Kathleen Cardone

  Research Specialist 

  A301 Richards Building 
  3700 Hamilton Walk, Philadelphia, PA 19104

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  https://sites.google.com/view/kathleen-cardone/home

Current Projects

• Determining genetic risk for various phenotypes with polygenic risk scores.
• Other broad research interests include neuroscience and pharmacology.

Education

Work Experience

• Geisinger Medical Center, Research Strategic Initiative Department Undergraduate Intern, 06/2021-05/2022
• Pennsylvania State University Department of Biobehavioral Health, Undergraduate Research Assistant, 11/2019-05/2022

Publications:

• Abner T. Apsley, Emma R. Domico, Max A. Verbiest, Carly A. Brogan, Evan R. Buck, Andrew J. Burich, Kathleen M. Cardone, Wesley J. Stone, Maria Anisimova, David J. Vandenbergh. Characterization of a Novel Hyper-Variable Variable Number Tandem Repeat in the Dopamine Transporter Gene (SLC6A3). Manuscript Submitted for Publication.

Nimay Kumar

  Application Developer

  A301 Richards Building 
  3700 Hamilton Walk, Philadelphia, PA 19104

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Current Projects

• PharmCAT HL7/EHR Reports

• LocoColoc

Education

• MSE in Data Science, University of Pennsylvania, Aug 2022 - Present
• BS in Electrical & Computer Engineering, The University of Texas at Austin, Aug 2016 - May 2020

 Work Experience

• Application Developer B, University of Pennsylvania, June 2022 - Present
• Software Engineer, IPT Global, June 2021 - June 2022
• Software Engineer, Odyssey Space Research, June 2020 - June 2021

Scott Dudek

Application Developer

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Current Projects

ATHENA – Platform for analyzing genetic data using evolutionary algorithms
PLATO – (PLatform for the Analysis, Translation, and Organization of large-scale data) incorporates a number of filters to select the important SNPs in a genome-wide association study.
Visualization – Developing tools for visualizing data and results for PheWAS projects

Education

B.A. Biology
Washington University

Washington University School of Medicine

Work Experience

Application Developer
Ritchie Lab
University of Pennsylvania

Software Developer
Ritchie Lab
Geisinger
2016-2017

Software Developer
Ritchie Lab
Pennsylvania State University
2011-2016

Software Developer
Ritchie Lab
Vanderbilt University
2004-2011

Software Developer
Bioinformatics Core
Center for Human Genetics Research
Vanderbilt University
2001-2004

Publications

• Bush W.S., Dudek S.M., Ritchie M.D. 2009. Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pacific Symposium on Biocomputing. 368-79.
• Motsinger A.A., Fanelli T.J., Dudek S.M., Ritchie M.D. 2008. Balanced accuracy as a fitness function in grammatical evolution neural networks is robust to imbalanced data. GECCO. In press.
• Edwards T.L., Lewis K.G., Velez D.R., Dudek S.M., Ritchie M.D. 2008. Exploring the Performance of Multifactor Dimensionality Reduction in Large Scale SNP Studies and in the Presence of Genetic Heterogeneity among Epistatic Disease Models. Human Heredity. 67(3):183-92.
• Bush W.S., Edwards T.L., Dudek S.M., McKinney B.A., Ritchie M.D. 2008. Alternative contingency table measures improves the power and detection of Multifactor Dimensionality Reduction. BMC Bioinformatics. 9:238
• Motsinger-Reif A.A., Dudek S.M., Hahn L.W., Ritchie M.D. 2008. Comparison of approaches for machine learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology. Genetic Epidemiology. 32(4):325-40.
• Edwards T.L., Bush W.S., Turner S.D., Dudek S.M., Torstenson E.S., Schmidt M., Martin E., Ritchie M.D. 2008 Generating linkage disequilibrium patterns in data simulations using genomeSIMLA. Lecture Notes in Computer Science. 4973: 24-35.
• Schwartz U.I., Ritchie M.D., Bradford Y., Dudek S., Frye-Anderson A., Kim R.B., Roden D.M., Stein C.M. 2008. Genetic determinants of response to warfarin during initial anticoagulation. NEJM. 358(10):999-1008. (PubMed)
• Motsinger A.A., Reif D.M., Dudek S.M., Ritchie M.D. 2006. Dissecting the evolutionary process of grammatical evolution optimized neural networks. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 1-8.
• Bush W.S., Dudek S.M., Ritchie M.D. 2006. Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. Bioinformatics. 22:2173-4. (PubMed)
• Motsinger A.A., Hahn L.W., Dudek S.M., Ryckman K.K., Ritchie M.D. 2006. Alternative Cross-Over Strategies and Selection Techniques for Grammatical Evolution Optimized Neural Networks. Proceedings of Genetic and Evolutionary Computation Conference. 947-949.
• Motsinger A.A., Dudek S.M., Hahn L.W., Ritchie M.D. 2006. Comparison of Neural Network Optimization Approaches for Studies of Human Genetics. Lecture Notes in Computer Science. 3907:103-114.
• Dudek SM, Motsinger AA, Velez DR, Williams SM, Ritchie MD. Data Simulation Software for Whole-Genome Association and Other Studies in Human Genetics. Pac Symp BioComput. 2006;:499-510.
• Reif DM, Dudek SM, Shaffer CM, Wang J, Moore JH. Exploratory visual analysis of pharmacogenomic results. Pac Symp BioComput. 2005;:296-307.
• Glossop NR, Houl JH, Zheng H, Ng FS, Dudek SM, Hardin PE. VRILLE feeds back to control circadian transcription of Clock in the Drosophila circadian oscillator. Neuron. 2003 Jan 23;37(2):249-61.
• Bergelson J, Stahl E, Dudek S, Kreitman M. Genetic variation within and among populations of Arabidopsis thaliana. Genetics. 1998 Mar;148(3):1311-23. (PubMed)

Xueqiong Li

Application Developer

A301 Richards Building 
3700 Hamilton Walk, Philadelphia, PA 19104

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Current Projects

• Development and maintenance of application tools

Education

• M.S. in Computer Science & Bioinformatics, Northern Illinois University, 2015 - 2019
• B.S. in Biological Engineering, Southeast University of China, 2011 - 2015

 Work Experience

• Application Developer, University of Pennsylvania, 2022 - Present
• Programmer, Noble Research Institute, 2019 - 2022
• Research Assistant & Teaching Assistant, Northern Illinois University, 2015 - 2019

 Publications 

 For the list of my publications please visit Google Scholar

Yuki Bradford