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: -- release of a new version of the pedigree simulation software SLINK, and publication of an associated paper in Human Heredity -- release of a new version of the genetic linkage and association software PSEUDOMARKER and publication in Human Heredity of a paper announcing the software -- publication in Neurogenetics of the discovery that a mutation in the canine form of the gene mitofusin 2 (MFN2) causes early-onset neuroaxonal dystrophy The work on SLINK was done in collaboration with Daniel Weeks (Univeristy of Pittsburgh) and Mathieu Lemire (Ontario Institute for Cancer Research). The work on PSEUDOMARKER was done in collaboration with Joseph Terwilliger (Columbia University) The work on canine MFN2 was done in collaboration with John Fyfe (Michigan State University) and Paula Henthorn (University of Pennsylvania).

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Joehanes, Roby; Zhang, Xiaoling; Huan, Tianxiao et al. (2017) Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies. Genome Biol 18:16
Witzel, Maximilian; Petersheim, Daniel; Fan, Yanxin et al. (2017) Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes. Nat Genet 49:742-752
Jin, Yumi; Schäffer, Alejandro A; Sherry, Stephen T et al. (2017) Quickly identifying identical and closely related subjects in large databases using genotype data. PLoS One 12:e0179106
Bhosale, Priyanka G; Cristea, Simona; Ambatipudi, Srikant et al. (2017) Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer. Transl Oncol 10:396-409
Schwartz, Russell; Schäffer, Alejandro A (2017) The evolution of tumour phylogenetics: principles and practice. Nat Rev Genet 18:213-229
Schubert, Desirée; Klein, Marie-Christine; Hassdenteufel, Sarah et al. (2017) Plasma cell deficiency in human subjects with heterozygous mutations in Sec61 translocon alpha 1 subunit (SEC61A1). J Allergy Clin Immunol :
Hatcher, Eneida L; Zhdanov, Sergey A; Bao, Yiming et al. (2017) Virus Variation Resource - improved response to emergent viral outbreaks. Nucleic Acids Res 45:D482-D490
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
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
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

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