Carl Kadie

Principal Research Software Design Engineer in the 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
Mail: One Microsoft Way, Redmond WA 98052-6399, USA

Papers

Papers

Title

Authors

Published In

Formats

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 (in press)

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

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

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

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, 2^nd 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.

Presentations and Interviews

"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.

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

Carl Kadie

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