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Principal Research Software Design Engineer in eScience at Microsoft Research. Also, an affiliate of the Machine Learning and Applied Statistics (MLAS) and Adaptive Systems and Interaction (ASI) groups. E-mail: carlk@microsoft.com |
| Podcast: "Microsoft battle HIV!" (Interview starts 7 min 55 sec in) |
| Papers | |||
| Title | Authors | Published In | Formats |
| HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef Proteins |
Zabrina L. Brumme, Mina John, Jonathan M. Carlson, Chanson J. Brumme, Dennison Chan, Mark A. Brockman, Luke C. Swenson, Iris Tao, Sharon Szeto, Pamela Rosato, Jennifer Sela, Carl Kadie, Nicole Frahm, Christian Brander, David W. Haas, Sharon Riddler, Richard Haubrich, Bruce D. Walker, P. Richard Harrigan, David Heckerman, Simon Mallal | PLos One, 2009, 4(8): e6687 | Abstract, PDF |
| Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles | Christine M. Rousseau, David W. Lockhart, Jennifer Listgarten, Carl Kadie, Gerald H. Learn, David C. Nickle, David E. Heckerman, Wenjie Deng, Christian Brander, Thumbi Ndung'u, Hoosen Coovadia, Philip J. R. Goulder, Bette T. Korber, Bruce D. Walker, James I. Mullins | AIDS Research and Human Retroviruses, 2009; 25(3):297-303 | Abstract |
| In silico resolution of ambiguous HLA typing data | Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Phillip Goulder, David Heckerman | ASHI (American Society for Histocompatibility and Immunogenetics) Quarterly, Volume 32, Number 2, 2008 | |
| Phylogenetic dependency networks: Inferring patterns of CTL escape and codon covariation in HIV-1 Gag | J. Carlson, Z. Brumme, C. Rousseau, C. Brumme, P. Matthews, C. Kadie, J. Mullins, B. Walker, P. Harrigan, P. Goulder, D. Heckerman | PLoS Computational Biology, 4(11): e1000225, November 2008 | Abstract, PDF |
| Design, expression, and processing of epitomized hepatitis C virus-encoded CTL epitopes. | D. Yerly, D. Heckerman, T. Allen, T. Suscovich, N. Jojic, C. Kadie, W. Pichler, A. Cerny, and C. Brander | Journal of Immunology, 181:6361-6370, November, 2008 | Abstract |
| Central role of reverting mutations in HLA associations with human immunodeficiency virus set point | P. Matthews, A. Prendergast, A. Leslie, H. Crawford, R. Payne, C. Rousseau, I. Honeyborne, J. Carlson, C. Kadie, C. Brander, J. Mullins, H. Coovadia, T. Nding.u, B. Walker, D. Heckerman, P. Goulder | Journal of Virology, 82:8548-59, September, 2008 | Abstract |
| 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 | Z. Brumme, C. Brumme, J. Carlson, H. Streeck, M. John, Q. Eichbaum, B. Block, B. Baker, C. Kadie, M. Markowitz, H. Jessen, A. Kelleher, E. Rosenberg, J. Kaldor, Y. Yuki, M. Carrington, T. Allen, S. Mallal, M. Altfeld, D. Heckerman, and B. Walker | Journal of Virology, 82:9216-9227, September 2008 | Abstract |
| Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection | Zabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Christian Brander, Bruce Walker, David Heckerman, P Richard Harrigan, Jonathan M Carlson, Dennison Chan, Carl Kadie, and Nicole Frahm | AIDS, vol. 22, no. 11, pp. 1277–1286, 2008 | Abstract, PDF |
| HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection |
| AIDS, 2008, doi: 10.1097/QAD.0b013e3283021a8c | Abstract, PDF |
| HLA Class-I Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: Immune Escape and Viral Load |
| Journal of Virology, doi:10.1128/JVI.02455-07 | Abstract |
| Statistical resolution of ambiguous HLA typing data |
| PLoS Computational Biology, 2008, 4(2):e1000016 | Abstract, PDF |
| A statistical framework for modeling HLA-dependent T-cell response data. |
| PLoS Computational Biology, 2007, 3(10):e188 | Abstract, PDF |
| Extensive HLA class I allele promiscuity among viral CTL epitopes |
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European Journal of Immunology, 2007 37(9):2419-2433. | Abstract |
| Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction |
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Journal of Computational Biology. 2007, 14(6): 736-746. doi:10.1089/cmb.2007.R013. | Abstract, PDF |
| Leveraging hierarchical population structure in discrete association studies. |
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PLoS One, 2(7):e591 (July 2007). |
Abstract, HTML, PDF |
| Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of Human Immunodeficiency Virus (HIV) type-1. |
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PLoS Pathogens, 3(7):e94 (July 2007). | Abstract, HTML, PDF |
| Founder effects in the assessment of HIV polymorphisms and HLA allele associations. |
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Science, 16 March 2007: Vol. 315. no. 5818 | Abstract |
| Estimate of the proportion of within-host sequence evolution in HIV-1 mediated by Human Leukocyte Antigen (HLA) class I selective pressures. |
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Presentation and poster, Keystone Symposium: Molecular and Cellular Determinants of HIV Pathogenesis, March 2007. | |
| Accumulation of HLA-class I-association CTL escape mutations in vivo during chronic infection is correlated with clinical markers of HIV-1 disease progression in a dose-dependent manner. |
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Poster, Keystone Symposium: Molecular and Cellular Determinants of HIV
Pathogenesis, March 2007. |
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| Presence of HLA class I-associated CTL escape mutations in chronic untreated HIV infection is significantly correlated with clinical markers of more severe disease progression. |
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Presentation, 14th Conference on Retroviruses and Opportunistic Infections (CROI), February 2007 | |
| Application of two bioinformatic methods to asses populational HIV evolution in response to HLA class-I mediated selection pressure reveals unprecedented levels of HLA-associated escape mutations across HIV nef. |
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Poster, 14th Conference on Retroviruses and Opportunistic Infections (CROI), February 2007. | |
| Identifying the effects of human immune pressure on the evolution of HIV. |
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Presentation, NIPS workshop on computational biology, December 2006 | Abstract |
| Learning MHC I - peptide binding |
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Bioinformatics. Vol. 22, Number 14, 15 July 2006. | Abstract, PDF |
| Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction |
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Research in Computational Molecular Biology: 10th Annual International Conference (RECOMB 2006), Venice, Italy, April 2-5, 2006. Lecture Notes in Computer Science, Volume 3909, Mar 2006, Pages 296 - 308 | |
| Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction |
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Microsoft Research Technical Report MSR-TR-2005-127, September, 2005. | Abstract, PDF |
| HLA-driven Optimization of an HIV Vaccine Immunogen |
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Presentation at the 12th Conference on Retroviruses and Opportunistic Infections, Boston, February 2005 | Abstract, PDF |
| Models of Attention in Computing and Communication: From Principles to Application |
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Communications of the ACM 46, 3 (March 2003), pp 52-59. | |
| CFW: A Collaborative Filtering System Using Posteriors Over Weights of Evidence |
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Proceedings of the Eighteenth Conference on Uncertainty in Artificial Intelligence, Edmonton, Alberta, August, 2002. | Abstract,
PDF, PS |
| Coordinate: Probabilistic Forecasting of Presence and Availability |
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Proceedings of the Eighteenth Conference on Uncertainty in Artificial Intelligence, Edmonton, Alberta, August, 2002. | Abstract, PDF |
| CFW: A Collaborative Filtering System Using Posteriors Over Weights of EvidenceNew Page 1 |
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Microsoft Research Technical Report MSR-TR-2002-46, March 2002. |
Abstract, PS |
| MSBNx: A Component-Centric Toolkit for Modeling and Inference with Bayesian Networks |
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Microsoft Research Technical Report MSR-TR-2001-67, July 2001. |
Abstract, Word, |
| Dependency Networks for Density Estimation, Collaborative Filtering, and Data Visualization |
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Journal of Machine Learning Research, Volume 1, October 2000, pp. 49-75. | Abstract, PDF, PS, HTML |
| Dependency Networks for Density Estimation, Collaborative Filtering, and Data Visualization |
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Proceedings of the Sixteenth Conference on Uncertainty in Artificial Intelligence, Stanford, CA, July, 2002. | Abstract, PDF |
| Dependency Networks for Density Estimation, Collaborative Filtering, and Data Visualization. |
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Technical Report MSR-TR-00-16, Microsoft Research, February, 2000. |
Abstract, |
| Empirical Analysis of Predictive Algorithms for Collaborative Filtering |
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Proceedings of the Fourteenth Conference on Uncertainty in Artificial Intelligence, Madison, WI, July, 1998. | Abstract, PS |
| Empirical Analysis of Predictive Algorithms for Collaborative Filtering |
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Technical Report MSR-TR-98-12, Microsoft Research, Redmond, WA, May, 1998. | Abstract, PS |
| Applying Library Intellectual Freedom Principles to Public and Academic Computers |
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In Computerization and Controversy: Value, Conflict, and Social Choices, 2nd Edition, edited by R. Kling, Academic Press, San Diego (1996). | |
| Computers and Academic Freedom News: List of Banned Computer Material on College Campuses |
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In Conceptual Issues on the Electronic Frontier, edited by Peter Ludlow, MIT Press, Cambridge, Massachusetts (1996). | Text |
| Seer: Maximum Likelihood Regression for Learning-Speed Curves |
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Technical Report UIUCDCS-R-95-1874, Department of Computer Science, University of Illinois, Urbana, IL, August 1995. Ph.D. Thesis. | PDF, Abstract, PS, HTML |
| Robot-Building Lab and Contest and the 1993 National AI Conference |
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AI Magazine, 14:4, Winter 1993. | Abstract, PDF, HTML |
| Continuous Conceptual Set Covering: Learning Robot Operators from Examples |
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Proceedings of the Eighth International Conference on Machine Learning, Evanston, Illinois, 1991. | Abstract, PS |
| Quantifying the Value of Constructive Induction, Knowledge, and Noise Filtering on Inductive Learning |
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Proceedings of the Eighth International Conference on Machine Learning, Evanston, Illinois, 1991. | Abstract, PS |
| Book Review of R.C. Johnson and C. Brown's Cognizers: Neural Networks and Machines that Think |
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Artificial Intelligence Review, 4:4, 1990. | Abstract, PS |
| Conceptual Set Covering: Improving Fit-and-Split Algorithms |
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Proceedings of the Seventh International Conference on Machine Learning, Austin, Texas, June 1990. | Abstract, PS |
| Diffy-S: Learning Robot Operators from Examples of Operator Effects |
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Technical Report UIUCDCS-R-89-1550, Department of Computer Science, University of Illinois, Urbana, IL, October 1989. Master's Thesis. | Abstract, PS |
| Rational Nonmonotonic Reasoning |
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Proceedings of the Fourth Workshop on Uncertainty in Artificial Intelligence, Minneapolis, August 1988. | Abstract, PS |
| Diffy-S: Learning Robot Operator Schemata From Examples, |
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Proceedings of the Fifth International Conference on Machine Learning, Ann Arbor, Michigan, June 1988. | |
Bachelor's, master's and doctoral degrees in Computer Science from the University of Illinois, Urbana-Champaign
19 patents and 30 published patent applications.