Portrait of Carl Kadie

Carl Kadie

Principal Research Software Design Engineer

About

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

Background

  • 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).

Projects

HIV Vaccine Design

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,…

Publications

2016

2014

2013

High-dimensional immunomonitoring models of HIV-1-specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control
Zaza 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, View abstract, Download PDF

2012

2011

2010

Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection
Mark 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, View abstract, View external link

2009

2008

HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: immune Escape and Viral Load
Christine 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, View abstract, View external link
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
Zabrina 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, View abstract, View external link

2007

Extensive HLA class I allele promiscuity among viral CTL epitopes
Nicole Frahm, Karina Yusim, Todd J. Suscovich, Sharon Adams, John Sidney, Peter Hraber, Hannah S. Hewitt, Caitlyn H. Linde, Daniel G. Kavanagh, Tonia Woodberry, Leah M. Henry, Kellie Faircloth, Jennifer Listgarten, Carl Kadie, Nebojsa Jojic, Kaori Sango, Nancy V. Brown, Eunice Pae, M. Tauheed Zaman, Florian Bihl, Ashok Khatri, Mina John, Simon Mallal, Francesco M. Marincola, Bruce D. Walker, Alessandro Sette, David Heckerman, Bette T. Korber, Christian Brander, September 1, 2007, View abstract, View external link
Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations
Tanmoy Bhattacharya, Marcus Daniels, David Heckerman, Brian Foley, Nicole Frahm, Carl Kadie, Jonathan Carlson, Karina Yusim, Ben McMahon, Brian Gaschen, Simon Mallal, James I. Mullins, David C. Nickle, Joshua Herbeck, Christine Rousseau, Gerald H. Learn, Toshiyuki Miura, Christian Brander, Bruce Walker, Bette Korber, in Science, American Association for the Advancement of Science, January 1, 2007, View abstract, View external link

2006

2005

2003

2002

2001

2000

1998

1995

1993

1991

1990

1988

Projects

Downloads

MSBNx

February 2016

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  • Website

Other

Presentations and Interviews