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.
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.
|Shaw, Laura A; BÃ©langer, 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; 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|
|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|
|Crotty, Shane (2015) A brief history of T cell help to B cells. Nat Rev Immunol 15:185-9|
|Nance, J Philip; BÃ©langer, Simon; Johnston, Robert J et al. (2015) Bcl6 middle domain repressor function is required for T follicular helper cell differentiation and utilizes the corepressor MTA3. Proc Natl Acad Sci U S A 112:13324-9|
|Martinez, Gustavo J; Pereira, Renata M; Ã„ijÃ¶, Tarmo et al. (2015) The transcription factor NFAT promotes exhaustion of activated CD8âº T cells. Immunity 42:265-78|
|Hatzi, Katerina; Nance, J Philip; Kroenke, Mark A et al. (2015) BCL6 orchestrates Tfh cell differentiation via multiple distinct mechanisms. J Exp Med 212:539-53|
|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|
|Nance, J Philip; BÃ©langer, Simon; Johnston, Robert J et al. (2015) Cutting edge: T follicular helper cell differentiation is defective in the absence of Bcl6 BTB repressor domain function. J Immunol 194:5599-603|
|Crotty, Shane; Pipkin, Matthew E (2015) In vivo RNAi screens: concepts and applications. Trends Immunol 36:315-22|
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