Projects

Rare Diseases in the UK Biobank

The purpose of this project is to catalog and investigate the information available about rare diseases in the UK Biobank. Click here to see the results.

Publications

Abstracts

Patrick, M. T., Sreeskandarajan, S., Shefler, A., Wasikowski, R., Sarkar, M. K., Chen, J., Prens, E., Hovnanian, A., Weidinger, S., Elder, J. T., Kuo, C., Gudjonsson, J. E., Tsoi, L. C. (2020). “273 Large scale functional inference for skin-expressing lncRNAs using expression and sequence information.” in Society of Investigative Dermatology, pp. S33 (read online).

Tsoi, L. C., Zhang, Z., Stuart, P., Zhang, Y., Patrick, M., Zhang, H., Wen, X., Nair, R., Elder, J. T. (2020). “303 Allele specific accessibility analysis to decipher molecular mechanism of psoriasis-associated loci.” in Society of Investigative Dermatology, pp. S37 (read online).

Wasikowksi, R., Billi, A. C., Zhang, H., Sutharzan, S., Shefler, S., Patrick, M., Chen, J., Gudjonsson, J. E., Tsoi, L. C. (2020). “300 Using single cell technique to reveal the expression landscape of lncRNAs in psoriasis.” in Society of Investigative Dermatology, pp. S37 (read online).

Gudjonsson, J. E., Tsoi, L. C., Billi, A. C., Plazyo, O., Wasikowski, R., Jiang, Y., Zeng, C., Kirma, J., Wilson, M. J., Patrick, M., Raja, K., Lafyatis, R., Kahlenberg, J., Khanna, D. (2020). “188 scRNA-seq and RNA-seq for Stiff Skin Syndrome identify pericytes as a key pathogenic cell population and avenue for therapeutic targeting.” in Society of Investigative Dermatology, pp. S22 (read online).

Verhaegen, M. E., Van Goor, J., Arche, J., Harms, P., Wilbert, D., Zabawa, H., Patrick, M., Tsoi, L. C., Chinnaiyan, A., Dlugosz, A.A. (2020). “118 In vivo cellular reprogramming facilitates viral T antigen-driven Merkel cell carcinoma development in adult mice.” in Society of Investigative Dermatology, pp. S14 (read online).

Patrick, M. T., Stuart, P. E., Yin, X., He, Z., Gudjonsson, J. E., Voorhees, J. J., Nair, R. P., Liu, D., Elder, J. T., Tsoi, L. C. (2019). “Psoriasis and type 2 diabetes trans-disease meta-analysis.” in National Psoriasis Foundation.

Patrick, M. T., Stuart, P. E., Yin, X., He, Z., Gudjonsson, J. E., Voorhees, J. J., Nair, R. P., Liu, D., Elder, J. T., Tsoi, L. C. (2019). “Trans-disease meta-analysis between psoriasis and type 2 diabetes reveals shared genetic signals.” in Society of Investigative Dermatology, pp. S10 (read online).

Patrick, M. T., Stuart, P. E., Raja, K., Abecasis, G. R., Voorhees, J. J., Tejasvi, T., Gudjonsson, J. E., Chandran, V., Rahman, P., Gladman, D. D., Nair, R. P., Elder, J. T. & Tsoi, L.C. (2018). “2325 Non-MHC loci associated with psoriatic arthritis reveal evidence of a potential mechanism for joint involvement.” in American Society of Human Genetics.

Yang, J., Nagpal, S., Epstein, M., Tsoi, L., Patrick, M., Wingo, A. & Wingo, T. (2018). “2356 Integrative functional genomics analysis of neuropathologic features of Alzheimer’s disease and related cognition decline reveals novel insights on previously identified loci.” in American Society of Human Genetics.

Patrick, M.T., Stuart, P. E., Yang, J., Raja, K., Yang, Y., Madu, D., Tejasvi, T., Voorhees, J. J., Kang, H. M., Gudjonsson, J. E., Abecasis, G., Nair, R. P., Wen, X., Elder, J. T. & Tsoi, L.C. (2018). “742 Identification of psoriasis-associated genes using genetically predicted transcriptomes.” in Journal of Investigative Dermatology, 138(5), pp. S126 (read online).

Patrick, M. T., Stuart, P. E., Raja, K., Yang, J., Zawistowski, M., Voorhees J. J., Tejasvi, T., Gudjonsson, J. E., Chandran, V., Rahman, P., Nair, R. P., Gladman, D. D., Elder, J. T. & Tsoi, L.C. (2018). “746 Challenges and opportunities for integrating genetics and health records in risk assessment for psoriasis subtypes.” in Journal of Investigative Dermatology, 138(5), pp. S127 (read online).

Tsoi, L. C., Rodrigues, E., Degenhardt, F., Baurecht, H., Wehkamp, U., Volks, N., Szymczak, S., Swindell, W., Sarkar, M., Raja, K., Patrick, M. T., Gao, Y., Uppala, R., Perez White, B. E., Getsios, S., Harms, P., Maverakis, E., Elder, J. T., Franke, A., Gudjonsson, J. E. & Weidinger, S. (2018). “480 Atopic dermatitis is an IL-13/IL10 driven disease with high molecular heterogeneity compared to psoriasis.” in Journal of Investigative Dermatology, 138(5), pp. S81 (read online).

Sarkar, M. K., Hile, G., Tsoi, L. C., Xing, X., Liu, J., Liang, Y., Berthier, C. C., Swindell, W. R., Patrick, M., Tsou, P., Uppala, R., Beamer, M., Srivastava, A., Bielas, S., Harms, P., Getsios, S., Elder, J. T., Voorhees, J. J., Kahlenberg, J. M. & Gudjonsson, J. E. (2018). “072 Photosensitivity and heightened type I IFN responses in cutaneous lupus are driven by elevated interferon kappa.” in Journal of Investigative Dermatology, 138(5), pp. S12 (read online).

Patrick, M.T., Stuart, P. E., Raja, K., Gudjonsson, J. E., Tejasvi, T., Voorhees, J. J., Gladman, D. D., Nair, R., Elder, J. T. & Tsoi, L.C. (2017). “193 Integrating health records and genetic signatures to enhance psoriatic arthritis risk assessment.” in Journal of Investigative Dermatology, 137(10), pp. S225 (read online).

Patrick, M.T., Stuart, P. E., Raja, K., Gudjonsson, J. E., Tejasvi, T., Voorhees, J. J., Gladman, D. D., Nair, R., Elder, J. T. & Tsoi, L.C. (2017). “Assessing the risk of Psoriatic Arthritis through Machine Learning Genetic Prediction.” in NPF Symposium.

Patrick, M.T., Stuart, P. E., Raja, K., Gudjonsson, J. E., Tejasvi, T., Voorhees, J. J., Gladman, D. D., Nair, R., Elder, J. T. & Tsoi, L.C. (2017). “485 Genetic signature to assess risk of psoriasis subtypes through machine learning approach.” in Journal of Investigative Dermatology, 137(5), pp. S83 (read online).

Sarkar, M.K., Xing, X., Tsoi, A., Liang, Y., Berthier, C.C., Roberts, L.W., Patrick, M.T., Hile, G., Beamer, M.A., Tsou, P., Harms, P.W., Elder, J.T., Voorhees, J.J., Johnston, A., Kahlenberg, J.M., Gudjonsson, J.E. (2017). “043 Interferon kappa is required for regulation of baseline type I interferon responses in keratinocytes and is dysregulated in cutaneous lupus.” in Journal of Investigative Dermatology, 137(5), pp. S8 (read online).

Raja, K., Patrick, M., Elder, J. T. & Tsoi, L.C. (2016). “Machine learning workflow to enhance predictions of adverse drug reactions through drug-drug interactions for cutaneous diseases.” in Int. Conf. Intelligent Biology and Medicine.

Book Chapters

Patrick, M. (2017). “Making scientific software easier to understand, test and communicate through software engineering.” in Software Engineering for Science. Carver, J. Abingdon, United Kingdom: Taylor & Francis, pp. 53-88 (read online).

Patrick, M. (2016). “Metaheuristic Optimisation and Mutation-Driven Test Data Generation” in Computational Intelligence and Quantitative Software Engineering. Pedrycz, W., Succi, G. & Sillitti, A. Heidelberg, Germany: Springer, pp. 89-115 (read online).

Journal Articles

Patrick, M.T., Bardhi, R., Raja, K., He, K., Tsoi, L.C. (2021). Advancement in predicting drug-drug interactions for drugs used to treat psoriasis and its comorbidities by integrating molecular and clinical resources. Journal of the American Medical Informatics Association, [in press].

Patrick, M.T., Zhang, H., Wasikowski, R., Prens, E.P., Weidinger, S., Gudjonsson, J.E., Elder, J.T., He, K., Tsoi, L.C. (2021). Associations between COVID-19 and skin conditions identified through epidemiology and genomic studies. Journal of Allergy and Clinical Immunology, [in press].

Patrick, M.T., Stuart, P.E., Zhang, H., Zhao, Q., Yin, X., He, K., Zhou, X., Mehta, N.N., Voorhees, M.D., Boehnke, M., Gudjonsson, J.E., Nair, R.P., Handelman, S.K., Elder, J.T., Liu, D.J., Tsoi, L.C. (2021). Causal relationship and shared genetic loci between psoriasis and type 2 diabetes through trans-disease meta-analysis. Journal of Investigative Dermatology, [in press] (read online).

Patrick, M. (2020). Exploring Software Reusability Metrics with Q&A Forum Data. Journal of Systems and Software, 168:110652 (read online).

Shao, S., Tsoi, L.C., Sarkar, M.K., Xing, X., Xue, K., Uppala, R., Berthier, C.C., Zheng, C., Patrick, M., Billi, A., Fullmer, J., Beamer, M.A., Perez-White, B., Getsios, S., Schuler, A., Voorhees, J.J., Choi, S., Harms, P., Kahlenberg, J.M., Gudjonsson, J.E. (2019). IFN-γ enhances cell-mediated cytotoxicity against keratinocytes via JAK2/STAT1 in lichen planus. Science Translational Medicine, 11:511 (read online).

Veniaminova, N.A., Grachtchouk, M., Doane O.J., Peterson, J.K., Quigley, D.A., Lull, M.V., Pyrozhenko, D.V., Nair, R.P., Patrick, M.T., Balmain, A., Dlugosz, A.A., Tsoi, L.C., Wong, S.Y. (2019). Niche-Specific Factors Dynamically Regulate Sebaceous Gland Stem Cells in the Skin. Developmental Cell, 51(3), pp. 326-340.e4 (read online).

Patrick, M.T., Stuart, P.E., Raja, K., Chi, S., He, Z., Voorhees, J., Tejasvi, T., Gudjonsson, J., Kahlenberg, M., Chandran, V., Rahman, P., Gladman, D.D., Nair, R., Elder, J.T., Tsoi, L.C. (2019). Integrative approach to reveal cell type specificity and gene candidates for psoriatic arthritis outside the MHC. Frontiers in Genetics, 10:304 (read online).

Tsoi, L.C., Hile, G., Berthier, C.C., Sarkar, M., Reed, T.J., Uppala, R., Patrick, M., Raja, K., He, Z., Gudjonsson, J.E., Kahlenberg, M. (2019). Hypersensitive IFN responses in lupus keratinocytes reveal key mechanistic determinants in cutaneous lupus. The Journal of Immunology, 202(7), pp. 2121-2130 (read online).

Tsoi, L.C., Rodriguez, E., Degenhardt, F., Baurecht, H., Wehkamp, U., Volks, N., Szymczak, S., Swindell, W.R., Sarkar, M.K., Raja, K., Shao, S., Patrick, M., Gao, Y., Uppala, R., White, B.E.P., Getsios, S., Harms, P.W., Maverakis, E., Weidinger, S. (2019). Atopic dermatitis is an IL-13 dominant disease with greater molecular heterogeneity compared to psoriasis. Journal of Investigative Dermatology 139(7), pp. 1480-1489 (read online).

Nagpal, S., Meng, X., Epstein, M.P., Tsoi, L.C., Patrick, M., Gibson, G., De Jager, P., Bennett, D.A., Wingo, A.P., Wingo, T.S., Yang, J. (2019). TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits. ASHG, 105, pp. 1-9 (read online).

Patrick, M., Tsoi, L.C., Gudjonsson, J.E. (2019). Making new connections – chromosome conformation capture for identification of disease-associated target genes. Journal of Investigative Dermatology, 139(3), pp. 514-517 (< href="https://doi.org/10.1016/j.jid.2018.11.026">read online).

Patrick, M., Raja, K., Miller, K., Sotzen, J., Gudjonsson, J.E., Elder, J.T. & Tsoi, L.C. (2019). Drug repurposing prediction for immune-mediated cutaneous diseases using a word-embedding based machine learning approach. Journal of Investigative Dermatology, 139(3), pp. 683-691 (read online).

Meng, G., Patrick, M., Xue, Y., Liu, Y., Zhang, J. (2018). Securing Android App Markets via Modelling and Predicting Malware Spread between Markets. IEEE Transactions on Information Forensics and Security, 14(7), pp. 1944-1959 (read online).

Patrick, M., Stuart, P.E., Raja, K., Gudjonsson, J.E., Tejasvi, T., Yang, J., Chandran, V., Das, S., Callis-Duffin, K., Ellinghaus, E., Enerbäck, C., Esko, T., Franke, A., Kang, H.M., Krueger, G.G., Lim, H.W., Rahman, P., Rosen, C.F., Weidinger, S., Weichenthal, M., Wen, X., Voorhees, J.J., Abecasis, G.R., Gladman, D.D., Nair, R.P., Elder, J.T. & Tsoi, L.C. (2018). Genetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients. Nature Communications 9(1):4178 (read online).

Tsoi, L.C., Patrick, M. & Elder, J.T. (2018). Research Techniques Made Simple: Using genome-wide association studies to understand complex cutaneous disorders. Journal of Investigate Dermatology 138, pp. e23-e29 (read online).

Sarkar, M.K., Hile, G.A., Tsoi, L.C., Xing, X., Liu, J., Liang, Y., Berther, C.C., Swindell, W.R., Patrick, M.T., Shao, S., Tsou, P.S., Uppalla, R., Beamer, M.A., Srivastava, A., Bielas, S.L., Harms, P.W., Gestsios, S., Elder, J.T., Voorhees, J.J., Gudjonsson, J.E. & Kahlenberg, J.M. (2018). Photosensitivity and type I IFN responses in cutaneous lupus are driven by epidermal-derived interferon kappa. Ann. Rheum. Dis. 21397 (read online).

Raja, K., Patrick, M., Elder, J.T. & Tsoi, L.C. (2017). Machine Learning Workflow to Enhance Predictions of Adverse Drug Reactions (ADRs) through Drug-Gene Interactions: Application to Drugs for Cutaneous Diseases. Scientific Reports 7, article 3690 (read online).

Raja, K., Patrick, M., Gao, Y., Madu, D., Yang, Y. & Tsoi, L.C. (2017). A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries. International Journal of Genomics, 2017, article 6213474 (read online).

Patrick, M. & Jia, Y. (2017). KD-ART: Should we intensify or diversify tests to kill mutants?. Information and Software Technology, 81, pp. 36-51 (read online).

Patrick, M., Alexander, R., Oriol, M. & Clark, J.A. (2015). Subdomain-Based Test Data Generation. Journal of Systems and Software, 103, pp. 328-342 (read online).

Conference Proceedings

Patrick, M., Donnelly, R. & Gilligan, C.A. (2017). A Toolkit for Testing Stochastic Simulations against Statistical Oracles. Int. Conf. Software Testing, pp. 448-453 (read online).

Patrick, M., Castle, M.D., Stutt R.O.J.H. (2016). Automated Test Image Generation Using Procedural Noise. Int. Conf. Automated Software Engineering, pp. 654-659 (read online).

Patrick, M. (2016). Interactive Tool for Iterative Test Suite Construction. Int. Conf. Software Engineering and Knowledge Engineering, no. 202 (read online).

Patrick, M., Craig, A.P., Cunniffe, N.J., Parry, M., Gilligan, C.A. (2016). Testing Stochastic Software using Pseudo-Oracles. Int. Symp. Software Testing Analysis, pp. 235-246 (,a href="https://doi.org/10.1145/2931037.2931063">read online).

Patrick, M., Elderfield, J., Stutt, R.O.J.H., Rice, A., Gilligan, C.A. (2016). Software Testing in a Scientific Research Group. ACM Symp. Applied Computing, pp. 1454-1459 (read online).

Patrick, M., Jia, Y. (2015). Exploring the Landscape of Non-Functional Program Properties using Spatial Analysis. Symp. Search Based Software Eng., pp. 332-338 (read online).

Patrick, M., Jia, Y. (2015). Kernel Density Adaptive Random Testing. IEEE Int. Conf. Software Testing, pp. 53-62 (read online).

Patrick, M., Stutt, R.O.J.H., & Gilligan, C.A. (2014). Rasterising Epidemiological Host Data Efficiently. IEEE Int. Conf. Modelling Simulation, pp. 232-237 (read online).

Patrick, M., Alexander, R., Manuel, O. & Clark, J.A. (2014). Probability-Based Semantic Interpretation of Mutants. IEEE Int. Conf. Software Testing, pp. 186-195 (read online).

Patrick, M., Alexander, R., Manuel, O. & Clark, J.A. (2013). Efficient Subdomains for Random Testing. Symp. Search Based Software Engineering, pp. 251-256 (read online).

Patrick, M., Alexander, R., Manuel, O. & Clark, J.A. (2013). Using Mutation Analysis to Evolve Subdomains for Random Testing. IEEE Int. Conf. Software Testing, pp. 53-62 (read online).

Patrick, M., Manuel, O. & Clark, J.A. (2012). MESSI: Mutant Evaluation by Static Semantic Interpretation. IEEE Int. Conf. Software Testing, pp. 711-719 (read online).

Patrick, M. (2010). Evaluating Yeti using Open Source Software, York Doctoral Symp (read online).

Patrick, M. (2010). Online Evolution in Unreal Tournament 2004, IEEE Conf. Computational Intelligence and Games, pp. 249-256 (read online).

Experience and Training

Professional Experience

2020 - Present: Research Investigator, University of Michigan, MI

Cutaneous Bioinformatics Group, Department of Dermatology

Post-doctoral Training

2016 - 2020: Post-doctoral Research Fellow, University of Michigan, MI

Cutaneous Bioinformatics Group, Department of Dermatology

2013 - 2016: Post-doctoral Research Associate, University of Cambridge, UK

Epidemiology and Modelling Group, Department of Plant Sciences

Education

2009 - 2013: PhD Computer Science, University of York, UK (fully funded by EPSRC)

Thesis: Mutation-Optimised Subdomains for Test Data Generation

2004 - 2009: MEng Computer Systems & Software Engineering, University of York, UK (1st class with honours)

Thesis: Online Evolution for Unreal Tournament 2004

Guest Lectures

'Testing Stochastic Simulations against Statistical Oracles' at NCHU, Taiwan (2017)

'Testing Stochastic Software', half-day tutorial at 31st IEEE/ACM International Conference on Automated Software Engineering (co-presented by Dr Guoxin Su), Singapore (2016)

'Software Reuse in a Scientific Research Group' at NCHU, Taiwan (2015)

'Evolution Strategies', as part of 2012/2013 module on Evolutionary Computing at University of York (2013)

'Mutation Testing and Search-Based Software Engineering' at Academia Sinica, NCCU, NCHU, NCTU and NTHU, Taiwan (2012)