PI

Leili Shahriyari

Associate Professor

Department of Mathematics and Statistics  

UMass Cancer Center

Institute for Applied Life Sciences (IALS)

University of Massachusetts Amherst

lshahriyari at umass.edu

Education:

• Ph.D. Mathematics, Johns Hopkins University, 2013.

  •       Dissertation: Translating graphs by mean curvature flow.

  •       Advisor: Professor William Minicozzi

• M.S.E. Computer Science, Johns Hopkins University, 2012.

• M.S. Mathematics, Sharif University of Technology, 2005.

  •       Dissertation: Molecular algorithms for TSP and set cover problems.

  •       Advisor: Professor Hayedeh Ahrabian

• B.S. Mathematics, Isfahan University of Technology, 2003.

Research Experience:

(Current positions)

Associate Professor, Department of Mathematics and Statistics, University of Massachusetts Amherst, Sep 2023 - now.

Assistant Professor, Department of Mathematics and Statistics, University of Massachusetts Amherst, Sep 2019 - Aug 2023.

Affiliated Faculty, UMass Cancer Center, April 2020 - Present.

(Former positions)

Assistant Professor, Department of Mathematics, University of Texas Arlington, Sep 2018 - Aug 2019.

Affiliated Faculty,  Department of Computer Science and Engineering, University of Texas Arlington, Sep 2018 - Aug 2019.

Affiliated Faculty,  Department of Biology, University of Texas Arlington, Oct 2018 - Aug 2019.

Visiting Scientist, Dana-Farber Cancer Institute, Nov 2018 - Dec 2018.

Visiting Scholar, Mathematical Biosciences Institute, Ohio State University, Sep 2017 - June 2018.

Data Science Fellow, The Data Incubator, Sep 2017 - Nov 2017.

Postdoctoral Fellow, Mathematical Biosciences Institute, Ohio State University, Sep 2014 - Sep 2017.

Postdoctoral Scholar, Institute for Genomics & Bioinformatics, University of California Irvine, Feb 2014 - Sep 2014.

Postdoctoral Scholar, Department of Mathematics & Department of Ecology and Evolutionary Biology, University of California Irvine, Jan 2013 - Jan 2014.

Grants:

• DOE, My Virtual Cancer, (Role: PI, Total Costs: $49,966), Jan 2021 - April 2022.

• NCI-Leidos Biomedical Research Inc., My Virtual Cancer, (Role: PI, Total Costs: $49,952), Jan 2021 - April 2022.

• DOE, Dynamic Multiscale Digital Twin for a Lung Cancer Patient, (Role: co-PI, PI: Qi Wang at U of South Carolina, Total Costs: $50,000), Jan 2021 - Nov 2021.

• NCI-Leidos Biomedical Research Inc., Dynamic Multiscale Digital Twin for a Lung Cancer Patient, (Role: co-PI, PI: Qi Wang at U of South Carolina, , Total Costs: $50,000), Jan 2021 - Nov 2021.

• NCI-CMU, Sociome: Integrating Social Determinants of Health and Multi-Omic Data to Predict Cancer Prognosis, (Role: PI), awarded Dec 2020.

• NCI/NIH, Integration of liquid biopsy and spatial profiling to predict immunotherapy response in triple-negative breast cancer through data-driven mechanistic model of tumor-immune interactions, (Role: PI, Total Costs: $110,498), awarded Sep 2020.

• NCI/NIH R21-02S1 supplementary project on Childhood Osteosarcoma, (period:9/1/2020-8/31/2022, Role: PI, Total Costs: $159,908).

• NCI/NIH R21, Data driven QSP model for personalized colon cancer treatments, (period:9/1/2019-8/31/2022, Role: PI, Total Costs: $386,767), impact score: 14, Percentile: 1.0.

• Center for Transportation Equity, Decisions and Dollars (CTEDD), United States Department of Transportation (USDOT), (Role: PI, Total Costs: $129,480).

• UMass Amherst, Mutual Mentoring Team Grant project,  Building Support Networks of Junior Women in Mathematics and Statistics,  (Role: co-PI, PI: Maryclare Griffin), (Total Costs: $5,502).

• IALS Midigrant: SARS-CoV2 nsp1: a master regulator of RNA stability, (Role: co-PI, PI: Mandy Muller, Total Costs:$17,500).

Publications:

(2024)

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, Volume 25, Issue 3, May 2024.

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.

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

(2023)

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

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

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

(2022)

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

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.

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

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.

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

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.

(2021)

N. Mohammad Mirzaei, S. Su, D. Sofia, M. Hegarty, M. Abdel-Rahman, A. Asadpoure, C.M. Cebulla, Y.H. Chang, W. Hao, P.R. Jackson, A.V. Lee, D.G. Stover, Z. Tatarova, I.K. Zervantonakis, L. Shahriyari, Mathematical model of breast tumors progression based on their immune infiltration, Journal of Personalized Medicine, 2021.

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

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

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

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

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

(2020)

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.

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.  

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

(2019)

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

(2018)

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.

A. Mahdipour Shirayeh*, L. Shahriyari*, New insights into initiation of colon and intestinal cancer: The significance of central stem cells in the crypt, Bulletin of mathematical biology, 2018. (*equal contribution) 

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.

(2017)

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.

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

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

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

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

(2016)

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

L. Shahriyari, A new hypothesis: some metastases are the result of inflammatory processes by adapted cells, especially adapted immune cells at sites of inflammation  [version 1; referees: 3 approved], F1000Research, 2016.

(2015)

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

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

(2014)

N. 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.

(2013)

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

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, to translate with products of novices: Teaching MT with competitive challenge problems,  Transactions of the Association for Computational Linguistics, 2013.

(2005)

L. Shahriyari, DNA Computing, Nanobiotechnology Magazine, Iran, 2005.

Conference Abstracts:

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.

L. Shahriyari, A  new perspective on cancer: Tumor initiation, failure of treatments, and metastasis. In: Proceedings of the AACR Special Conference on Tumor Metastasis,  Cancer Research,  2016.

L. Shahriyari, N. Komarova,  Role of stem cell niche structure in cancer, qbio.org, 2015.

L. Shahriyari, N. Komarova, Symmetric vs. asymmetric stem cell divisions, qbio.org, 2014.

Honors and Awards:

• Invited Panelist on "Digital Twins in Medicine" panel at the Fifth HPC Applications in Precision Medicine Workshop (HAPM22) organized by NIH/NCI-Frederick National Laboratory for Cancer Research at ISC High Performance 2022.

• Invited Panelist at Computational Approaches for Cancer Workshop (CAFCW) organized by NIH/NCI-Frederick National Laboratory for Cancer Research at Supercomputing (SC) 2021.

• Rising STARs award UT System $300,000, 2018.

• MBI/NSF postdoctoral fellowship, 2014-2017.

• Full tuition fellowship, teaching and research assistant, Johns Hopkins University, 2007 - 2012.

• Award of Iranian nanotechnology organization for master's thesis, 2005.

• Travel Grants:

  • • NSF/SIAM travel award to attend ICIAM 2023, Tokyo, Japan. 

    • Landahl-Busenberg travel award, SMB annual meeting, 2017.

• • AWM-NSF Travel Grant, 2016.

  • IMA Annual Program Year Workshop, Biological Systems and Networks, 2015.

  • Mathematical methods in systems biology workshop, University College Dublin, Ireland, 2015.

  • International conference on micro and macro systems in life sciences, Poland, 2015

  • Landahl-Busenberg travel award, SMB annual meeting, Atlanta 2015.

  • The Eighth Q-bio Summer School and Conference, New Mexico, USA 2014.

  • The 18th Southern California Geometric Analysis Seminar (SCGAS), UC San Diego, 2011.

  • Connections for Women and Introductory Workshop: Free Boundary Problems, MSRI 2011.

  • 35th Univ. of Arkansas Spring Lecture series; Minimal surfaces and mean curvature flow, 2010.

  • Research period on geometric flows and geometric operators, Centro De Giorgi, Italy, 2009.

Professional Services:

Organizer:

• Mini-symposium, ICIAM 2023, Tokyo, Japan, summer 2023.

• Mini-symposium, SMB annual meeting, summer 2023.

• Mathematical and Computational Biology Workshop, ICERM, June 2023.

• UMass Virtual Mathematical and Computational Biology, Since Summer 2020.

• Mini-symposium entitled  "Mathematical models for cancer growth and cellular mechanics" at CMBE2019 in Japan.

• Mini-symposium entitled "Modeling and Simulation of Cancer" at the 5th International Conference on Computational and Mathematical Biomedical Engineering – CMBE2017, Pittsburgh, 10–12 April, 2017.

• Mathematical Biosciences Institute Postdoc Seminar, Academic year 2015 - 2016.

• Mini-symposium entitled "Quantifying the Role of Stem Cells in Cancer" at the annual meeting of the Society for Mathematical Biology, Atlanta, June 30-July 3, 2015.

Reviewer:

• Geometriae Dedicate

• PLOS Computational Biology

• Theoretical Biology (JTB)

• Mathematical Biosciences

• Computational and Applied Mathematics

• Mathematical Biology

• Computers in Biology and Medicine

• Briefings in Bioinformatics 

• IEEE Access

• International Journal of Radiation Biology

• Computational and Mathematical Methods in Medicine

• Bulletin of Mathematical Biology

• Scientific Reports

• NSF grant proposals for a joint program with NIH

• Otto-Hahn-Medal of Max Planck Institute

• Grant proposals for NIH/NCI programs

• BMC Cancer

• Royal Society Interface 

• Biophysical Journal

• Molecular Therapy - Nucleic Acids

• Mathematical Biosciences and Engineering

• Technology in Cancer Research & Treatment 

• Cancers

• Computational Science

• npj Digital Medicine

• Personalized Medicine

• Entropy

• Acta Biotheoretica

• Briefings in Bioinformatics

• iScience

• The Lancet Digital Health

• Mathematical Biosciences

• Translational Cancer Research

Representative:

• Mathematics Graduate students, Johns Hopkins University, Academic year 2012 - 2013.

Member:

• American Association for Cancer Research (AACR)

• Society for Industrial and Applied Mathematics (SIAM)

• Society for Mathematical Biology (SMB)

• IEEE Computer Society Technical Committee on Computational Life Sciences

• Association for Computing Machinery (ACM)

Conferences and Presentations:

Invited Talks:

1. Mini-symposium at WCCM, July 2024.

2. Mini-symposium at CAIMS, June 2024.

3. Mini-symposium at ECCOMAS, Lisbon, June 2024.

4. University of British Columbia, May 2024.

5. Webinar, NCI, April 2024.

6. University of California Riverside, April 2024.

7. Mini-symposium at CMPD6, Winnipeg, Canada, May 2023.

8. Biomedical Digital Twins Workshop at Bio-IT World Conference, Boston, May 2023.

9. University of Alberta, Nov 28, 2022.

10. Perdue University, Nov 21, 2022.

11. University of Texas Austin, Oct 5th, 2022.

12. Mini-symposium at AMS sectional meeting, Oct 2nd, 2022.

13. NCI ITCR Annual meeting, Sep 2022.

14. Department of Mathematics, University of Minnesota, April 11, 2022.

15. Mini-symposium at SMB annual meeting, June 2021.

16. Department of Mathematics, Tufts University, March 8th, 2021.

17. Global Seminar on Mathematical Modeling and Applications, Online, June 2020.

18. Department of Mathematics, Penn State University, November 2019.

19. NCI/NIH - ITCR teleconference, November 2019.

20. Symposium at SMB annual meeting, Montreal, Canada, July 2019.

21. Symposium at ICIAM 2019, Valencia, Spain, July 2019.

22. Department of Computer Science, UMass Lowell, April 2019.

23. Department of Mathematics and Statistics, UMass Amherst, April 2019.

24. Department of Earth and Environmental Sciences, UT Arlington, March 2019. 

25. CTEDD, UT Arlington, March 2019.

26. Amazon, Cambridge MA, May 2018.

27. University of Texas Arlington, April 2018. 

28. Omega Therapeutics Inc., Boston MA, April 2018.

29. Bristol-Myers Squibb, Lawrenceville, April 2018.

30. George Mason University, April 2018.

31. University of Tennessee Knoxville, March 2018.

32. Gritstone Oncology, Boston MA, February  2018.

33. Iowa State University, January 2018.

34. University of Massachusetts Dartmouth, December 2017.

35. OM1, Boston MA, November 2017.

36. Broad Institute of MIT and Harvard, September 2017.

37. Celgene Corporation, Cambridge MA, August 2017.

38. Symposium at SMB meeting, Salt Lake City, July 2017.

39. St. Jude Children's Research Hospital, Webinar, May 2017.

40. George Mason University, April 2017.

41. Rutgers University - Camden, April 2017.

42. Symposium at AMS JMM meeting, Atlanta, January 2017.

43. Sharif University of Technology, Iran, July 2016.

44. Symposium at SIAM Life Science, Boston, July 2016.

45. Iranian International Conference on Systems Biology, December 2015.

46. University of Notre Dame, September 2015.

47. MMSB, University College Dublin, Ireland, June 2015.

48. Micro and Macro Systems in Life Sciences, Poland, June 2015. 

49. the Fifth Annual SAGE Workshop, UT Austin, January 2012.

50. CUNY, March 2011.

51. Department of Mathematical Sciences, Isfahan University of Technology, 2005.

52. Department of Electrical Engineering and Computer Engineering, Isfahan University of Technology, 2005.

Contributed Talks:

• What is computational and mathematical oncology?, UMass Amherst TWIGS, Fall 2022.

• Collaborative research toward data driven mathematical modeling of cancer to arrive at effective treatments, Department colloquium, Oct 13, 2022.

• A path toward personalized cancer treatments, UMass Amherst Applied Mathematics and Computation Seminar, 2020.

• What is Computational Oncology, UMass Amherst TWIGS, 2020.

• Computational modeling of cell dynamics in colon and intestinal crypts, MBI Postdoc seminar, 2016.

• Stochastic modeling of tumor's initiation and new hypothesis on metastasis, MBI Postdoc Seminar, 2015.

• The role of stem cell niche in cancer, MBI Postdoc Seminar, 2015.

• Symmetric vs asymmetric stem cell divisions, The Eighth Q-bio Conference, NM, 2014.

• Stem cell divisions, The Eighth Q-bio Summer School, NM, 2014.

• The curve shrinking flow, Analysis & PDE Seminar, Johns Hopkins University, 2009.

• Width and mean curvature flow, Centro di Ricerca Matematica Ennio De Giorgi, Italy, 2009.

Poster Presentations:

• AACR Meeting on Tumor Metastasis, Austin, Dec 2015.

• The 2015 Hallmarks of Cancer Symposium, Houston, Oct 2015.

• Micro and Macro Systems in Life Sciences, Poland, June 2015. 

Teaching Experience:

Solo Instructor:

• STAT 697BD: ST-Biomedical and Health Data Analysis, University of Massachusetts Amherst, Fall 2020.

• MATH 456.1: Mathematical Modeling, University of Massachusetts Amherst, Spring 2020.

• STAT 697BD: ST-Biomedical and Health Data Analysis, University of Massachusetts Amherst, Fall 2019.

• Biomedical Data Analytics, University of Texas Arlington, Spring 2019.

• Biomedical Informatics, University of Texas Arlington, Spring 2019.

• Calculus 2B, University of California Irvine, Winter 2014.

• Calculus 2D, University of California Irvine, Winter 2014.

• Calculus I(Bio), Johns Hopkins University, Summer 2011.

• Qualifying Exam Problems (Analysis), Johns Hopkins University, Spring 2011.

• Pre Calculus, CTY Online course, Johns Hopkins University, Summer 2008.

• Fundamentals of Computer & Programming, University of Tehran, Spring 2006.

• Fundamentals of Computer & Programming, University of Culture & Sciences, Spring 2006.

Teaching Assistant:

 Johns Hopkins University: 

• Analysis I (Spring 2011)

• Introduction to real analysis (Fall 2010)

• Calculus II(Eng)  (Spring 2010)

• Analysis II (Spring 2010)

• Analysis II (Spring 2009)

• Honors analysis II (Spring 2009)

• Introduction to real analysis (Fall 2009)

• Calculus II(Eng)(Fall 2008)

Isfahan University of Technology:

• Analysis I, (Spring 2003)

Grader:

Johns Hopkins University: 

• Dynamical systems (Spring 2011)

• Real variables (Fall 2010)

• Riemannian geometry (Fall 2009)

• Calculus of variation (Fall 2007)

Additional Research Experience:

Research Assistant, Department of Mathematics, Johns Hopkins University, 2009 - 2012.

• Differential Geometry: Classified translating graphs by mean curvature flow in R3.

Director of DNA Computing & Bioinformatics Division, New Ideas Research Institute 2005 - 2006.

• Supervised and trained staff and conducted research on the following projects:

• Microarray Data Analysis (Collaboration with Dr. Assadi, UW Madison)

• Protein Folding (Collaboration with R. Behrouzi)

Research Assistant, Department of Computer Science, University of Tehran, 2003 - 2005.

• DNA Computing: Proposed a molecular algorithm with time order O(1) for HPP, and improved time and volume complexity for set cover and dominating set problems.

• Bioinformatics: Studied algorithms for pairwise structural alignment of RNA sequences.

Research Assistant, Sharif University of Technology, 2003 - 2005.

• Graph Theory: Proved Behzad (or Vizing) total coloring conjecture for almost all graphs.