Podcast: "Microsoft battle HIV!" (Interview starts 7 min 55 sec in)

 

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Contents

• Development and Research Interests and Activities
• Papers
• Presentations and Interviews
• Background

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Development and Research Interests and Activities

• Machine Learning and Artificial Intelligence
• Bioinformatics and HIV Vaccine Design (e.g. Microsoft Computational Biology Tools)
• Graphical Models and Bayesian Reasoning Systems (e.g. MSBNx)
• Fighting Spam with Machine Learning
• Collaborative Filtering

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Papers

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	PDF Web tool source code
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	Z. Brumme I. Tao S. Szeto C. Brumme J.M. Carlson D. Chan, C. Kadie N. Frahm C. Brander B.D. Walker D. Heckerman P.R. Harrigan	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	C.M. Rousseau M.G. Daniels, J.M. Carlson C. Kadie, H. Crawford, A. Prendergast, P. Matthews, D.N. Raugi, B.S. Maust G.H. Learn D.C. Nickle N. Frahm, C. Brander, B.D. Walker P.J.R. Goulder, T. Bhattacharya,, D.E. Heckerman,  B.T. Korber, J.I. Mullins	Journal of Virology, doi:10.1128/JVI.02455-07	Abstract
Statistical resolution of ambiguous HLA typing data	J. Listgarten Z.L. Brumme C. Kadie G. Xiaojiang B. Walker M. Carrington P. Goulder D. Heckerman	PLoS Computational Biology, 2008, 4(2):e1000016	Abstract,  PDF PLoS Press Release Tech Report Web tool source code coverage in the magazine BioInform
A statistical framework for modeling HLA-dependent T-cell response data.	J. Listgarten N. Frahm C. Kadie C. Brander D. Heckerman	PLoS Computational Biology, 2007, 3(10):e188	Abstract,  PDF PLoS Press Release Web tool and source code
Extensive HLA class I allele promiscuity among viral CTL epitopes	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	European Journal of Immunology, 2007 37(9):2419-2433.	Abstract
Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction	D. Heckerman C.M. Kadie J. Listgarten	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.	J.M. Carlson C. Kadie S. Mallal D. Heckerman	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.	Z.L. Brumme C.J. Brumme D. Heckerman B.T. Korber M. Daniels J.M. Carlson C. Kadie T. Bhattacharya C. Chui J. Szinger T. Mo R.S. Hogg J.S.G. Montaner N. Frahm C. Brander B.D. Walker P.R. Harrigan	PLoS Pathogens, 3(7):e94 (July 2007).	Abstract, HTML, PDF Mass. Gen. Press Release
Founder effects in the assessment of HIV polymorphisms and HLA allele associations.	T. Bhattacharya M. Daniels D. Heckerman B. Foley N. Frahm C. Kadie J.M. Carlson K. Yusim B. McMahon B. Gashen S. Mallal J. Mullins D. Nickle J. Herbeck C. Rousseau G. Learn T. Miura C. Brander B. Walker B. Korber	Science, 16 March 2007: Vol. 315. no. 5818	Abstract Readable Commentary C|NET article MS Press Release
Estimate of the proportion of within-host sequence evolution in HIV-1 mediated by Human Leukocyte Antigen (HLA) class I selective pressures.	J. Carlson CJ Brumme C Kadie M. Daniels T. Bhattacharya S. Mallal B.D. Walker P.R. Harrigan B.T. Korber D. Heckerman	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.	Z. Brumme C. Brumme C. Kadie B. Korber C. Daniels T. Bhattacharya J. Carlson T. Mo C. Chui J. Montaner B. Walker D. Heckerman P.R. Harrigan	Poster, Keystone Symposium: Molecular and Cellular Determinants of HIV Pathogenesis, March 2007.
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.	Z. Brumme C. Brumme C. Kadie J. Carlson C. Chui T. Mo J. Montaner B. Walker D. Heckerman P. Harrigan	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.	C. Brumme Z. Brumme J. Carlson C. Kadie C. Chui J. Montaner B. Walker P. Harrigan D. Heckerman	Poster, 14th Conference on Retroviruses and Opportunistic Infections (CROI), February 2007.
Identifying the effects of human immune pressure on the evolution of HIV.	J. Carlson C. Kadie D. Heckerman	Presentation, NIPS workshop on computational biology, December 2006	Abstract
Learning MHC I - peptide binding	N. Jojic Manuel Reyes-Gomez D. Heckerman C.M. Kadie Ora Schueler-Furman	Bioinformatics. Vol. 22, Number 14, 15 July 2006.	Abstract, PDF
Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction	D. Heckerman C.M. Kadie J. Listgarten	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	PDF
Leveraging Information Across HLA Alleles/Supertypes Improves HLA-Specific Epitope Prediction	D. Heckerman C.M. Kadie J. Listgarten	Microsoft Research Technical Report MSR-TR-2005-127, September, 2005.	Abstract, PDF
HLA-driven Optimization of an HIV Vaccine Immunogen	V. Jojic D. Heckerman C.M. Kadie C. Meek M. John S. Mallal	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	E. Horvitz C.M. Kadie T. Paek D. Hovel	Communications of the ACM 46, 3 (March 2003), pp 52-59.	PDF
CFW: A Collaborative Filtering System Using Posteriors Over Weights of Evidence	C.M. Kadie C. Meek D. Heckerman	Proceedings of the Eighteenth Conference on Uncertainty in Artificial Intelligence, Edmonton, Alberta, August, 2002.	Abstract, PDF, PS
Coordinate: Probabilistic Forecasting of Presence and Availability	E. Horvitz P. Koch C.M. Kadie A. Jacobs	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	C.M. Kadie C. Meek D. Heckerman	Microsoft Research Technical Report MSR-TR-2002-46, March 2002.	Abstract, PS
MSBNx: A Component-Centric Toolkit for Modeling and Inference with Bayesian Networks	C.M. Kadie D. Hovel E. Horvitz	Microsoft Research Technical Report MSR-TR-2001-67, July 2001.	Abstract, Word, PDF
Dependency Networks for Density Estimation, Collaborative Filtering, and Data Visualization	D. Heckerman D. Chickering C. Meek R. Rounthwaite C.M. Kadie	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	D. Heckerman D. Chickering C. Meek R. Rounthwaite C.M. Kadie	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.	D. Heckerman D. Chickering C. Meek R. Rounthwaite C.M. Kadie	Technical Report MSR-TR-00-16, Microsoft Research, February, 2000.	Abstract, PDF
Empirical Analysis of Predictive Algorithms for Collaborative Filtering	J. Breese D. Heckerman C.M. Kadie	Proceedings of the Fourteenth Conference on Uncertainty in Artificial Intelligence, Madison, WI, July, 1998.	Abstract, PS
Empirical Analysis of Predictive Algorithms for Collaborative Filtering	J. Breese D. Heckerman C.M. Kadie	Technical Report MSR-TR-98-12, Microsoft Research, Redmond, WA, May, 1998.	Abstract, PS
Applying Library Intellectual Freedom Principles to Public and Academic Computers	C.M. Kadie	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	C.M. Kadie	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	C.M. Kadie	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	C.M. Kadie	AI Magazine, 14:4, Winter 1993.	Abstract, PDF, HTML
Continuous Conceptual Set Covering: Learning Robot Operators from Examples	C.M. Kadie	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	C.M. Kadie	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	C.M. Kadie	Artificial Intelligence Review, 4:4, 1990.	Abstract, PS
Conceptual Set Covering: Improving Fit-and-Split Algorithms	C.M. Kadie	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	C.M. Kadie	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	C.M. Kadie	Proceedings of the Fourth Workshop on Uncertainty in Artificial Intelligence, Minneapolis, August 1988.	Abstract, PS
Diffy-S: Learning Robot Operator Schemata From Examples,	C.M. Kadie	Proceedings of the Fifth International Conference on Machine Learning, Ann Arbor, Michigan, June 1988.

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Presentations and Interviews

• "Microsoft battles HIV!", .NET Rocks, September 10, 2009. Interview starts at 7 min 55 sec.
  • Carl and Richard talk to Jonathan Carlson, Bob Davidson, David Heckerman, and Carl Kadie from Microsoft Research about their efforts to find vaccines for HIV using Microsoft technologies.
• "Microsoft Research Releases Tools to Help Science Progress Toward an AIDS Vaccine", Microsoft PressPass, June 13, 2007.
• "Microsoft Researchers Boost Task Productivity Fiftyfold with Cluster Server Software", Microsoft Server Product Portfolio Customer Solution Case Study, 2007.
• "The Role of HPC in AIDS Vaccine Designs", HPC Wire, 2007.
• Technical advisor to Slugco Inc., winners of First Prize in the Youth Division of the Seattle Times’ “Three-Minute Masterpiece” contest.
• Interview, Slashdot, March 2, 2001, http://slashdot.org/article.pl?sid=01/03/02/1614248.
• C. M. Kadie, "Computers and Academic Freedom," Presented at the National Academy of Sciences Workshop on Rights and Responsibilities of Participants in Networked Communities, November, 1992.
• C. M. Kadie, "Quantifying the Effects of Representation, Noise, and Method on Inductive Learning," Presented at the first Workshop on Computational Learning Theory and Natural Learning Systems, 1990.

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Background

Bachelor's, master's and doctoral degrees in Computer Science from the University of Illinois, Urbana-Champaign

19 patents and 30 published patent applications.

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