David Heckerman


Senior Director, eScience Research Group, Microsoft Research

E-mail: heckerma@microsoft.com
Mail: 1100 Glendon Ave Suite PH1, Los Angeles CA 90024

We are currently taking applications for internships from Ph.D. students with expertise in genomics and computational biology.  Please contact me if you are interested.


Research activities

I am interested in learning from data. The models and methods I use are inspired by work in the fields of statistics and data analysis, machine learning, probability theory, decision theory, decision analysis, and artificial intelligence. My recent work has concentrated on using graphical models for data analysis and visualization in biology and medicine with a special focus on the design of HIV vaccines and genome-wide association studies.

Selected publications

·         D. Heckerman.  A Tutorial on Learning with Bayesian Networks.  In Learning in Graphical Models, M. Jordan, ed.. MIT Press, Cambridge, MA, 1999.  Also appears as Technical Report MSR-TR-95-06, Microsoft Research, March, 1995.  An earlier version appears as Bayesian Networks for Data Mining, Data Mining and Knowledge Discovery, 1: 79-119, 1997.

 

·         J. Listgarten, C. Lippert, and D. Heckerman. FaST-LMM-Select for addressing confounding from spatial structure and rare variants.  Nature Genetics, 45: 470-471, April 2013 (doi:10.1038/ng.2620).

 

·         J. Listgarten, C. Lippert, C.M. Kadie, R.I. Davidson, E. Eskin, and D. Heckerman.  Improved linear mixed models for genome-wide association studies.  Nature Methods, 9: 525-526, June 2012 (doi:10.1038/nmeth.2037).

 

·         C. Lippert, J. Listgarten, Y. Liu, C.M. Kadie, R.I. Davidson, and D. Heckerman.  FaST linear mixed models for genome-wide association studies.  Nature Methods, 8: 833-835, Oct 2011 (doi:10.1038/nmeth.1681).

 

·         J. Listgarten, C. Lippert, E.Y. Kang, J. Xiang, C.M. Kadie, and D. Heckerman.  A powerful and efficient set test for genetic markers that handles confounders.  Bioinformatics, May 2013 (doi: 10.1093/bioinformatics/btt177).

 

·         J. Listgarten, C. Kadie, E. Schadt, D. Heckerman.  Correction for hidden confounders in the genetic analysis of gene expression. PNAS, 107 (38): 16465-16470, September 2010 (doi: 10.1073/pnas.1002425107).

 

·         G. Alter, D. Heckerman, A. Schneidewind, L. Fadda, C. Kadie, J. Carlson, C. Oniangue-Ndza, M. Martin, B. Li, S. Khakoo, M. Carrington, T. Allen, M. Altfeld M.  HIV-1 adaptation to NK-cell-mediated immune pressure.  Nature, 476 (7358): 96-100, August 2011.

 

·         J. Carlson, Z. Brumme, C. Rousseau, C. Brumme, P. Matthews, C. Kadie, J. Mullins, B. Walker, P. Harrigan, P. Goulder, D. Heckerman.  Phylogenetic dependency networks: Inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Computational Biology, 4(11): e1000225, November 2008.

 

·         J. Goodman, D. Heckerman, and R. Rounthwaite.  Stopping Spam.  Scientific American, April, 2005.

 

·         D. Heckerman.  Probabilistic interpretations for MYCIN's certainty factors.  In Proceedings of the Workshop on Uncertainty and Probability in Artificial Intelligence, Los Angeles, CA, pages 9-20. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, August 1985.  Also in L. Kanal. and J. Lemmer, editors, Uncertainty in Artificial Intelligence, pages 167-196. North-Holland, New York, 1986.

 

·         D. Heckerman.  Probabilistic Similarity Networks.  MIT Press, Cambridge, MA, 1991.

All publications

·         N. Furlotte, D. Heckerman, and C. Lippert.  Quantifying the uncertainty in heritability.  Journal of Human Genetics 27, March 2014 (doi: 10.1038/jhg.2014.15).

 

·         J. Zou, C. Lippert, D. Heckerman, M. Aryee, and J. Listgarten.  Epigenome-wide association studies without the need for cell-type composition.  Nature Methods 11:309–311, Jan 2014 (doi:10.1038/nmeth.2815).

 

·         J. Sunshine, M. Kim, J. Carlson, D. Heckerman, J. Czartoski, S. Migueles, J. Maenza, M. McElrath, J. Mullins, and N. Frahm. Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication.  Journal of Virology 88(2):1354-65, Jan 2013 (doi: 10.1128/JVI.02361-13).

 

·         I. Bartha, J.Carlson, C. Brumme, P. McLaren, Z. Brumme, M. John, D. Haas, J. Martinez-Picado, J. Dalmau, C. López-Galíndez, C. Casado, A. Rauch, H. Günthard, E. Bernasconi, P. Vernazza, T. Klimkait, S. Yerly, S. O’Brien, J. Listgarten, N. Pfeifer, C. Lippert, N. Fusi, Z. Kutalik, T. Allen, V. Müller, P. Harrigan, D. Heckerman, A. Telenti, and J. Fellay.  A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.  eLife 2013;2:e01123, October 2013 (http://dx.doi.org/10.7554/eLife.01123).

 

·         C. Lippert, G. Quon, E.Y. Kang, C.M. Kadie, J. Listgarten, and D. Heckerman.  The benefits of selecting phenotype-specific variants for applications of mixed models in genomics.  Scientific Reports, 3, May 2013 (doi:10.1038/srep01815).

 

·         J. Listgarten, C. Lippert, E.Y. Kang, J. Xiang, C.M. Kadie, and D. Heckerman.  A powerful and efficient set test for genetic markers that handles confounders.  Bioinformatics, May 2013 (doi: 10.1093/bioinformatics/btt177).

 

·         J. Listgarten, C. Lippert, and D. Heckerman. FaST-LMM-Select for addressing confounding from spatial structure and rare variants.  Nature Genetics, 45: 470-471, April 2013 (doi:10.1038/ng.2620).

 

·         C. Boutwell, J.M. Carlson, T. Lin, A. Seese, K. Power, J. Peng, Y. Tang, Z. Brumme, D. Heckerman, A. Schneidewind, and T. Allen.  Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins.  Journal of Virology, 87(7): 3952-3965, April 2013 (10.1128/JVI.03233-12).

 

·         G. Quon, C. Lippert, D. Heckerman, and J. Listgarten.  Patterns of methylation heritability in a genome-wide analysis of four brain regions.  Nucleic Acids Research, March 2013 (doi: 10.1093/nar/gks1449).

 

·         C. Bronke, C.A. Almeida, E. McKinnon, S.G. Roberts, N.M.  Keane, A. Chopra, J.M. Carlson, D. Heckerman, S. Mallal, and M. John.  HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes.  AIDS, 27(6): 899–905, March 2013 (doi: 10.1097/QAD.0b013e32835e1616).

 

·         V. Kulkarni, M. Rosati, A. Valentin, B. Ganneru, A.K. Singh, J. Yan, M. Rolland, C. Alicea, R.K. Beach, G. Zhang, S. Le Gall, K.E. Broderick, N.Y. Sardesai, D. Heckerman, B. Mothe, C. Brander, D.B. Weiner, J.I. Mullins, G.N. Pavlakis, B.K. Felber.  HIV-1 p24-Gag derived conserved element DNA vaccine increases the breadth of immune response in mice.  PLoS ONE 8(3): e60245, March 2013 (doi:10.1371/journal.pone.0060245).

 

·         C. Lippert, J. Listgarten, R.I. Davidson, J. Baxter, H. Poon, C.M. Kadie, and  D. Heckerman.  An Exhaustive Epistatic SNP Association Analysis on Expanded Wellcome Trust Data.  Scientific Reports, 3, Jan 2013 (doi:10.1038/srep01099).

 

·         Z.M. Ndhlovu, L.B. Chibnik, J. Proudfoot, S. Vine, A. McMullen, K. Cesa, F. Porichis, R.B. Jones, D.M. Alvino, M.G. Hart, E. Stampouloglou, A. Piechocka-Trocha, C.M. Kadie, F. Pereyra, D. Heckerman, P.L. De Jager, B.D. Walker, and D.E. Kaufmann.  High-dimensional immunomonitoring models of HIV-1–specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control.  Blood, 121(5): 801-811, Jan 2013 (doi: 10.1182/blood-2012-06-436295).

 

·         J. Carlson, C. Brumme, E. Martin, J. Listgarten, M. Brockman, A. Le, C. Chui, L. Cotton, D. Knapp, S. Riddler, R. Haubrich, G. Nelson, N. Pfeifer, C. DeZiel, D. Heckerman, R. Apps, M. Carrington, S. Mallal, R. Harrigan, M. John, and Z. Brumme.  Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1.  Journal of Virology, 86(24): 13202-13216, Dec 2012 (doi: 10.1128/JVI.01998-12).

 

·         P. C. Matthews, M. Koyanagi, H. N. Kloverpris, M. Harndahl, A. Stryhn, T. Akahoshi, H. Gatanaga  S. Oka, C. Juarez Molina, P. H. Valenzuela, R. Avila Rios, D. Cole, J. Carlson, R. P. Payne, A. Ogwu, A. Bere, T. Ndung'u, K. Gounder, F. Chen, L. Riddell, G. Luzzi, R. Shapiro, C. Brander, B. Walker, A. K. Sewell, G. Reyes Teran, D. Heckerman, E. Hunter, S. Buus, M. Takiguchi, P. J. GoulderJ.  Differential clade-specific HLA-B*3501 association with HIV-1 disease outcome is linked to immunogenicity of a single Gag epitope.  Journal of Virololgy, 86(23): 12643-54, Dec 2012 (doi: 10.1128/JVI.01381-12).

 

·         R. Apps, Y. Qi, J. M. Carlson, H. Chen, X. Gao, R. Thomas, Y. Yuki, G. Q. Del Prete, P. Goulder, Z. L. Brumme, C. J. Brumme, M John, S. Mallal, G. Nelson, R. Bosch, D. Heckerman, J. L. Stein, K. A. Soderberg, M. A. Moody, T. N. Denny, Xue Zeng, J. Fang, A. Moffett, J. D. Lifson, J. J. Goedert, S. Buchbinder, G. D. Kirk, J. Fellay, P. McLaren, S. G. Deeks, F. Pereyra, B. Walker, N. L. Michael, A. Weintrob, S. Wolinsky, W. Liao, M. Carrington.  Influence of HLA-C Expression Level on HIV Control.  Science, 340(6128): 87-91, Nov 2012 (doi: 10.1128/JVI.02122-12).

 

·         J.L. Prince, D.T. Claiborne, J.M. Carlson, M. Schaefer, T. Yu, S. Lahki, H.A. Prentice, L.Yue, S.A. Vishwanathan, W. Kilembe, P. Goepfert, M.A. Price, J. Gilmour, J. Mulenga, P. Farmer, C.A. Derdeyn, J. Tang, D. Heckerman, R.A. Kaslow, and S.A. Allen.  Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis.  PLoS Pathogens 8(11): e1003041, Nov 2012 (doi:10.1371/journal.ppat.1003041).

 

·         S. Nomura, N. Hosoya, Z. Brumme, M. Brockman, T. Kikuchi, M. Koga, H. Nakamura, T. Koibuchi, T. Fujii, J. Carlson, D. Heckerman, A. Tachikawa, A. Iwamoto, and T. Miura.  Significant reductions in Gag-protease mediated HIV-1 replication capacity over the course of the epidemic in Japan.  Journal of Virology, 87(3): 1465-1476, Nov 2012 (doi: 10.1128/JVI.02122-12).

 

·         P.C. Matthews, J. Listgarten, J.M. Carlson, R. Payne, K.G. Huang, J. Frater, D. Goedhals, D. Steyn, C. van Vuuren, P. Paioni, P. Jooste, A. Ogwu, R. Shapiro, Z. Mncube, T. Ndung'u, B.D. Walker, D. Heckerman, and P.J.R. Goulder.  Co-operative additive effects between HLA alleles in control of HIV-1.  PLoS One 7(10): e47799, Oct 2012 (doi:10.1371/journal.pone.0047799).

 

·         J. Listgarten, C. Lippert, C.M. Kadie, R.I. Davidson, E. Eskin, and D. Heckerman.  Improved linear mixed models for genome-wide association studies.  Nature Methods, 9: 525-526, June 2012 (doi:10.1038/nmeth.2037).

 

·         P.J. McLaren, S. Ripke, K. Pelak, A.C. Weintrob, N.A. Patsopoulos, X. Jia, R.L. Erlich, N.J. Lennon, C.M. Kadie, D. Heckerman, N. Gupta, D.W. Haas, S.G. Deeks, F. Pereyra, B.D. Walker, P.I.W. de Bakker, and the International HIV Controllers Study.  Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans.  Human Molecular Genetics, 21(19): 4334-4347, June 2012 (doi: 10.1093/hmg/dds226).

 

 

  • M. Brockman, D. Chopera, A. Olvera, C. Brumme, J. Sela, T. Markle, E Martin, J.Carlson, A. Le, R. McGovern, P. Cheung, A. Kelleher, H. Jessen, M. Markowitz, E. Rosenberg, N. Frahm, J. Sanchez, S. Mallal, M. John, P. Harrigan, D. Heckerman, C. Brander, B. Walker, and Z. Brumme.  Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity.  Journal of Virology, April, 2012 (doi: 10.1128/JVI.07133-11).

 

 

 

  • B. Mothe, A. Llano, J. Ibarrondo, M. Daniels, C. Miranda, J. Zamarreno, V. Bach, R. Zuniga, S. Perez-Alvarez, C. Berger, M. Puertas, J. Martinez-Picado, M. Rolland, M. Farfan, J. Szinger, W. Hildebrand, O. Yang, V. Sanchez-Merino, C. Brumme, Z. Brumme, D. Heckerman, T. Allen, J. Mullins, G. Gomez, P. Goulder, B.Walker, J. Gatell, B. Clotet, B. Korber, J. Sanchez and C. Brander.  Definition of the viral targets of protective HIV-1-specific T cell responses.  Journal of Translational Medicine, 9: 208, Dec 2011 (doi:10.1186/1479-5876-9-208).

 

 

 

 

  • G. Alter, D. Heckerman, A. Schneidewind, L. Fadda, C. Kadie, J. Carlson, C. Oniangue-Ndza, M. Martin, B. Li, S. Khakoo, M. Carrington, T. Allen, M. and Altfeld M.  HIV-1 adaptation to NK-cell-mediated immune pressure.  Nature, 476 (7358): 96-100, August 2011.

 

 

·         E. Lazaro, C. Kadie, P. Stamegna, S. Zhang, P. Gourdain, N. Lai, M. Zhang, S. Martinez, D. Heckerman, and S. Le Gall.  Variable HIV peptide stability in human cytosol is critical to epitope presentation and immune escape.  J Clin Invest., 121(6): 2480-2492, June 2011.

 

·         N. Keane, S. Roberts, C. Almeida, T. Krishnan, A. Chopra, E. Demaine, R. Laird, M. Tschochner, J. Carlson, S. Mallal, D. Heckerman, I. James, and M. John.  High-avidity, high-IFNg-producing CD8 T-cell responses following immune selection during HIV-1 infection.  Immunology and Cell Biology, doi:10.1038/icb.2011.34, May, 2011.

 

·         P. Matthews, E. Adland, J. Listgarten, A. Leslie, N. Mkhwanazi, J. Carlson, M. Harndahl, A. Stryhn, R. Payne, A. Ogwu, K. Huang, J. Frater, P. Paioni, H. Kloverpris, P.Jooste, D. Goedhals, C. van Vuuren, D. Steyn, L. Riddell, F. Chen, G. Luzzi, T. Balachandran, T. Ndung'u, S. Buus, M. Carrington, R. Shapiro, D. Heckerman, and P. Goulder.  HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703.  Journal of Immunology, doi: 10.4049, April 2011.

 

·         K. Huang, D. Goedhals, J. Carlson, M. Brockman, S. Mishra, Z. Brumme, S. Hickling, C. Tang, T. Miura7, C. Seebregts, D. Heckerman, T. Ndung'u, B. Walker, P. Klenerman, D. Steyn, P. Goulder, R. Phillips, Bloemfontein-Oxford Collaborative Group, C. van Vuuren, and J. Frater.  Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations.  PLoS One, 6(4):e19018, April, 2011.

 

·         M. Rolland, N. Frahm, D. Nickle, N. Jojic, W. Deng, T. Allen, C. Brander, D. Heckerman, J. Mullins.  Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences.  PLoS One, 28;6(3):e17969, March 2011.

 

·         J. Wright, V. Novitsky, M. Brockman, Z. Brumme, C. Brumme, J. Carlson, D. Heckerman, B. Wang, E. Losina, M. Leshwedi, M. van der Stok, L. Maphumulo, N. Mkhwanazi, F. Chonco, P. Goulder, M. Essex, B. Walker, and T. Ndung'u.  Influence of Gag-Protease-mediated replication vapacity on disease progression in individuals recently infected with HIV-1 subtype C.  Journal of Virology, doi:10.1128/JVI.02520-10, February, 2010.

 

·         The International HIV Controllers Study.  The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation, Science, 330: 1551-1557, December 10 2010.

 

·         H. Crawford, P. Matthews, M. Schaefer, J. Carlson, A. Leslie, W. Kilembe, S. Allen, T. Ndung'u, D. Heckerman, E. Hunter, and P. Goulder.  The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms.  Journal of Virology, doi:10.1128/JVI.01879-10, November, 2010.

 

·         M. Brockman, Z. Brumme, C. Brumme, T. Miura, J. Sela, P. Rosato, C. Kadie, J. Carlson, T. Markle, H. Streeck, A. Kelleher, M. Markowitz, H. Jessen, E. Rosenberg, M. Altfeld, P. Harrigan, D. Heckerman, B. Walker, and T. Allen.  Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection.  Journal of Virology, 84(22): 11937-11949, November 2010.

 

·         A. Leslie, P. Matthews, J. Listgarten, J. Carlson, C. Kadie, T. Ndung'u, C. Brander, H. Coovadia, B. Walker, D. Heckerman and P. Goulder. Additive contribution of HLA class I alleles in the immune control of HIV-1 infection. Journal of Virology, 84(19):9879-9888, October 2010.

 

·         H. Laaksovirta, T. Peuralinna, J. Schymick, S. Scholz, S. Lai, L. Myllykangas, R. Sulkava, L. Jansson, D. Hernandez, J. Gibbs, M. Nalls, D. Heckerman, P. Tienari, B. Traynor.  Chromosome 9p21 in amyotrophic lateral sclerosis in Finland: A genome-wide association study.  The Lancet Neurology, 9(10): 978-985, October 2010.

 

·         J. Listgarten, C. Kadie, E. Schadt, D. Heckerman.  Correction for hidden confounders in the genetic analysis of gene expression. PNAS, 107 (38): 16465-16470, September 2010 (doi: 10.1073/pnas.1002425107).

 

·         M. Rolland, J. Carlson, S. Manocheewa, J. Swain, E. Lanxon-Cookson, W. Deng,  C. Rousseau, D. Raugi, G. Learn, B. Maust, H. Coovadia, T. Ndung'u, P. Goulder, B. Walker, C. Brander, D. Heckerman, J. Mullins.  Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics.  PLoS One, 5(9), September 1, 2010.

 

·         A. S, V.Y.F. Tan, J. Winn, M. Svens, C.M. Bishop, D. Heckerman, I. Buchan, and A. Custovic, Beyond atopy: Multiple patterns of sensitization in relation to asthma in a birth cohort study.  American Journal of Respiratory and Critical Care Medicine, 181(11):1200-6, June 2010.

 

·         R. Shachter and D. Heckerman.  Pearl Causality and the Value of Control.  In Heuristics, Probability and Causality: A Tribute to Judea Pearl, R. Dechter, H. Geffner, and J. Halpern eds.  2010.

 

·         M. John, D. Heckerman, I. James, L. Park, J. Carlson, A. Chopra, S. Gaudieri, D. Nolan, D. Haas, S. Riddler, R. Haubrich, and Simon Mallal.  Adaptive interactions between HLA and HIV-1: Highly divergent selection imposed by HLA class I molecules with common supertype motifs.  The Journal of Immunology, 184:4368-4377, March 2010.

 

·         M. Koga, A. Kawana-Tachikawa, D. Heckerman, T. Odawara, H. Nakamura, T. Koibuchi, T. Fujii, T. Miura, and A. Iwamoto.  Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time.  Microbiology and Immunology, 54(4): 196-205.  January 2010.

 

·         A. Bansal, J. Carlson, J. Yan, O. Akinsiku, M. Schaefer, S. Sabbaj, A. Bet, D. Levy, S. Heath, J. Tang, R. Kaslow, B. Walker, T. Ndungu, P. Goulder, D. Heckerman, E. Hunter, and P. Goepfert.  CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription.  JEM, 10.1084/jem.20092060, January 2010.

 

·         C. Berger, J. Carlson, C. Brumme, K. Hartman, Z. Brumme, L. Henry, P. Rosato, A. Piechocka-Trocha, M. Brockman, P. Harrigan, D. Heckerman, D. Kaufmann, and Ch. Brander.  Viral adaptation to immune selection pressure by HLA class I-restricted CTL responses targeting epitopes in HIV frameshift sequences.  JEM, 10.1084/jem.20091808, January 2010.

 

·         B. Lee, L. Nachmanson, G. Robertson, J. Carlson, and D. Heckerman.  PhyloDet: A scalable visualization tool for mapping multiple traits to large evolutionary trees.  Bioinformatics, 25(19):2611-2612.  October 2009.

 

·         S. Avila-Rios, C. Ormsby, J. Carlson, H. Valenzuela-Ponce, J. Blanco-Heredia, D. Garrido-Rodriguez, C. Garcia-Morales, D. Heckerman, Z. Brumme, S. Mallal, M. John, E. Espinosa, and G. Reyes-Teran.  Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study.  Retrovirology, 6:72doi:10.1186/1742-4690-6-72, August 2009.

 

·         Z. Brumme, M. John., J. Carlson, C. Brumme, D. Chan, M. Brockman, L. Swenson, I. Tao, S. Szeto, P. Rosato, J. Sela, C. Kadie, N. Frahm, C. Brander, D. Haas, S. Riddler, R. Haubrich, B. Walker, P. Harrigan, D. Heckerman, and S. Mallal.  HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS ONE, 4(8):e6687. doi:10.1371/journal.pone.0006687.  August 2009.

 

·         B. Lee, L. Nachmanson, G. Robertson, J. Carlson, and D. Heckerman.  PhyloDet: A scalable visualization tool for mapping multiple traits to large evolutionary trees.  Bioinformatics, 25(9): 2611-2612, July 2009.

 

·         C. Rousseau, D. Lockhart, J. Listgarten, S. Maley, C. Kadie, G. Learn, D. Nickle, D. Heckerman, W. Deng, C. Brander, T. Ndung'u, H. Coovadia, P. Goulder, B. Korber, B. Walker, J. Mullins.  Rare HLA drive additional HIV evolution compared to more frequent alleles.  AIDS Res Hum Retroviruses, 25:297-303, March 2009.

 

·         Y. Kawashima, K. Pfafferott, J. Frater, P. Matthews, R. Payne, M. Addo, H. Gatanaga, M. Fujiwara, A. Hachiya, H. Koizumi, N. Kuse, S. Oka, A. Duda, A. Prendergast, H. Crawford, A. Leslie, Z. Brumme, C. Brumme, T. Allen, C. Brander, R. Kaslow, J. Tang, E. Hunter, S. Allen, J. Mulenga, S. Branch, T. Roach, M. John, S. Mallal, A. Ogwu, R. Shapiro, J. Prado, S. Fidler, J. Weber, O. Pybus, P. Klenerman, T. Ndung'u, R. Phillips, D. Heckerman, P. Harrigan, B. Walker, M. Takiguchi, and P. Goulder.  Adaptation of HIV-1 to human leukocyte antigen class I.  Nature, February 2009.

 

·         T. Miura, M. Brockman, Z. Brumme, C. Brumme, F. Pereyra, A. Trocha, B. Block, A. Schneidewind, T. Allen, D. Heckerman, and B. Walker.  HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1.  Journal of Virology, 83:140-149. January 2009.

 

·         J. Carlson, Z. Brumme, C. Rousseau, C. Brumme, P. Matthews, C. Kadie, J. Mullins, B. Walker, P. Harrigan, P. Goulder, D. Heckerman.  Phylogenetic dependency networks: Inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Computational Biology, 4(11): e1000225, November 2008.

 

 

 

 

 

 

  • T. Kuntzen, J. Timm, A. Berical, N. Lennon, A. Berlin, S. Young, B. Lee, D. Heckerman, J. Carlson, L. Reyor, M. Kleyman, C. McMahon, C. Birch, J. Schulze Zur Wiesch, T. Ledlie, M. Koehrsen, C. Kodira, A. Roberts, G. Lauer, H. Rosen, F. Bihl, A. Cerny, U. Spengler, Z. Liu, A. Kim, Y. Xing, A. Schneidewind, M. Madey, J. Fleckenstein, V. Park, J. Galagan, C. Nusbaum, B. Walker, G. Lake-Bakaar, E. Daar, I. Jacobson, E. Gomperts, B. Edlin, S. Donfield, R. Chung, A. Talal, T. Marion, B. Birren, M. Henn, T. Allen.  Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients.  Hepatology, 48:1769-1778, July 2008.

 

 

 

 

 

 

 

 

 

 

 

 

 

  • 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.

 

 

 

 

 

 

 

  • 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.

 

 

 

  • J. Goodman, D. Heckerman, and R. Rounthwaite.  Stopping Spam.  Scientific American, April, 2005.

 

 

 

 

 

 

 

  • B. Thiesson, D. Chickering, D. Heckerman, and C. Meek, ARMA Time-Series Modeling with Graphical Models.  In Proceedings of Twentieth Conference on Uncertainty in Artificial Intelligence, Banff, Canada, UAI Press, July 2004.  Also appears as Technical Report MSR-TR-04-86, Microsoft Research, July, 2004.  Local copy.

 

 

 

 

 

  • C. Meek, B. Thiesson, and D. Heckerman,  Staged Mixture Modeling and Boosting.  In Proceedings of Eighteenth Conference on Uncertainty in Artificial Intelligence, Edmonton, Alberta, Morgan Kaufmann, August 2002.  Local copy.  Also appears as Technical Report MSR-TR-02-45, Microsoft Research, February, 2001.

 

 

 

 

 

 

  • B. Thiesson, C. Meek, and D. Heckerman. Accelerating EM for Large Databases.   Machine Learning, 45:279-299, 2001.  Also appears as Technical Report MSR-TR-99-31, Microsoft Research, May, 1999 (Revised February, 2001).

 

 

 

 

  • D. Chickering and D. Heckerman. Fast Learning from Sparse Data.  In Proceedings of Fifteenth Conference on Uncertainty in Artificial Intelligence, Stockholm, Sweden, Morgan Kaufmann, August 1999.  Local copy.  Also appears as Technical Report MSR-TR-00-15, Microsoft Research, February, 1999 (Revised May, 1999).

 

  • D. Heckerman, C. Meek, and G. Cooper A Bayesian Approach to Causal Discovery.  In C. Glymour and G. Cooper, editors, Computation, Causation, and Discovery, pages 141-165.  MIT Press, Cambridge, MA, 1999.  Also appears as Technical Report MSR-TR-97-05, Microsoft Research, February, 1997.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  • J. Breese and D. Heckerman.  Decision-theoretic case-based reasoning.  IEEE Transactions on Systems, Man, and Cybernetics, 26:838-842, 1996.  Local copy.  Also appears as MSR-TR-95-03, Microsoft Research, November, 1994 (revised August, 1995).

 

 

  • D. Geiger and D. Heckerman.  Beyond Bayesian networks: Similarity networks and Bayesian multinets.  Artificial Intelligence, 82:45-74, 1996.

 

 

 

 

 

 

  • D. Heckerman. A Bayesian approach to learning causal networks.  In Proceedings of Eleventh Conference on Uncertainty in Artificial Intelligence, Montreal, Quebec, pages 285-295. Morgan Kaufmann, August 1995.  Local copy.  Also appears as Technical Report MSR-TR-95-04, Microsoft Research, March, 1995.

 

 

 

 

  • J. Breese and D. Heckerman.  Decision-theoretic case-based reasoning.  In Proceedings of Fifth Conference on Artificial Intelligence and Statistics, Ft. Lauderdale, FL. Society for Artificial Intelligence in Statistics, January 1995.

 

  • D. Heckerman and R. Shachter.  A decision-based view of causality.  In Proceedings of Fifth Conference on Artificial Intelligence and Statistics, Ft. Lauderdale, FL. Society for Artificial Intelligence in Statistics, January 1995.

 

 

·         D. Heckerman, J. Breese, and K. Rommelse.  Troubleshooting under uncertainty.  In Proceedings of Fifth International Workshop on Principles of Diagnosis, New Paltz, NY, pages 121-130, October 1994.  Also appears as Technical Report MSR-TR-94-07, Microsoft Research, March, 1994.

 

·         D. Heckerman, D. Geiger, and D. Chickering. Learning Bayesian networks: The combination of knowledge and statistical data.  In Proceedings of Tenth Conference on Uncertainty in Artificial  Intelligence, Seattle, WA, pages 293-301. Morgan Kaufmann, July 1994.  Local copy.

 

·         D. Geiger and D. Heckerman. Learning Gaussian networks.  In Proceedings of Tenth Conference on Uncertainty in Artificial Intelligence, Seattle, WA, pages 235-243. Morgan Kaufmann, July 1994.

 

·         D. Heckerman and J. Breese.  A new look at causal independence.  In Proceedings of Tenth Conference on Uncertainty in Artificial  Intelligence, Seattle, WA, pages 286-292. Morgan Kaufmann, July 1994.  Local copy.

 

·         D. Heckerman and R. Shachter.  A decision-based view of causality.  In Proceedings of Tenth Conference on Uncertainty in Artificial Intelligence, Seattle, WA, pages 302-310. Morgan Kaufmann, July 1994.  Local copy.

 

·         D. Geiger and D. Heckerman.  Inference algorithms for similarity networks.  In Proceedings of Ninth Conference on Uncertainty in Artificial Intelligence, Washington, DC, pages 326-334. Morgan Kaufmann, July 1993.  Local copy.

 

·         D. Heckerman.  Causal independence for knowledge acquisition and inference.  In Proceedings of Ninth Conference on Uncertainty in Artificial Intelligence, Washington, DC, pages 122-127. Morgan Kaufmann, July 1993.  Local copy.

 

·         D. Heckerman and M. Shwe.  Diagnosis of multiple faults: A sensitivity analysis.  In Proceedings of Ninth Conference on Uncertainty in Artificial Intelligence, Washington, DC, pages 80-87. Morgan Kaufmann, July 1993.  Local copy.

 

·         D. Heckerman and E. Horvitz.  Problem formulation as the reduction of a decision model.  In Proceedings of Ninth Conference on Uncertainty in Artificial Intelligence, Washington, DC, pages 80-87. Morgan Kaufmann, July 1993.  Local copy.

 

·         D. Heckerman, E. Horvitz, and B. Middleton.  An approximate nonmyopic computation for value of information.  IEEE Transactions on Pattern Analysis and Machine Intelligence, 15:292-298, 1993.

 

·         D. Heckerman, E. Horvitz, and B. Nathwani.  Toward normative expert systems: Part I.  The Pathfinder project.  Methods of Information in Medicine, 31:90-105, 1992.  Local copy.

 

·         D. Heckerman and B. Nathwani.  Toward normative expert systems: Part II. Probability-based representations for efficient knowledge acquisition and inference.  Methods of Information in Medicine, 31:106-116, 1992.  Also in van Bemmel, J., McCray, A., editors, Yearbook of Medical Informatics, pages 430-440. International Medical Informatics Association, Rotterdam, The Netherlands, 1993.  Local copy.

 

·         D. Heckerman.  The certainty-factor model.  In S. Shapiro, editor, Encyclopedia of Artificial Intelligence, Second Edition, pages 131-138.  Wiley, New York, 1992.

 

·         D. Heckerman and E. Shortliffe.  From certainty factors to belief networks.  Artificial Intelligence in Medicine, 4:35-52, 1992.  Local copy.

 

·         D. Heckerman and B. Nathwani.  An evaluation of the diagnostic accuracy of Pathfinder.  Computers and Biomedical Research, 25:56-74, 1992.  Local copy.

 

·         M. Shwe, B. Middleton, D. Heckerman, M. Henrion, E. Horvitz, H. Lehmann, and G. Cooper.  Probabilistic diagnosis using a reformulation of the INTERNIST-1/QMR knowledge base:  Part 1. The probabilistic model and inference algorithms.  Methods of Information in Medicine, 30:241-255, 1991.

 

·         B. Middleton, M. Shwe, D. Heckerman, M. Henrion, E. Horvitz, H. Lehmann, and G. Cooper.  Probabilistic diagnosis using a reformulation of the INTERNIST-1/QMR knowledge base:  Part 2.  Evaluation of diagnostic performance.  Methods of Information in Medicine, 30:256-267, 1991.

 

·         D. Heckerman, E. Horvitz, and B. Middleton.  An approximate nonmyopic computation for value of information.  In Proceedings of the Seventh Conference on Uncertainty in Artificial Intelligence, Los Angeles, CA, pages 135-141. Morgan Kaufmann, July 1991.  Local copy.

 

·         D. Geiger and D. Heckerman.  Advances in probabilistic reasoning.  In Proceedings of the Seventh Conference on Uncertainty in Artificial Intelligence, Los Angeles, CA, pages 118-126. Morgan Kaufmann, July 1991.  Local copy.

 

·         D. Heckerman.  Probabilistic Similarity Networks.  MIT Press, Cambridge, MA, 1991.  Review.

 

·         D. Heckerman.  Probabilistic similarity networks.  Networks, 20:607-636, 1990.

 

·         B. Nathwani, D. Heckerman, E. Horvitz, and T. Lincoln.  Integrated expert systems and videodisc in surgical pathology: An overview. Human Pathology, 21:11-27, 1990.

 

·         D. Heckerman.  Similarity networks for the construction of multiple-fault belief  networks.  In Proceedings of the Sixth Conference on Uncertainty in Artificial Intelligence, Boston, MA, pages 32-39. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, July 1990.  Also in P. Bonissone, M. Henrion, L. Kanal, and J. Lemmer, editors, Uncertainty in Artificial Intelligence 6, pages 51-64.  North-Holland, New York, 1990.  Local copy.

 

·         D. Heckerman and E. Horvitz.  Problem formulation as the reduction of a decision model.  In Proceedings of the Sixth Conference on Uncertainty in Artificial Intelligence, Boston, MA, pages 82-89. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, July 1990.  Also in P. Bonissone, M. Henrion, L. Kanal, and J. Lemmer, editors, Uncertainty in Artificial Intelligence 6, pages 159-170.  North-Holland, New York, 1990.

 

·         D. Geiger and D. Heckerman.  Separable and transitive graphoids.  In Proceedings of the Sixth Conference on Uncertainty in Artificial Intelligence, Boston, MA, pages 538-545. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, July 1990.  Local copy.

 

·         H. Suermondt, G. Cooper, and D. Heckerman.  A combination of cutset conditioning with clique-tree propagation in the Pathfinder system.  In Proceedings of the Sixth Conference on Uncertainty in Artificial Intelligence, Boston, MA, pages 273-279. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, July 1990.  Local copy.

 

·         D. Heckerman.  A tractable algorithm for diagnosing multiple diseases.  In Proceedings of the Fifth Workshop on Uncertainty in Artificial Intelligence, Windsor, ON, pages 174-181. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, August 1989.  Also in M. Henrion, R. Shachter, L. Kanal, and J. Lemmer, editors, Uncertainty in Artificial Intelligence 5, pages 163-171.  North-Holland, New York, 1990.  Local copy.

 

·         D. Heckerman, J. Breese, and E. Horvitz.  The compilation of decision models.  In Proceedings of Fifth Workshop on Uncertainty in Artificial Intelligence, Windsor, ON, pages 162-173. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, August 1989.  Local copy.

 

·         D. Heckerman, E. Horvitz, and B. Nathwani.  Update on the Pathfinder project.  In Proceedings of the Thirteenth Symposium on Computer Applications in Medical Care, Washington, D, pages 203-207.  IEEE Computer Society Press, Silver Spring, MD, November 1989.  Local copy.

 

·         E. Horvitz, G. Cooper, and D. Heckerman.  Reflection and action under scarce resources: Theoretical principles and empirical study.  In Proceedings of the Eleventh International Joint Conference on Artificial Intelligence, Detroit, MI, pages 1121-1127. Morgan Kaufmann, San Mateo, CA, August 1989.  Local copy.

 

·         E. Horvitz, D. Heckerman, K. Ng, and B. Nathwani.  Heuristic abstraction in the decision-theoretic Pathfinder system.  In Proceedings of the Thirteenth Symposium on Computer Applications in Medical Care, Washington, DC, pages 178-182. IEEE Computer Society Press, Silver Spring, MD, November 1989.

 

·         D. Heckerman.  An empirical comparison of three inference methods.  In Proceedings of the Fourth Workshop on Uncertainty in Artificial Intelligence, Minneapolis, MN, pages 158-169. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, August 1988.  Also in R. Shachter, T. Levitt, L. Kanal, and J. Lemmer, editors, Uncertainty in Artificial Intelligence 4, pages 283-302.  North-Holland, New York, 1990.  Local copy.

 

·         D. Heckerman and E. Horvitz.  On the expressiveness of rule-based systems for reasoning under uncertainty.  In Proceedings AAAI-87 Sixth National Conference on Artificial Intelligence, Seattle, WA, pages 121-126. Morgan Kaufmann, San Mateo, CA, July 1987.  Local copy.

 

·         D. Heckerman and H. Jimison.  A perspective on confidence and its use in focusing attention during knowledge acquisition.  In Proceedings of the Third Workshop on Uncertainty in Artificial Intelligence, Seattle, WA, pages 123-131. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, July 1987.  Also in L. Kanal, T. Levitt, and J. Lemmer, editors, Uncertainty in Artificial Intelligence 3, pages 123-131. North-Holland, New York, 1989.  Local copy.

 

·         R. Shachter and D. Heckerman.  Thinking backward for knowledge acquisition.  AI Magazine, 8:55-63, 1987.  Local copy.

 

·         D. Heckerman.  An axiomatic framework for belief updates.  In Proceedings of the Second Workshop on Uncertainty in Artificial Intelligence, Philadelphia, PA, pages 123-128. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, August 1986.  Also in L. Kanal and J. Lemmer, editors, Uncertainty in Artificial Intelligence 2, pages 11-22. North-Holland, New York, 1988.  Local copy.

 

·         D. Heckerman and E. Horvitz.  The myth of modularity in rule-based systems.  In Proceedings of the Second Workshop on Uncertainty in Artificial Intelligence, Philadelphia, PA, pages 115-121. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, August 1986.  Also in L. Kanal and J. Lemmer, editors, Uncertainty in Artificial Intelligence 2, pages 23-34. North-Holland, New York, 1988.

 

·         D. Heckerman and R. Miller.  Towards a better understanding of the INTERNIST-1 knowledge base.  In Proceedings of Medinfo, Washington, DC, pages 27-31.  North-Holland, New York, October 1986.

 

·         E. Horvitz, D. Heckerman, and C. Langlotz.  A framework for comparing alternative formalisms for plausible reasoning.  In Proceedings AAAI-86 Fifth National Conference on Artificial Intelligence, Philadelphia, PA, pages 210-214. Morgan Kaufmann, San Mateo, CA, August 1986.  Local copy.

 

·         E. Horvitz, D. Heckerman, B. Nathwani, and L. Fagan.  The use of a heuristic problem-solving hierarchy to facilitate the explanation of hypothesis-directed reasoning.  In Proceedings of Medinfo, Washington, DC, pages 27-31.  North-Holland, New York, October 1986.

 

·         E. Horvitz and D. Heckerman.  The inconsistent use of measures of certainty in artificial intelligence research.  In Proceedings of the Workshop on Uncertainty and Probability in Artificial Intelligence, Los Angeles, CA. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, August 1985.  Also in L. Kanal and J. Lemmer, editors, Uncertainty in Artificial Intelligence, pages 137-151. North-Holland, New York, 1986.

 

·         D. Heckerman.  Probabilistic interpretations for MYCIN's certainty factors.  In Proceedings of the Workshop on Uncertainty and Probability in Artificial Intelligence, Los Angeles, CA, pages 9-20. Association for Uncertainty in Artificial Intelligence, Mountain View, CA, August 1985.  Also in L. Kanal. and J. Lemmer, editors, Uncertainty in Artificial Intelligence, pages 167-196. North-Holland, New York, 1986.

 

·         D. Heckerman, R. Rosenbaum, S. Putterman, and G. Williams.  Pressure release superleak sound modes in He II.  Journal of Low Temperature Physics, 38:629, 1980.

 

·         D. Heckerman, S. Garrett, G.A. Williams, and P. Weidman.  Surface tension restoring forces on gravity waves in narrow channels.  Physics of Fluids, 22, 1979.

 

·         S. Putterman, D. Heckerman, R. Rosenbaum, and G. Williams.  Superfluid two-phase sound.  Physics Review Letters, 42:580, 1979.

 

·         R. Rosenbaum, G. Williams, D. Heckerman, J. Marcus, D. Scholler, J. Maynard, and I. Rudnick.  Surface tension sound in superfluid helium films adsorbed on alumina powder.  Journal of Low Temperature Physics, 37:663, 1979.

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