Pejman Mohammadi, PhD

Assistant Professor
Department of Integrative Structural and Computational Biology
California Campus


Scripps Research Joint Appointments

Assistant professor, Scripps Translational Science Institute
Faculty, Graduate Program

Research Focus

Dr. Mohammadi is a computational biologist with a background primarily in statistical machine learning and probabilistic data modeling. His work focuses on design of mathematical models that leverage known biochemical principles to facilitate decision-making from limited data in modern biomedical research applications. Currently, his work is focused on analysis of regulatory variation in the genome and its application to rare diseases. Additionally, he is interested in application of modern technologies, including data from wearable sensors, and other large-scale health related data to personalized medicine.


Ph.D. (Computational Biology), Swiss Federal Institute of Technology Zurich (ETH), 2014
M.S. (Computer Science (Bioinformatics)), Aalto University, 2010
B.S. (Computer Engineering (Software)), Isfahan University of Technology, 2008

Professional Experience

2015-2017 Postdoctoral Researcher, New York Genome Center
2015-2017 Postdoctoral Fellow, Columbia University
2014-2014 Postdoctoral Researcher, CHUV- Lausanne University Hospital
2010-2014 Doctoral Researcher, Swiss Federal Institute of Technology Zurich (ETH)
2008-2010 Research Assistant, Helsinki Institute for Information Technology
2007-2008 Research Assistant, The Institute for Research in Fundamental Sciences (IPM)
2005-2007 Research Assistant, Isfahan University of Technology

Selected References

All Publications

Zou, J., Huss, M., Abid, A., Mohammadi, P., Torkamani, A. & Telenti, A. A primer on deep learning in genomics. (2019). Nature Genetics, 51(1), 12-18.

Mohammadi, P., Castel, S. E., Cummings, B. B., Einson, J., Sousa, C., Hoffman, P., Donkervoort, S., Jiang, Z., Mohassel, P., Foley, A. R., Wheeler, H. E., Im, H. K., et al. Genetic regulatory variation in populations informs transcriptome analysis in rare disease. (2019). Science, 366(6463), 351-356. PMCID: PMC6814274.

Castel, S. E., Cervera, A., Mohammadi, P., Aguet, F., Reverter, F., Wolman, A., Guigo, R., Iossifov, I., Vasileva, A. & Lappalainen, T. Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. (2018). Nature Genetics, 50(9), 1327-1334. PMCID: PMC6119105.

Mohammadi, P., Beerenwinkel, N. & Benenson, Y. Automated design of synthetic cell classifier circuits using a two-step optimization strategy. (2017). Cell Systems, 4(2), 207-218.

Aguet, F., Brown, A. A., Castel, S. E., Davis, J. R., He, Y., Jo, B., Mohammadi, P., Park, Y., Parsana, P., Segre, A. V., Strober, B. J., Zappala, Z., et al. Genetic effects on gene expression across human tissues. (2017). Nature, 550(7675), 204-213.

Kim-Hellmuth, S., Bechheim, M., Putz, B., Mohammadi, P., Nedelec, Y., Giangreco, N., Becker, J., Kaiser, V., Fricker, N., Beier, E., Boor, P., Castel, S. E., et al. Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. (2017). Nature Communications, 8. PMCID: PMC5559603.

Jonsson, K. L., Laustsen, A., Krapp, C., Skipper, K. A., Thavachelvam, K., Hotter, D., Egedal, J. H., Kjolby, M., Mohammadi, P., Prabakaran, T., Sorensen, L. K., Sun, C., et al. IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP. (2017). Nature Communications, 8. PMCID: PMC5309897.

Mohammadi, P., Castel, S. E., Brown, A. A. & Lappalainen, T. Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. (2017). Genome Research, 27(11), 1872-1884. PMCID: PMC5668944.

Golumbeanu, M., Mohammadi, P. & Beerenwinkel, N. BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. (2016). Bioinformatics, 32(7), 976-983.

Trypsteen, W., Mohammadi, P., Van Hecke, C., Mestdagh, P., Lefever, S., Saeys, Y., De Bleser, P., Vandesompele, J., Ciuffi, A., Vandekerckhove, L. & De Spiegelaere, W. Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay. (2016). Scientific Reports, 6. PMCID: PMC5080576.