During my career I have worked on several projects creating software (FASTLINK, CASPAR, rh_tsp_map, PedHunter, etc.) and a database (Anabaptist Genealogy database) for genetic studies. My association with this software and a past track record of effective collaboration with wet lab scientists leads to more such collaborations. Three highlights from my publications of the past year are: -- characterization of the first human patients known to have the rare human disease "IL21R deficiency", which was published in Journal of Experimental Medicine; -- characterization of version 5 of the Anabaptist Genealogy Database (AGDB), which was published in PLoS One -- initial description of the software FISHtrees for analysis of single-cell copy number data, which was published in Bioinformatics The work on IL21R was done in collaboration with Christoph Klein (Munich, Germany). The work on epidemiology studies with AGDB is being done in collaboration with Professor Braxton Mitchell (Baltimore, MD) The work on FISHtrees is being done in collaboration with Thomas Ried (NCI/NIH) and Russell Schartz (Pittsburgh, PA) The paper on this topic that Dr. Schwartz presented at the July 2013 ISMB meeting in Berlin shared the prize for best paper in translational bioinformatics.

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Gertz, E Michael; Chowdhury, Salim Akhter; Lee, Woei-Jyh et al. (2016) FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe. PLoS One 11:e0158569
Richard, Arianne C; Peters, James E; Lee, James C et al. (2016) Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network. Genome Med 8:76
Wangsa, Darawalee; Chowdhury, Salim Akhter; Ryott, Michael et al. (2016) Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis. Int J Cancer 138:98-109
Catanzaro, Daniele; Shackney, Stanley E; Schaffer, Alejandro A et al. (2016) Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study. IEEE/ACM Trans Comput Biol Bioinform 13:643-55
Abuhatzira, Liron; Xu, Huanyu; Tahhan, Georges et al. (2015) Multiple microRNAs within the 14q32 cluster target the mRNAs of major type 1 diabetes autoantigens IA-2, IA-2β, and GAD65. FASEB J :
Lanternier, Fanny; Mahdaviani, Seyed Alireza; Barbati, Elisa et al. (2015) Inherited CARD9 deficiency in otherwise healthy children and adults with Candida species-induced meningoencephalitis, colitis, or both. J Allergy Clin Immunol 135:1558-68.e2
Sei, Yoshitatsu; Zhao, Xilin; Forbes, Joanne et al. (2015) A Hereditary Form of Small Intestinal Carcinoid Associated With a Germline Mutation in Inositol Polyphosphate Multikinase. Gastroenterology 149:67-78
Fliegauf, Manfred; Bryant, Vanessa L; Frede, Natalie et al. (2015) Haploinsufficiency of the NF-κB1 Subunit p50 in Common Variable Immunodeficiency. Am J Hum Genet 97:389-403
Volk, Timo; Pannicke, Ulrich; Reisli, Ismail et al. (2015) DCLRE1C (ARTEMIS) mutations causing phenotypes ranging from atypical severe combined immunodeficiency to mere antibody deficiency. Hum Mol Genet 24:7361-72
Engelhardt, Karin R; Gertz, Michael E; Keles, Sevgi et al. (2015) The extended clinical phenotype of 64 patients with dedicator of cytokinesis 8 deficiency. J Allergy Clin Immunol 136:402-12

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