My research has been mainly focused on studying problems in the intersection of math, computation, and biological applications.
As a PhD student, I worked on computationally difficult problems in the study of evolution. This led to several (discrete and stochastic) models for inferring gene duplications and horizontal gene transfers (aka lateral gene transfers). Part of this work has been published in a textbook on phylogenetic networks, written by Daniel Huson et al.
During the last year of my PhD studies, I became involved in projects related to cancer, which led to the development of a stochastic model of evolution in cancer tumors.
I was a postdoctoral fellow at McGill University for four years, working with Professor Michael Hallett on breast cancer related projects. My current research is focused on studying breast cancer prognostic predictors, developing network models that capture interactions between tumor and tumor microenvironment, and modeling of cancer evolution using next-generation high-throughput sequencing data from tumor cells.
2003-2009 PhD in Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden. Thesis: Using Trees to Capture Reticulate Evolution: Lateral Gene Transfers and Cancer Progression
1997-2002 Master of Science in Engineering, Degree Programme in Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.
(* = shared first authorship)
Lai, A. Z., Cory, S., Zhao, H., Gigoux, M., Monast, A., Guiot, M.-C., Sidong, H., Tofigh, A., et al. (2014). Dynamic Reprogramming of Signaling Upon Met Inhibition Reveals a Mechanism of Drug Resistance in Gastric Cancer. Science Signaling, 7(322), ra38. doi:10.1126/scisignal.2004839
Sjostrand, J.*, Tofigh, A.*, Daubin, V., Arvestad, L., Sennblad, B., & Lagergren, J. (2014). A bayesian method for analyzing lateral gene transfer. Systematic Biology, 63(3), 409–420. doi:10.1093/sysbio/syu007
Tofigh, A., Hallett, M., & Lagergren, J. (2011a). Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM, 8(2), 517–535. doi:10.1109/TCBB.2010.14
Tofigh, A., Sjölund, E., Höglund, M., & Lagergren, J. (2011b). A Global Structural EM Algorithm for a Model of Cancer Progression. Advances in Neural Information Processing Systems 24 (NIPS 2011), In J. Shawe-Taylor, R. S. Zemel, P. Bartlett, F. C. N. Pereira, & K. Q. Weinberger (Eds.), (pp. 163–171).
Sehat, B., Tofigh, A., Lin, Y., Trocmé, E., Liljedahl, U., Lagergren, J., & Larsson, O. (2010). SUMOylation mediates the nuclear translocation and signaling of the IGF-1 receptor. Science Signaling, 3(108), ra10. doi:10.1126/scisignal.2000628