The immune system, by any standard is complex. As the number of components in a system and interactions between components grows, our ability to fully comprehend the system diminishes significantly. Principally, humans in comparison to computers, do poorly in tasks such as memorizing, searching and constructing multi-component, multi-scale images. The need to """"""""free our knowledge"""""""" from free text, and place it in a computer system which will memorize our knowledge, allow for easy searching and visualization of our understanding of the immune system is apparent. The use of natural language processing to represent molecular findings from the scientific literature, and the use of network visualization have both made a clear impact across biology. Here, we plan to build a new informatics tool that uses both of these techniques to represent the complex network between cells, immunological processes, secreted cytokines, expressed transcripts, and phosphorylated signaling proteins, called ImuuneXpresso. We will then apply this tool to the multiple type of molecular measurements made throughout this program, to suggest the cellular cause of influenza vaccine non-response. Our tools will be available for beta tested to investigators within this program and released to the general community.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Program--Cooperative Agreements (U19)
Project #
2U19AI057229-06
Application #
7701556
Study Section
Special Emphasis Panel (ZAI1-KS-I (J4))
Project Start
2009-04-01
Project End
2014-03-31
Budget Start
2009-04-01
Budget End
2010-03-31
Support Year
6
Fiscal Year
2009
Total Cost
$186,076
Indirect Cost
Name
Stanford University
Department
Type
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
Davis, Mark M; Tato, Cristina M (2018) Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? Seeing the Forest Rather than a Few Trees. Cold Spring Harb Perspect Biol 10:
Gee, Marvin H; Han, Arnold; Lofgren, Shane M et al. (2018) Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes. Cell 172:549-563.e16
Keeffe, Jennifer R; Van Rompay, Koen K A; Olsen, Priscilla C et al. (2018) A Combination of Two Human Monoclonal Antibodies Prevents Zika Virus Escape Mutations in Non-human Primates. Cell Rep 25:1385-1394.e7
Wagar, Lisa E; DiFazio, Robert M; Davis, Mark M (2018) Advanced model systems and tools for basic and translational human immunology. Genome Med 10:73
Good, Zinaida; Sarno, Jolanda; Jager, Astraea et al. (2018) Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse. Nat Med 24:474-483
Satpathy, Ansuman T; Saligrama, Naresha; Buenrostro, Jason D et al. (2018) Transcript-indexed ATAC-seq for precision immune profiling. Nat Med 24:580-590
Vallania, Francesco; Tam, Andrew; Lofgren, Shane et al. (2018) Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases. Nat Commun 9:4735
Bongen, Erika; Vallania, Francesco; Utz, Paul J et al. (2018) KLRD1-expressing natural killer cells predict influenza susceptibility. Genome Med 10:45
Sweeney, Timothy E; Azad, Tej D; Donato, Michele et al. (2018) Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters. Crit Care Med 46:915-925
Lin, Dongxia; Maecker, Holden T (2018) Mass Cytometry Assays for Antigen-Specific T Cells Using CyTOF. Methods Mol Biol 1678:37-47

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