Biology Publications
- J. Listgarten, Z. Brumme, C. Kadie, G. Xiaojiang, B. Walker, M. Carrington, P. Goulder, and D. Heckerman. Statistical resolution of ambiguous HLA typing data. PLoS Computational Biology, to appear.
- D. Yerly, D. Heckerman, T. Allen, J. Chisholm, K. Faircloth, C. Linde, N. Frahm, J. Timm, W. Pichler, A. Cerny, and C. Brander. Increased CTL epitope variant cross-recognition and functional avidity are associated with HCV clearance.J. Virol, January 2008.
- D. Nickle, N. Jojic, D. Heckerman, V. Jojic, D. Kirovski, M. Rolland, S. Pond, J. Mullins. Comparison of immunogen designs that optimize peptide coverage: Reply to Fischer et al.,PLoS Computational Biology, 4(1):e25, January 2008.
- M. Rolland, D. Heckerman, W. Deng, C. Rousseau, H. Coovadia K. Bishop, P. Goulder, B. Walker, C. Brander, J. Mullins. Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads. PLoS ONE, 3(1): e1424, January, 2008.
- J. Listgarten, N. Frahm, C. Kadie, C. Brander, D. Heckerman. A statistical framework for modeling HLA-dependent T cell response data, PLoS Computational Biology, 3(10): e188, October 2007.
- J. Bockhorst, F. Lu, J. H. Janes, J. Keebler, B. Gamain, P. Awadalla, X.Z. Su, R. Samurdala, N. Jojic, and J.D. Smith, Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. Mol Biochem Parasitol. 155(2):103-12, October 2007.
- D. Heckerman, C. Kadie, and J. Listgarten. Leveraging information across HLA alleles/supertypes improves epitope prediction.J. of Comp. Bio, 14(6): 736-746, August 2007.
- N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, Ca. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten, C. Kadie, N. Jojic, K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman, B. Korber, C. Brander. Extensive HLA class I allele promiscuity among viral CTL epitopes. EJI, 37, August 2007.
- Z. Brumme, C. Brumme, D. Heckerman, B. Korber, M. Daniels, J. Carlson, C. Kadie, T. Bhattacharya, C. Chui, T. Mo, R. Hogg, J. Montaner, N. Frahm, C. Brander, B. Walker, P. Harrigan. Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1.PLoS Pathogens, 3(7): e94, July 2007.
- J. Carlson, C. Kadie, S. Mallal, and D. Heckerman. Leveraging hierarchical population structure in discrete association studies.PLoS ONE, 2(7): e591, July 2007.
- J. Listgarten and D. Heckerman, Determining the number of non-spurious arcs in a learned DAG model: Investigation of a Bayesian and a frequentist approach. In Proceedings of Twenty Third Conference on Uncertainty in Artificial Intelligence, Vancouver, Canada, UAI Press, July 2007. Also appears as Technical Report MSR-TR-07-60, Microsoft Research, May, 2007.
- C. Rousseau, G. Learn, T. Bhattacharya, D. Nickle, D. Heckerman, S. Chetty, C. Brander, P. Goulder, B. Walker, P. Kiepiela, B. Korber, and J. Mullins. Extensive intrasubtype recombination in South African Human Immunodeficiency Virus type I subtype C infections. J Virol, 81(9): 4492-4500. May, 2007.
- D. Nickle, M. Rolland, M. Jensen, S. Pond, W. Deng, M. Seligman, D. Heckerman, J. Mullins, and N. Jojic. Coping with viral diversity in HIV vaccine design, PLoS Computational Biology, 3(4): e75, April 2007.
- T. Bhattacharya, M. Daniels, D. Heckerman, B. Foley, N. Frahm, C. Kadie, J. Carlson, K. Yusim, B. McMahon, B. Gaschen, S. Mallal, J. Mullins, D. Nickle, J. Herbeck, C. Rousseau, G. Learn, T. Miura, C. Brander, B. Walker, B. Korber. Founder effects in the assessment of HIV polymorphisms and HLA allele associations, Science, 315, 1583-1586, March 16 2007.
- P. Kiepiela, K. Ngumbela, C. Thobakgale, D. Ramduth, I. Honeyborne, E. Moodley, S. Reddy, C. de Pierres, Z. Mncube, N. Mkhwanazi, K. Bishop, M. van der Stok, K. Nair, N. Khan, H. Crawford, R. Payne, A. Leslie, J. Prado, A. Prendergast, J. Frater, N. McCarthy, C. Brander, G. Learn, D. Nickle, C. Rousseau, H. Coovadia, J. Mullins, D. Heckerman, B. Walker, and P. Goulder. CD8+ T-cell responses to different HIV proteins have discordant associations with viral load, Nature Medicine, December 17 2006.
- N. Jojic, V. Jojic, B. Frey, C. Meek, and D. Heckerman. Using epitomes to model genetic diversity: Rational design of HIV vaccine cocktails. NIPS 2005.
- V. Jojic, N. Jojic, C. Meek, D. Geiger, A. Siepel, D. Haussler, and D. Heckerman: Efficient approximations for learning phylogenetic HMM models from data. ISMB/ECCB (Supplement of Bioinformatics) 161-168, 2004. Also appears as Technical Report MSR-TR-2003-62, Microsoft Research, October, 2003.
