HIV is one of the world's primary health concerns. Researchers at Microsoft are collaborating with leading HIV scientific centers to bring together research expertise and cutting-edge computing technology in to the fight against the virus. Computational tools are available here. In the news Washington Post, 2016 Geek Wire, 2013 Fast Company, 2012 Microsoft Blog, 2011 Selected references F. Pereyra, D. Heckerman, J. Carlson, C. Kadie, D. Soghoian, D. Karel, A. Goldenthal, O. Davis, C. DeZiel,…
I’m a Principal Research Software Design Engineer in Microsoft Research’s Genomics group (previously, the eScience group). I’m also an affiliate of the Machine Learning and Applied Statistics (MLAS) and Adaptive Systems and Interaction (ASI) groups.
Development and Research Interest and Activities
- Machine Learning and Artificial Intelligence
- Genomics (e.g. Microsoft Genomics Tools on GitHub and PySnpTools)
- Graphical Models and Bayesian Reasoning Systems (e.g. MSBNx)
- Fighting Spam with Machine Learning
- Collaborative Filtering
- Bachelor’s, master’s and doctoral degrees in Computer Science & Machine Learning from the University of Illinois, Urbana-Champaign
- 50 patents and 42 published patent applications.
- Erdős-Bacon number of 6 (Erdős→Charles K. Chui→Zabrina L. Brumme→Carl Kadie and Bacon→Rachel Blanchard→Andrew Tribolini→Carl Kadie).
Greater power and computational efficiency for kernel-based association testing of sets of genetic variantsChristoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Kadie, David Heckerman, Jennifer Listgarten, in Bioinformatics, Oxford University Press, September 1, 2014,
High-dimensional immunomonitoring models of HIV-1-specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral controlZaza M. Ndhlovu, Lori B. Chibnik, Jacqueline Proudfoot, Seanna Vine, Ashley McMullen, Kevin Cesa, Filippos Porichis, R. Brad Jones, Donna Marie Alvino, Meghan G. Hart, Eleni Stampouloglou, Alicja Piechocka-Trocha, Carl Kadie, Florencia Pereyra, David Heckerman, Philip L. De Jager, Bruce D. Walker, Daniel E. Kaufmann, January 31, 2013,
Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African AmericansPaul J. McLaren, Stephan Ripke, Kimberly Pelak, Amy C. Weintrob, Nikolaos A. Patsopoulos, Xiaoming Jia, Rachel L. Erlich, Niall J. Lennon, Carl Kadie, David Heckerman, Namrata Gupta, David W. Haas, Steven G. Deeks, Florencia Pereyra, Bruce D. Walker, Paul I. W. de Bakker, June 19, 2012,
Translation of HLA-HIV Associations to the Cellular Level: HIV Adapts To Inflate CD8 T Cell Responses against Nef and HLA-Adapted Variant EpitopesCoral-Ann M. Almeida, Corine Bronke, Steven G. Roberts, Elizabeth McKinnon, Niamh M. Keane, Abha Chopra, Carl Kadie, Jonathan Carlson, David W. Haas, Sharon A. Riddler, Richard Haubrich, David Heckerman, Simon Mallal , Mina John, in The Journal of Immunology, September 1, 2011,
Variable HIV Peptide Stability in Human Cytosol is Critical to Epitope Presentation and Immune EscapeEstibaliz Lazaro, Carl Kadie, Pamela Stamegna, Shao Chong Zhang, Pauline Gourdain, Nicole Y. Lai, Mei Zhang, Sergio A. Martinez, David Heckerman, Sylvie Le Gall, in J Clin Invest, June 1, 2011,
Reduced Replication Capacity of NL4-3 Recombinant Viruses Encoding Reverse Transcriptase Integrase Sequences From HIV-1 Elite ControllersZabrina L. Brumme, Chun Li, Toshiyuki Miura, Jennifer Sela, Pamela C. Rosato, Chanson J. Brumme, Tristan J. Markle, Eric Martin, Brian L. Block, Alicja Trocha, Carl Kadie, Todd M. Allen, Florencia Pereyra, David Heckerman, Bruce D. Walker, Mark A. Brockman, in J Acquir Immune Defic Syndr., February 1, 2011,
Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic InfectionMark A Brockman, Zabrina L Brumme, Chanson J Brumme, Toshiyuki Miura, Jennifer Sela, Pamela C Rosato, Carl Kadie, Jonathan Carlson, Tristan J Markle, Hendrik Streeck, Anthony D Kelleher, Martin Markowitz, Heiko Jessen, Eric Rosenberg, Marcus Altfeld, P Richard Harrigan, David Heckerman, Bruce D Walker, Todd M Allen, in Journal of Virology, November 1, 2010,
Gag-Protease-Mediated Replication Capacity in HIV-1 1 Subtype C Chronic Infection: Associations with HLA Type and Clinical ParametersJaclyn K. Wright, Zabrina L. Brumme, Jonathan Carlson, David Heckerman, Carl Kadie, Chanson J. Brumme, Bingxia Wang, Elena Losina, Toshiyuki Miura, Fundisiwe Chonco, Mary van der Stok, Zenele Mncube, Karen Bishop, Philip J.R. Goulder , Bruce D. Walker, Mark A. Brockman, Thumbi Ndung'u, October 1, 2010,
HLA-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infectionZabrina L. Brumme, Iris Tao, Sharon Szeto, Chanson J. Brumme, Jonathan Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan, July 11, 2009,
Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 GagJonathan Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, David Heckerman, in PLoS Computational Biology, PLoS Computational Biology (Public Library of Science Computational Biology), November 1, 2008,
HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral LoadChristine M. Rousseau, Marcus G. Daniels, Jonathan Carlson, Carl Kadie, Hayley Crawford, Andrew Prendergast, Philippa Matthews, Rebecca Payne, Morgane Rolland, Dana N. Raugi, Brandon S. Maust, Gerald H. Learn, David C. Nickle, Hoosen Coovadia, Thumbi Ndung'u, Nicole Frahm, Christian Brander, Bruce D. Walker, Philip J. R. Goulder, Tanmoy Bhattacharya, David Heckerman, Bette T. Korber, James I. Mullins, in Journal of Virology, January 1, 2008,
Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infectionZabrina L Brumme, Iris Tao, Sharon Szeto, Chanson J Brumme, Jonathan Carlson, Dennison Chan, Carl Kadie, Nicole Frahm, Christian Brander, Bruce Walker, David Heckerman, P. Richard Harrigan, in AIDS, January 1, 2008,
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 InfectionZabrina L. Brumme, Chanson J. Brumme, Jonathan Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L. Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, Bruce D. Walker, in Journal of Virology, January 1, 2008,
Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, Jonathan Carlson, Carl Kadie, Tanmoy Bhattacharya, Celia Chui, James Szinger, Theresa Mo, Robert S Hogg, Julio S. G Montaner, Nicole Frahm, Christian Brander, Bruce D Walker, P. Richard Harrigan, in PLoS Pathogens, July 1, 2007,
Quantifying the Value of Constructive Induction, Knowledge, and Noise Filtering on Inductive LearningCarl Kadie, Morgan Kaufmann Publishers, January 1, 1991,
February 17, 2017
October 16, 2009
Presentations and Interviews
- “PySnpTools: A New Open-Source Library for Reading and Manipulating Matrix Data (including Genomics Data)”, 24 July 2015, PyData Seattle 2015
- Excel Fun-Build 3D graphics from a spreadsheet (guest blog for Excel team), 18 February 2015
- “Supercomputing on Demand with Windows Azure“, 12 Nov 2012. Microsoft Research Connections Blog
- “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 young filmmaker Ben Kadie (aka Slugco Films), whose 15 films have screened around the world, as far as Nepal, won five top festival awards and 37 top youth awards.
- Slashdot “Interview with Carl Kadie“, March 2, 2001.
- 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.