Abstract

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.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Program--Cooperative Agreements (U19)
Project #
5U19AI057229-08
Application #
8249152
Study Section
Special Emphasis Panel (ZAI1)
Project Start
Project End
Budget Start
2011-04-01
Budget End
2012-03-31
Support Year
8
Fiscal Year
2011
Total Cost
$181,546
Indirect Cost

  Institution

Name
Stanford University
Department
Type
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305

  Publications

Bukhari, Syed Ahmad Chan; O'Connor, Martin J; Martínez-Romero, Marcos et al. (2018) The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. Front Immunol 9:1877
Azad, Tej D; Donato, Michele; Heylen, Line et al. (2018) Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival. JCI Insight 3:
Leipold, Michael D; Obermoser, Gerlinde; Fenwick, Craig et al. (2018) Comparison of CyTOF assays across sites: Results of a six-center pilot study. J Immunol Methods 453:37-43
Sibener, Leah V; Fernandes, Ricardo A; Kolawole, Elizabeth M et al. (2018) Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding. Cell 174:672-687.e27
Ju, Chia-Hsin; Blum, Lisa K; Kongpachith, Sarah et al. (2018) Plasmablast antibody repertoires in elderly influenza vaccine responders exhibit restricted diversity but increased breadth of binding across influenza strains. Clin Immunol 193:70-79
Sweeney, Timothy E; Perumal, Thanneer M; Henao, Ricardo et al. (2018) A community approach to mortality prediction in sepsis via gene expression analysis. Nat Commun 9:694
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

Showing the most recent 10 out of 249 publications