Abstract

The purpose of Core D is to provide the bioinformatics and statistics support necessary for completing shRNAmir-based genetic screens using deep sequencing technology. The Director of Core D is Bjoern Peters. Dr. Peters has long and successful track record of scientific publications on bioinformatics intensive topics. Drs. Peters and Crotty have multiple scientific publications together, and have been collaborators on studies of antiviral immunity for six years. Drs. Peters and Pipkin have also worked together for multiple years on bioinformatics intensive projects, and they currently have two co-authored research papers submitted for publication.
The Specific Aims of the Bioinformatics and Statistics Core are as follows: 1. To provide the bioinformatics support necessary for completing shRNAmir-based genetic screens using deep sequencing technology. 2. To provide statistics support for data analysis and interpretation.

Public Health Relevance

Bioinformatics and statistics are essential parts of data processing and analysis for all three Projects in this U19, and almost all individual Aims of each Project. Drs. Peters, Pipkin, and Crotty have collaborated over the past 18 months to develop the necessary bioinformatics to rapidly analyze shRNAmir sequences from an lon Torrent output and rigorous match the correct DNA seqeunces.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Program--Cooperative Agreements (U19)
Project #
5U19AI109976-03
Application #
9024445
Study Section
Special Emphasis Panel (ZAI1)
Project Start
Project End
Budget Start
2016-03-01
Budget End
2017-02-28
Support Year
3
Fiscal Year
2016
Total Cost
Indirect Cost

  Institution

Name
La Jolla Institute
Department
Type
DUNS #
603880287
City
La Jolla
State
CA
Country
United States
Zip Code
92037

  Publications

Milner, J Justin; Goldrath, Ananda W (2018) Transcriptional programming of tissue-resident memory CD8+ T cells. Curr Opin Immunol 51:162-169
Wang, Dapeng; Diao, Huitian; Getzler, Adam J et al. (2018) The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation. Immunity 48:659-674.e6
Milner, J Justin; Toma, Clara; Yu, Bingfei et al. (2017) Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours. Nature 552:253-257
Yu, Bingfei; Zhang, Kai; Milner, J Justin et al. (2017) Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation. Nat Immunol 18:573-582
Pedros, Christophe; Zhang, Yaoyang; Hu, Joyce K et al. (2016) A TRAF-like motif of the inducible costimulator ICOS controls development of germinal center TFH cells via the kinase TBK1. Nat Immunol 17:825-33
Martinez, Gustavo J; Hu, Joyce K; Pereira, Renata M et al. (2016) Cutting Edge: NFAT Transcription Factors Promote the Generation of Follicular Helper T Cells in Response to Acute Viral Infection. J Immunol 196:2015-9
Shaw, Laura A; Bélanger, Simon; Omilusik, Kyla D et al. (2016) Id2 reinforces TH1 differentiation and inhibits E2A to repress TFH differentiation. Nat Immunol 17:834-43
Martinez, Gustavo J; Pereira, Renata M; Äijö, Tarmo et al. (2015) The transcription factor NFAT promotes exhaustion of activated CD8? T cells. Immunity 42:265-278
Choi, Youn Soo; Gullicksrud, Jodi A; Xing, Shaojun et al. (2015) LEF-1 and TCF-1 orchestrate T(FH) differentiation by regulating differentiation circuits upstream of the transcriptional repressor Bcl6. Nat Immunol 16:980-90
Crotty, Shane; Pipkin, Matthew E (2015) In vivo RNAi screens: concepts and applications. Trends Immunol 36:315-22

Showing the most recent 10 out of 16 publications