Portrait of David Heckerman

David Heckerman

Distinguished Scientist & Senior Director of Microsoft Genomics

About

I am developing machine learning and statistical approaches for biological and medical applications including HIV vaccine design and genomics (see https://github.com/microsoftgenomics).  In my early work, I demonstrated the importance of probability theory in Artificial Intelligence, and developed methods to learn graphical models from data, including methods for causal discovery.

At Microsoft, I have developed numerous applications including data-mining tools in SQL Server and Commerce Server, the junk-mail filters in Outlook, Exchange, and Hotmail, handwriting recognition in the Tablet PC, text mining software in Sharepoint Portal Server, troubleshooters in Windows, and the Answer Wizard in Office.

Selected Publications

Projects

Microsoft Genomics BWA & GATK Acceleration

Established: October 18, 2016

Click here to sign up Microsoft has made a substantial increase in the speed of the Broad Institute best practices pipeline for genome reassembly of high-throughput sequencing data—the Burroughs Wheeler Aligner (BWA) and the Genome Analysis Toolkit (GATK).   We applied…

FaST-LMM

Established: October 14, 2006

Click here to download latest version of FaST-LMM   FaST-LMM, (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets. FaST-LMM runs on both Windows…

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.…

Publications

2016

Impact of Pre-Adapted HIV Transmission
Jonathan Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent T. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter, Paul A. Goepfert, May 16, 2016, View abstract, View external link

2015

2014

2013

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
Istvan Bartha, Jonathan Carlson, Chanson J Brumme, Paul J McLaren, Zabrina L Brumme, Mina John, David W Haas, Javier Martinez-Picado, Judith Dalmau, Cecilio López-Galíndez, Concepción Casado, Andri Rauch, Huldrych F Günthard, Enos Bernasconi, Pietro Vernazza, Thomas Klimkait, Sabine Yerly, Stephen J O’Brien, Jennifer Listgarten, Nico Pfeifer, Christoph Lippert, Nicolo Fusi, Zoltán Kutalik, Todd M Allen, Viktor Müller, P Richard Harrigan, David Heckerman, Amalio Telenti, Jacques Fellay, in eLife, October 29, 2013, View abstract, Download PDF
Influence of HLA-C Expression Level on HIV Control
Richard Apps, Ying Qi, Jonathan Carlson, Haoyan Chen, Xiaojiang Gao, Rasmi Thomas, Yuko Yuki, Greg Q. Del Prete, Philip Goulder, Zabrina L. Brumme, Chanson J. Brumme, Mina John, Simon Mallal, George Nelson, Ronald Bosch, David Heckerman, Judy L. Stein, Kelly A. Soderberg, M. Anthony Moody, Thomas N. Denny, Xue Zeng, Jingyuan Fang, Ashley Moffett, Jeffrey D. Lifson, James J. Goedert, Susan Buchbinder, Gregory D. Kirk, Jacques Fellay, Paul McLaren, Steven G. Deeks, Florencia Pereyra, Bruce Walker, Nelson L. Michael, Amy Weintrob, Steven Wolinsky, Wilson Liao, Mary Carrington, in Science, April 5, 2013, View abstract, View external link
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

Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1
Jonathan Carlson, Chanson J. Brumme, Eric Martin, Jennifer Listgarten, Mark A. Brockman, Anh Q. Le, Celia K. S. Chui, Laura A. Cotton, David J. H. F. Knapp, Sharon A. Riddler, Richard Haubrich, George Nelson, Nico Pfeifer, Charles E. DeZiel, David Heckerman, Richard Apps, Mary Carrington, Simon Mallal, P. Richard Harrigan, Mina John, Zabrina L. Brumme, in Journal of Virololgy, December 5, 2012, View abstract, View external link
Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope
Philippa C. Matthews, Madoka Koyanagi, Henrik N. Kloverpris, Mikkel Harndahl, Anette Stryhn, Tomohiro Akahoshi, Hiroyuki Gatanaga, Shinichi Oka, Claudia Juarez Molina, Humberto Valenzuela Ponce, Santiago Avila Rios, David Cole, Jonathan Carlson, Rebecca P. Payne, Anthony Ogwu, Alfred Bere, Thumbi Ndung'u, Kamini Gounder, Fabian Chen, Lynn Riddell, Graz Luzzi, Roger Shaprio, Christian Brander, Bruce Walker, Andrew K. sewell, Gustavo Reyes Teran, David Heckerman, Eric Hunter, Soren Buus, Masafumi Takiguchi, Philip J.R. Goulder, December 4, 2012, View abstract, View external link
CTL Responses of High Functional Avidity and Broad Variant Cross-Reactivity Are Associated with HIV Control
Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Jennifer Zamarreno, Mattia Schiaulini, Cristina Miranda, Marta Ruiz-Riol, Christoph T. Berger, M. Jose Herrero, Eduard Palou, Montse Plana, Morgane Rolland, Ashok Khatri, David Heckerman, Florencia Pereyra, Bruce D. Walker, David Weiner, Roger Paredes, Bonaventura Clotet, Barbara K. Felber, George N. Pavlakis, James I. Mullins, Chirstian Brander, January 4, 2012, View abstract, View external link

2011

A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD
Alan E. Renton, Elisa Majounie, Adrian Waite, Javier Simon-Sanchez, Sara Rollinson, J. Raphael Gibbs, Jennifer C Scymick, Hannu Laaksovirta, John. C. van Swieten, Liisa Myllykangas, Hannu Kalimo, Anders Paetau, Yevgeniya Abramzon, Anne M. Remes, Alice Kaganovich, Sonja W. Scholz, Jamie Duckworth, Jinhui Ding, Daniel W. Harmer, Dena G. Hernandez, Janel O. Johnson, Kin Mok, Mina Ryten, Danyah Trabzuni, Rita J. Guerreiro, Richard W. Orrell, James Neal, Alex Murray, Justin Pearson, Iris E. Jansen, David Sondervan, Harro Seelaar, Derek Blake, Kate Young, Nicola Halliwell, Janis Bennion Callister, Greg Toulson, Anna Richardson, Alex Gerhard, Julie Snowden, David Mann, David Neary, Michael A. Nalls, Terhi Peuralinna, Lilja Jansson, Veli-Matti Isovaiita, Anna-Lotta Kaivorinne, Maarit Holtta-Vuori, Elina Ikonen, Raimo Sulkava, MIchael Benatar, Joanne Wuu, Adriano Chio, Garbiella Restagno, Giuseppe Borghero, Mario Sabatelli, The ITALSGEN Consortium, David Heckerman, Ekaterina ROgaeva, Lorne Zinman, Jeffrey D. Rothstein, MIchael Sendtner, Carsten Drepper, Evan E. Eichler, Can Alkan, Ziedulla Abdullaev, Svetlana D. Pack, Amalia Dutra, Evengenia Pak, John Hardy, Andrew SIngleton, Nigel M. Williams, Peter Heutink, Stuart Pickering-Brown, Huw R. Morris, Pentti J. Tienari, Bryan J. Traynor, September 21, 2011, View abstract, View external link
Definition of the viral targets of protective HIV-1-specific T cell responses
Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Marcus Daniels, Cristina Miranda, Jennifer Zamarreno, Vanessa Bach, Rosario Zuniga, Susana Perez-Alvarez, Chirstoph T. Berger, Maria C. Puertas, Javier Martinez-Picado, Morgane Rolland, Marilu Farfan, James J. Szinger, William H. Hildebrand, Otto O. Yang, Victor Sanchez-Merino, Chanson J. Brumme, Zabrina L. Brumme, David Heckerman, Todd M. Allen, James I. Mullins, Guadalupe Gomez, Philip J. Goulder, Bruce D. Walker, Jose M. Gatell, Bonaventura Clotet, Better T. Korber, Jorge Sanchez, Chirstian Brander, August 6, 2011, View abstract, View external link
HLA-A*7401–Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703
Philippa C. Matthews, Emily Adland, Jennifer Listgarten, Alasdair Leslie, Nompumelelo Mkhwanazi, Jonathan Carlson, Mikkel Harndahl, Anette Stryhn, Rebecca P. Payne, Anthony Ogwu, Kuan-Hsiang Gary Huang, John Frater, Paolo Paioni, Henrik Kolverpris, Pieter Jooste, Dominique Goedhals, Cloete van Vuuren, Dewald Steyn, Lynn Riddell, Fabian Chen, Graz Luzzi, Thambiah Balachandran, Thumbi Ndung'u, Soren Buus, Mary Carrington, Roger Shapiro, David Heckerman, Philip J. R. Goulder, April 15, 2011, View abstract, View external link
Influence of Gag-Protease-Mediated Replication Capacity on Disease Progression in Individuals Recently Infected with HIV-1 Subtype C
Jaclyn K. Wright, Vladimir Novitsky, Mark A. Brockman, Zabrina L. Brumme, Chanson J. Brumme, Jonathan Carlson, David Heckerman, Bingxia Wang, Elena Losina, Mopo Leshwedi, Mary van der Stok, Lungile Maphumulo, Nompumelelo Mkhwanazi, Fundisiwe Chonco, Philip J. R. Goulder, Max Essex, Bruce D. Walker, Thumbi Ndung'u, February 2, 2011, View abstract, View external link

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

Adaptation of HIV-1 to Human Leukocyte Antigen Class I
Yuka Kawashima, Katja Pfafferott, John Frater, Philippa Matthews, Rebecca Payne, Marylyn Addo, Hiroyuki Gatanaga, Mamoru Fujiwara, Atsuko Hachiya, Hirokazu Koizumi, Nozomi Kuse, Shinichi Oka, Anna Duda, Andrew Pendergast, Hayley Crawford, Alasdair Leslie, Zabrina Brumme, Chanson Brumme, Todd Allen, Christian Brander, Richard Kaslow, James Tang, Eric Hunter, Susan Allen, Joseph Mulenga, Songee Branch, Tim Roach, Mina John, Simon Mallal, Anthony Ogwu, Roger Shapiro, Julia G. Prado, Sarah Fidler, Jonathan Weber, Oliver G. Pybus, Paul Klenerman, Thumbi Ndung'u, Rodney Phillips, David Heckerman, P. Richard Harrigan, Bruce D. Walker, Masafumi Takiguchi, Philip Goulder, April 2, 2009, View abstract, View external link

2008

Genetic Characterization of Human Immunodeficiency Virus type 1 in Elite Controllers: Lack of gross genetic defects or common amino acid changes
Toshiyuki Miura, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Jonathan Carlson, Florencia Pereyra, Alicja Trocha, Marylyn M. Addo, Brian L. Block, Alissa C. Rothchild, Brett M. Baker, Theresa Flynn, Arne Schneidewind, Bin Li, Yaoyu E. Wang, David Heckerman, Todd M. Allen, Bruce D. Walker, January 1, 2008, View abstract, Download PDF, View external link
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

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

CD8+ T-cell responses to different HIV proteins have discordant associations with viral load
Photini Kiepiela, Kholiswa Ngumbela, Christina Thobakgale, Dhanwanthia Ramduth, Isobella Honeyborne, Eshia Moodley, Shabashini Reddy, Chantal de Pierres, Zenele Mncube, Nompumelelo Mkhwanazi, Karen Bishop, Mary van der Stok, Kriebashnie Nair, Nasreen Khan, Hayley Crawford, Rebecca Payne, Alasdair Leslie, Julia Prado, Andrew Pendergast, John Frater, Noel McCarthy, Christian Brander, Gerald H. Learn, David Nickle, Christine Rousseau, Hoosen Coovadia, James I. Mullins, David Heckerman, Bruce D. Walker, Philip Goulder, December 17, 2006, View abstract, View external link

2005

2004

2003

2002

2001

2000

1999

1998

1997

1996

1995

1994

1993

1992

1991

1990

1989

1988

1987

1986

1984

Projects

Link description

The Coming Genomics Software Revolution?

Date

July 16, 2013

Speakers

David Haussler, David Heckerman, David Patterson, and George Varghese

Affiliation

University of California, Microsoft Research