Highlights

"Multiparameter phospho-flow analysis of lymphocytes in early rheumatoid arthritis," published in PLOSOne, discusses levels of 15 phospho-proteins across 3 cell lineages (CD3+CD4+, CD3+CD8+, and CD20+) in patients with rheumatoid arthritis.  It's a nice presentation of a "big data" study, with data from 77 donors.  There are some interesting findings about  leflunomide, systemic steroids and anti-TNF therapy reducing the levels of the phospho-proteins.

"An analyical workflow for investigating cytokine profiles," by Siebert et al., was published in the conference proceedings issue of Cytometry Part A. Ms. Siebert also presented this paper at the 2008 ISAC Congress.  Using an iterative process of population-level analysis followed by donor-level analysis, the authors identified findings that were not immediately obvious with standard analytical techniques.

In August of 2007, "Functional T cell responses to tumor antigens in breast cancer patients have a distinct phenotype and cytokine signature," by Inokuma et al. appeared in the Journal of Immunology. Ms. Siebert is a coauthor on this paper. She helped the other members of the team with some data normalization techniques that supported statistical confirmation of differences between responses to tumor associated antigens and viruses such as CMV and Flu.

All of these works build on "A rich analytical environment for flow cytometry experimental results," which  presents advantages of combining the cytometer's output with clinical data and aliquot handling information. Parsed fcs files are loaded into a relational database, where the analyst can query based on donor characteristics such as species, gender, diet type; or aliquot data such as stain type.

Citations

1. Galligan CL, Siebert JC, Siminovitch KA, Keystone EC, Bykerk V, Perez OD, Fish EN. Multiparameter phospho-flow analysis of lymphocytes in early rheumatoid arthritis: implications for diagnosis and monitoring drug therapy. PLoS One. 2009 Aug 20;4(8):e6703.
2. Siebert JC, Inokuma M, Waid DM, Pennock ND, Vaitaitis GM, Disis ML, Dunne JF, Wagner DH Jr, Maecker HT. An analytical workflow for investigating cytokine profiles. Cytometry A. 2008 Apr;73(4):289-98.
3. Inokuma M, dela Rosa C, Schmitt C, Haaland P, Siebert J, Petry D, Tang M, Suni MA, Ghanekar SA, Gladding D, Dunne JF, Maino VC, Disis ML, Maecker HT. Functional T cell responses to tumor antigens in breast cancer patients have a distinct phenotype and cytokine signature. J Immunol. 2007 Aug 15;179(4):2627-33.
4. Siebert J, Cios KJ, and Newell MK. A rich analytical environment for flow cytometry experimental results. Int. J. Bioinformatics Research and Applications. 2006; 2(1):52-62.
5. Siebert J. Improving the performance of data analysis in data warehouses:a methodology and case study.P roceedings of the 1999 ACM SIGMETRICS international conference on measurement and modeling of computer systems SIGMETRICS '99; 27(1):234-235.