RC, Pujet HC, Ramgopal M, Rathod A, Rausch M, Ravishankar J, Rhame FS, Richards CS, Richman DD, Rodes B, Rodriguez M, Rose RC 3rd, Rosenberg ES, Rosenthal D, Ross PE, Rubin DS, Rumbaugh E, Saenz L, Salvaggio MR, Sanchez WC, Sanjana VM, Santiago S, Schmidt W, Schuitemaker H, Sestak PM, Shalit P, Shay W, Shirvani VN, Silebi VI, Sizemore JM Jr, Skolnik PR, Sokol-Anderson M, Sosman JM, Stabile P, Stapleton JT, Starrett S, Stein F, Stellbrink HJ, Sterman FL, Stone VE, Stone DR, Tambussi G, Taplitz RA, Tedaldi EM, Telenti A, Theisen W, Torres R, Tosiello L, Tremblay C, Tribble MA, Trinh PD, Tsao A, Ueda P, Vaccaro A, Valadas E, Vanig TJ, Vecino I, Vega VM, Veikley W, Wade BH, Walworth C, Wanidworanun C, Ward DJ, Warner DA, Weber RD, Webster D, Weis S, Wheeler DA, White DJ, Wilkins E, Winston A, Wlodaver CG, van't Wout A, Wright DP, Yang OO, Yurdin DL, Zabukovic BW, Zachary KC, Zeeman B, Zhao M.

Science. 2010 Dec 10;330(6010):1551-7. doi: 10.1126/science.1195271. Epub 2010 Nov 4.

20.

Correction for hidden confounders in the genetic analysis of gene expression.

Listgarten J, Kadie C, Schadt EE, Heckerman D.

Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16465-70. doi: 10.1073/pnas.1002425107. Epub 2010 Sep 1.

21.

Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection.

Brockman MA, Brumme ZL, Brumme CJ, Miura T, Sela J, Rosato PC, Kadie CM, Carlson JM, Markle TJ, Streeck H, Kelleher AD, Markowitz M, Jessen H, Rosenberg E, Altfeld M, Harrigan PR, Heckerman D, Walker BD, Allen TM.

J Virol. 2010 Nov;84(22):11937-49. doi: 10.1128/JVI.01086-10. Epub 2010 Sep 1.

22.

Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters.

Wright JK, Brumme ZL, Carlson JM, Heckerman D, Kadie CM, Brumme CJ, Wang B, Losina E, Miura T, Chonco F, van der Stok M, Mncube Z, Bishop K, Goulder PJ, Walker BD, Brockman MA, Ndung'u T.

J Virol. 2010 Oct;84(20):10820-31. doi: 10.1128/JVI.01084-10. Epub 2010 Aug 11.

23.

Additive contribution of HLA class I alleles in the immune control of HIV-1 infection.

Leslie A, Matthews PC, Listgarten J, Carlson JM, Kadie C, Ndung'u T, Brander C, Coovadia H, Walker BD, Heckerman D, Goulder PJ.

J Virol. 2010 Oct;84(19):9879-88. doi: 10.1128/JVI.00320-10. Epub 2010 Jul 21.

24.

Exploiting knowledge of immune selection in HIV-1 to detect HIV-specific CD8 T-cell responses.

Almeida CA, Roberts SG, Laird R, McKinnon E, Ahmad I, Keane NM, Chopra A, Kadie C, Heckerman D, Mallal S, John M.

Vaccine. 2010 Aug 23;28(37):6052-7. doi: 10.1016/j.vaccine.2010.06.091. Epub 2010 Jul 7.

25.

HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins.

Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, Brockman MA, Swenson LC, Tao I, Szeto S, Rosato P, Sela J, Kadie CM, Frahm N, Brander C, Haas DW, Riddler SA, Haubrich R, Walker BD, Harrigan PR, Heckerman D, Mallal S.

PLoS One. 2009 Aug 19;4(8):e6687. doi: 10.1371/journal.pone.0006687.

26.

Rare HLA drive additional HIV evolution compared to more frequent alleles.

Rousseau CM, Lockhart DW, Listgarten J, Maley SN, Kadie C, Learn GH, Nickle DC, Heckerman DE, Deng W, Brander C, Ndung'u T, Coovadia H, Goulder PJ, Korber BT, Walker BD, Mullins JI.

AIDS Res Hum Retroviruses. 2009 Mar;25(3):297-303. doi: 10.1089/aid.2008.0208.

27.

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.

Carlson JM, Brumme ZL, Rousseau CM, Brumme CJ, Matthews P, Kadie C, Mullins JI, Walker BD, Harrigan PR, Goulder PJ, Heckerman D.

PLoS Comput Biol. 2008 Nov;4(11):e1000225. doi: 10.1371/journal.pcbi.1000225. Epub 2008 Nov 21.

28.

Design, expression, and processing of epitomized hepatitis C virus-encoded CTL epitopes.

Yerly D, Heckerman D, Allen T, Suscovich TJ, Jojic N, Kadie C, Pichler WJ, Cerny A, Brander C.

J Immunol. 2008 Nov 1;181(9):6361-70.

29.

Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection.

Brumme ZL, Brumme CJ, Carlson J, Streeck H, John M, Eichbaum Q, Block BL, Baker B, Kadie C, Markowitz M, Jessen H, Kelleher AD, Rosenberg E, Kaldor J, Yuki Y, Carrington M, Allen TM, Mallal S, Altfeld M, Heckerman D, Walker BD.

J Virol. 2008 Sep;82(18):9216-27. doi: 10.1128/JVI.01041-08. Epub 2008 Jul 9.

30.

Central role of reverting mutations in HLA associations with human immunodeficiency virus set point.

Matthews PC, Prendergast A, Leslie A, Crawford H, Payne R, Rousseau C, Rolland M, Honeyborne I, Carlson J, Kadie C, Brander C, Bishop K, Mlotshwa N, Mullins JI, Coovadia H, Ndung'u T, Walker BD, Heckerman D, Goulder PJ.

J Virol. 2008 Sep;82(17):8548-59. doi: 10.1128/JVI.00580-08. Epub 2008 Jul 2.

31.

Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection.

Brumme ZL, Tao I, Szeto S, Brumme CJ, Carlson JM, Chan D, Kadie C, Frahm N, Brander C, Walker B, Heckerman D, Harrigan PR.

AIDS. 2008 Jul 11;22(11):1277-86. doi: 10.1097/QAD.0b013e3283021a8c.

PMID:
18580606
32.

HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load.

Rousseau CM, Daniels MG, Carlson JM, Kadie C, Crawford H, Prendergast A, Matthews P, Payne R, Rolland M, Raugi DN, Maust BS, Learn GH, Nickle DC, Coovadia H, Ndung'u T, Frahm N, Brander C, Walker BD, Goulder PJ, Bhattacharya T, Heckerman DE, Korber BT, Mullins JI.

J Virol. 2008 Jul;82(13):6434-46. doi: 10.1128/JVI.02455-07. Epub 2008 Apr 23.

33.

Statistical resolution of ambiguous HLA typing data.

Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, Carrington M, Goulder P, Heckerman D.

PLoS Comput Biol. 2008 Feb 29;4(2):e1000016. doi: 10.1371/journal.pcbi.1000016.

34.

A statistical framework for modeling HLA-dependent T cell response data.

Listgarten J, Frahm N, Kadie C, Brander C, Heckerman D.

PLoS Comput Biol. 2007 Oct;3(10):1879-86.

35.

Extensive HLA class I allele promiscuity among viral CTL epitopes.

Frahm N, Yusim K, Suscovich TJ, Adams S, Sidney J, Hraber P, Hewitt HS, Linde CH, Kavanagh DG, Woodberry T, Henry LM, Faircloth K, Listgarten J, Kadie C, Jojic N, Sango K, Brown NV, Pae E, Zaman MT, Bihl F, Khatri A, John M, Mallal S, Marincola FM, Walker BD, Sette A, Heckerman D, Korber BT, Brander C.

Eur J Immunol. 2007 Sep;37(9):2419-33.

36.

Leveraging information across HLA alleles/supertypes improves epitope prediction.

Heckerman D, Kadie C, Listgarten J.

J Comput Biol. 2007 Jul-Aug;14(6):736-46.

PMID:
17691891
37.

Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1.

Brumme ZL, Brumme CJ, Heckerman D, Korber BT, Daniels M, Carlson J, Kadie C, Bhattacharya T, Chui C, Szinger J, Mo T, Hogg RS, Montaner JS, Frahm N, Brander C, Walker BD, Harrigan PR.

PLoS Pathog. 2007 Jul;3(7):e94. Erratum in: PLoS Pathog. 2007 Aug 10;3(8):e121.

38.

Leveraging hierarchical population structure in discrete association studies.

Carlson J, Kadie C, Mallal S, Heckerman D.

PLoS One. 2007 Jul 4;2(7):e591.

39.

Founder effects in the assessment of HIV polymorphisms and HLA allele associations.

Bhattacharya T, Daniels M, Heckerman D, Foley B, Frahm N, Kadie C, Carlson J, Yusim K, McMahon B, Gaschen B, Mallal S, Mullins JI, Nickle DC, Herbeck J, Rousseau C, Learn GH, Miura T, Brander C, Walker B, Korber B.

Science. 2007 Mar 16;315(5818):1583-6.

40.

Learning MHC I--peptide binding.

Jojic N, Reyes-Gomez M, Heckerman D, Kadie C, Schueler-Furman O.

Bioinformatics. 2006 Jul 15;22(14):e227-35.

PMID:
16873476

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