Publications

(Google Scholar)

1. Trang Nguyen, Anthony Campbell, Ankit Kumar, Edwin Amponsah, Madalina Fiterau, Leili Shahriyari, Optimal fusion of genotype and drug embeddings in predicting cancer drug response, Briefings in Bioinformatics, 2024.

2. E. Katsoulakis, Q. Wang, H. Wu, L. Shahriyari, R. Fletcher, J. Liu, L. Achenie, H. Liu, P. Jackson, Y. Xiao, T. Syeda-Mahmood, R. Tuli, J. Deng, Digital twins for health: a scoping review, npj digital medicine, 2024.

3. N. Mirzaei, L. Shahriyari, Modeling Cancer Progression: An Integrated Workflow Extending Data-Driven Kinetic Models to Bio-Mechanical PDE Models, Physical Biology, 2024.

4. D. Sofia, Q. Zhou, L. Shahriyari, Mathematical and Machine Learning Models of Renal Cell Carcinoma: A Review, Bioengineering, 2023. 

5. N. Mohammad Mirzaei, W. Hao, L. Shahriyari, Investigating the spatial interaction of immune cells in colon cancer, iScience, 2023.

6. S. Gong, L. Shahriyari, A Review of Stochastic and Deterministic Modeling of Stem Cell Dynamics, Current Stem Cell Reports, 2023. 

7. Y Hu, N Mohammad Mirzaei, L Shahriyari, Bio-Mechanical Model of Osteosarcoma Tumor Microenvironment: A Porous Media Approach, Cancers, 2022.

8. Stahlberg EA, Abdel-Rahman M, Aguilar B, Asadpoure A, Beckman RA, Borkon LL, Bryan JN, Cebulla CM, Chang YH, Chatterjee A, Deng J, Dolatshahi S, Gevaert O, Greenspan EJ, Hao W, Hernandez-Boussard T, Jackson PR, Kuijjer M, Lee A, Macklin P, Madhavan S, McCoy MD, Mohammad Mirzaei N, Razzaghi T, Rocha HL, Shahriyari L, Shmulevich I, Stover DG, Sun Y, Syeda-Mahmood T, Wang J, Wang Q and Zervantonakis I, Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation, Front. Digit. Health, 2022. 

9. D. Sofia, N. Mohammad Mirzaei, L. Shahriyari, Patient-Specific Mathematical Model of the Clear Cell Renal Cell Carcinoma Microenvironment, Journal of Personalized Medicine, 2022.

10. N. Mohammad Mirzaei, Z. Tatarova, W. Hao, N. Changizi, A. Asadpoure, Y. Hu, I.K. Zervantonakis, Y.H. Chang,  L. Shahriyari, A PDE model of breast tumor progression in MMTV-PyMT mice, Journal of Personalized Medicine, 2022.

11. R.A. Aronow, S. Akbarinejad, T. Le, S. Su, L. Shahriyari, TumorDecon: A digital cytometry software, SoftwareX, 2022.

12. N. Mohammad Mirzaei, N. Changizi, A. Asadpoure, S. Su, D. Sofia, Z. Tatarova, I.K. Zervantonakis, Y.H. Chang, L. Shahriyari, Investigating key cell types and molecules dynamics in PyMT mice model of breast cancer through a mathematical model, PLoS Computational Biology, 2022.

13. N. Mohammad Mirzaei, S. Su, D. Sofia, M. Hegarty, M.H. Abdel-Rahman, A. Asadpoure, C. Cebulla, Y.H. Chang, W. Hao, P.R. Jackson, A.V. Lee, D.G. Stover, Z. Tatarova, I.K. Zervantonakis, L. Shahriyari, A Mathematical Model of Breast Tumor Progression Based on Immune Infiltration, Journal of Personalized Medicine, 2021.

14. T. Le, S. Su, L. Shahriyari, Investigating optimal chemotherapy options for osteosarcoma patients through a mathematical model, Cells, 2021. 

15. A. Budithi, S. Su, A. Kirshtein, L. Shahriyari, Data driven mathematical model of FOLFIRI treatment for colon cancer, Cancers, 2021.

16. T. Le, S. Su, A. Kirshtein, L. Shahriyari, Data driven mathematical model of osteosarcoma, Cancers, 2021.

17. T. Le, S. Su, L. Shahriyari, Immune Classification of Osteosarcoma, Mathematical Biosciences and Engineering, 2021.

18. S.Su, S. Akbarinejad, L. Shahriyari, Immune Classification of Clear Cell Renal Cell Carcinoma, Scientific Reports, 2021.

19. A. Kirshtein, S. Akbarinejad, W. Hao, T. Le, S. Su, R. Aronow, L. Shahriyari, Data driven mathematical model of colon cancer progression, Journal of Clinical Medicine, 2020.

20. T. Le, R. Aronow, A. Kirshtein, L. Shahriyari, A review of digital cytometry methods: estimating the relative abundance of cell types in a bulk of cells,  Briefing in Bioinformatics, 2020.  

21. S. Su, L. Shahriyari, RGS5 plays a significant role in renal cell carcinoma, Royal Society Open Science, 2020.

22. L. Shahriyari, M. Abdel-Rahman, C. Cebulla, BAP1 expression is prognostic in breast and uveal melanoma but not colon cancer, PLOS ONE, 2019.

23. M. Abdel-Rahman, L. Shahriyari, J. Massengill, K. Kendra, T. Olencki, F. Davidorf, C. Cebulla, Identification of novel targeted therapies for BAP1 mutated tumors, Investigative Ophthalmology & Visual Science 59 (9), 4958-4958, 2018.

24. W. Strychalski, S. Bryant, B. Jadamba, E. Kilikian, X. Lai, L. Shahriyari, R. Segal, N. Wei, L. Miller, Fluid Dynamics of Nematocyst Prey Capture. In: Radunskaya A., Segal R., Shtylla B. (eds) Understanding Complex Biological Systems with Mathematics. Association for Women in Mathematics Series, vol 14. Springer, Cham, 2018.

25. A. Mahdipour Shirayeh*, L. Shahriyari*, Modeling cell dynamics in colon and intestinal crypts: The significance of central stem cells in tumorigenesis, Bulletin of mathematical biology, 2018. (*equal contribution)

26. M. Renardy, A. Jilkine, L. Shahriyari, C. Chou, Control of cell fraction and population recovery during tissue regeneration in stem cell lineages, Journal of Theoretical Biology, 2018.

27. L. Shahriyari, Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ datasets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma, Briefings in Bioinformatics, 2017. (Patent application in progress)

28. A. Bollas, L. Shahriyari, The role of backward cell migration in two-hit mutants’ production in the stem cell niche, PLOS ONE, 2017. 

29. L. Shahriyari, Cell dynamics in tumor environment after treatments, Journal of The Royal Society Interface, 2017. (bioRxiv)

30. L. Shahriyari, Chronic inflammation leads to adapted immune cells forming local and distant tumors at sites of inflammation, Cancer Hypotheses, 2017. (Invited Article)

31. L. Shahriyari, A. Mahdipour Shirayeh, Modeling dynamics of mutants in heterogeneous stem cell niche, Physical Biology, 2017. (bioRxiv) 

32. L. Shahriyari, N.L. Komarova, A. Jilkine, The role of cell location and spatial gradients in the evolutionary dynamics of colon and intestinal crypts, Biology Direct, 2016.

33. L. Shahriyari, Abstract A07: A new perspective on cancer: Tumor initiation, failure of treatments, and metastasis, Cancer Research 76, A07--A07, 2016.

34. L. Shahriyari, A new hypothesis: some metastases are the result of inflammatory processes by adapted cells, especially adapted immune cells at sites of inflammation, F1000Research, 2016.

35. L. Shahriyari, N.L. Komarova, The role of the bi-compartmental stem cell niche in delaying cancer, Physical Biology, 2015. (preprint)

36. L. Shahriyari, Translating graphs by mean curvature flow, Geometriae Dedicata, 2015.

37. N.L. Komarova,  L. Shahriyari, D. Wodarz, Complex role of space in the crossing of fitness valleys by asexual populations, Journal of The Royal Society Interface, 2014.

38. L. Shahriyari, N.L. Komarova, Symmetric vs asymmetric stem cell divisions: an adaptation against cancer? PLOS ONE, 2013.

39. A. Lopez, M. Post, C. CallisonBurch, J. Weese, J. Ganitkevitch, N. Ahmidi, O. Buzek, L. Hanson, B. Jamil, M. Lee, Y. Lin,H. Pao, F. Rivera, L. Shahriyari, D. Sinha, A. Teichert, S. Wampler, M. Weinberger, D. Xu, L. Yang, and S. Zhao, Learning to translate with products of novices: Teaching MT with competitive challenge problems, Transaction of the association for computational linguistics, 2013.

40. L. Shahriyari, DNA Computing, Nanobiotechnology magazine, Iran, 2005.