Nature + Computing

Established: July 15, 2015

Nature + Computing

The intersection of computer science and the natural sciences

Computer science research and applications have grown increasingly data driven. At the same time, the natural sciences have experienced an explosion of data, and are being increasingly driven by computation. While historically the tools created in these two disciplines have been created in relative isolation of each other, increasingly there is bidirectional flow, with insights from machine learning, system modeling, visualization, and software engineering rapidly advancing the pace of scientific discovery, and the statistical rigor of the empirical sciences, driven by a desire to fundamentally understand how the world works, pushing the computational sciences.

The Nature + Computing team at MSR-Redmond is a diverse collection of researchers drawn from across the organization who develop and apply the tools of data science to scientific data and whose research interests are focused on the study of nature.

Precision Medicine

The broad aim of precision medicine is to understand the causal mechanisms underlying variation in clinical outcomes and to improve the efficiency of all aspects of medicine—from scientific discovery to bedside application and disease prevention. Our group is working on projects ranging from vaccine design, to cancer therapeutics, knowledge extraction and basic science using the tools of computational biology.

Heath & Wellbeing

Our group focuses on improving mental health, developing personalized systems to recommend behavioral changes that affect a wide variety of outcomes, and developing technologies that transform the lives of individuals living with physical impairments.


We are committed to using the tools of computer science and machine learning to tackle some of the hardest challenges in environmental sustainability, including conserving biodiversity, ensuring robust food systems, and mitigating climate change.

Engineering with Biology

The recent advances in biotechnology and the increasing challenges in electronics make this a good time to study how these two areas may interact. We are investigating how to apply biology to address current engineering challenges and how to apply engineering principles to the design and optimization of biological systems.




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



Impact of HLA-Driven HIV Adaptation on Virulence in Populations of High HIV Seroprevalence
Rebecca Payne, Maximilian Muenchhoff, Jaclyn Mann, Hannah E. Roberts, Philippa Matthews, Emily Adland, Allison Hempenstall, Kuan-Hsiang Huang, Mark Brockman, Zabrina Brumme, Marc Sinclair, Toshiyuki Miura, John Frater, Myron Essex, Roger Shapiro, Bruce D. Walker, Thumbi Ndung'u, Angela R. McLean, Jonathan Carlson, Philip J. R. Goulder, in Proceedings of the National Academy of Sciences of the United States of America, October 31, 2014, View abstract, View external link
Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck
Jonathan Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J. R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter, in Science, Science, July 12, 2014, View abstract, Download PDF, View external link


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


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




Protective HLA class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1
Yaoyu E. Wang, Bin Li, Jonathan Carlson, Hendrik Streeck, Adrianne D. Gladden, Robert Goodman, Arne Schneidewind, Karen A. Power, Ildiko Toth, Nicole Frahm, Galit Alter, Christian Brander, Mary Carrington, Bruce D. Walker, Marcus Altfeld, David Heckerman, Todd M. Allen, January 1, 2009, View abstract, View external link


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
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
Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients
Thomas Kuntzen, Joerg Timm, Andrew Berical, Niall Lennon, Aaron M. Berlin, Sarah K. Young, Bongshin Lee, David Heckerman, Jonathan Carlson, Laura L. Reyor, Marianna Kleyman, Cory M. McMahon, Christopher Birch, Julian Schulze zur Wiesch, Timothy Ledlie, Michael Koehrsen, Chinnappa Kodira, Andrew D. Roberts, Georg M. Lauer, Hugo R. Rosen, Florian Bihl, Andreas Cerny, Ulrich Spengler, Zhimin Liu, Arthur Y. Kim, Yanming Xing, Arne Schneidewind, Margaret A. Madey, Jaquelyn F. Fleckenstein, Vicki M. Park, James E. Galagan, Chad Nusbaum, Bruce D. Walker, Gerond V. Lake-Bakaar, Eric S. Daar, Ira M. Jacobson, Edward D. Gomperts, Brian R. Edlin, Sharyne M. Donfield, Raymond T. Chung, Andrew H. Talal, Tony Marion, Bruce W. Birren, Matthew R. Henn, Todd M. Allen, in Hepatology, January 1, 2008, 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




Project Florence

Established: August 3, 2015

Nature has its own language; specifically, plants use electro-chemical signals to communicate their needs. Project Florence is a speculative glimpse into our Future where both our Natural and Digital worlds could co-exist in harmony through enhanced communication. Combining Natural Language Research, Biology, Design, and Engineering… we have created the first instantiation of a plant to human interface through the power of language. In this system, the user first attempts to communicate with or influence the…


Established: January 1, 2011

FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for performing efficient genome-wide association studies (GWAS) on large data sets. FaST-LMM runs on both Windows and Linux, and has been tested on data sets with over one million samples. FaST-LMM applications include single-SNP testing, SNP-set testing, tests for epistasis, and heritability estimation. Software versions for FaST-LMM FaST-LMM (python): This version is our most up-to-date release and available on GitHub.  It supports univariate…


Putting Threats to Wildlife on the Map

By Rob Knies, Managing Editor, Microsoft Research In an era of rising temperatures, shrinking ice caps, and widespread drought, the world’s attention is focused on environmental concerns. It seems like every business, every organization, every government has plans to “go green,” and information-technology firms are no exception. No company, though, is better prepared to do so than Microsoft. Not only does it enjoy an abundance of software-engineering talent, but it also has a dedicated team of…

September 2012

Microsoft Research Blog