This U19 project brings together a large number of investigators of varied expertise generating different forms of data to characterize immune responses to vaccinated and infected subjects in several sample collections. The resulting multidimensional dataset will be an extremely rich substrate for systematic analyses that not only answer specific questions but also investigate the possibility of coordinated responses to vaccination across multiple platforms. Leveraging existing database infrastructure at the Broad Institute, we will build a database for this U19 project by adding functionality that accommodates the unique features of different immunophenotypic data. In particular, we will implement an automated pipeline for cytometric data preparation, quality control, and analysis based on our FLAME program. This novel method models multidimensional data and extracts parameters such as geometric descriptions of cell population clusters and the orientation of these clusters in multidimensional space. This method illustrates the cutting-edge computational methods that we will deploy in this project. Additional methods will be written and implemented as needed in close collaboration with the Analysis Team, whose members are also physically located at the Broad Institute.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-QV-I (M2))
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Yale University
New Haven
United States
Zip Code
Murray, Kristy O; Garcia, Melissa N; Rahbar, Mohammad H et al. (2014) Survival analysis, long-term outcomes, and percentage of recovery up to 8 years post-infection among the Houston West Nile virus cohort. PLoS One 9:e102953
Yao, Yi; Liu, Rebecca; Shin, Min Sun et al. (2014) CyTOF supports efficient detection of immune cell subsets from small samples. J Immunol Methods 415:1-5
Olivieri, Fabiola; Procopio, Antonio Domenico; Montgomery, Ruth R (2014) Effect of aging on microRNAs and regulation of pathogen recognition receptors. Curr Opin Immunol 29:29-37
Vander Heiden, Jason A; Yaari, Gur; Uduman, Mohamed et al. (2014) pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics 30:1930-2
Zapata, Heidi J; Shaw, Albert C (2014) Aging of the human innate immune system in HIV infection. Curr Opin Immunol 29:127-36
Qian, Feng; Thakar, Juilee; Yuan, Xiaoling et al. (2014) Immune markers associated with host susceptibility to infection with West Nile virus. Viral Immunol 27:39-47
Lee, Naeun; Shin, Min Sun; Kang, Ki Soo et al. (2014) Human monocytes have increased IFN-?-mediated IL-15 production with age alongside altered IFN-? receptor signaling. Clin Immunol 152:101-10
Chattopadhyay, Pratip K; Gierahn, Todd M; Roederer, Mario et al. (2014) Single-cell technologies for monitoring immune systems. Nat Immunol 15:128-35
Gierahn, Todd M; Loginov, Denis; Love, J Christopher (2014) Crossword: a fully automated algorithm for the segmentation and quality control of protein microarray images. J Proteome Res 13:362-71
Goel, Gautam; Conway, Kara L; Jaeger, Martin et al. (2014) Multivariate inference of pathway activity in host immunity and response to therapeutics. Nucleic Acids Res 42:10288-306

Showing the most recent 10 out of 24 publications