Publications

24. Nabet* BY, Esfahani* MS, Hamilton EG, et al, Alizadeh AA, Diehn M, “A noninvasive approach for early prediction of therapeutic benefit from immune checkpoint inhibition for lung cancer”, in press at Cell, (2020).

23. Alig S, Jurinovic V, Esfahani MS, et al., “Evaluating upfront high-dose consolidation after R-CHOP for follicular lymphoma by clinical and genetic risk models”, Blood Advances 4 (18): 4451–4462, (2020).

22. Chabon* JJ, Hamilton* EG, Kurtz* DM, Esfahani* MS, Moding EJ, et al., Alizadeh AA, Diehn M, “Integrating genomic features for noninvasive early lung cancer detection”, Nature, 580, 245–251, (2020).

21. Esfahani* MS, Lee LJ, Jeon YJ, Flynn RA, et al., Chang H, Alizadeh AA, Diehn M, “Functional significance of U2AF1 S34F mutations in lung adenocarcinomas,” Nature Communications, Volume 10, Issue 1, 1-13, (2019).

20. Kurtz DM*, Esfahani MS*, Scherer* F, et al., Diehn M, Alizadeh AA, “Dynamic Risk Profiling Using Serial Tumor Biomarkers for Personalized Outcome Prediction”, Cell, Volume 178, Issue 3, 699-713, (2019).

19. Azad TD, Chaudhuri AA, Fang P, Qiao Y, Esfahani MS, et al, SH Lin, Alizadeh AA, Diehn M, “Circulating tumor DNA analysis for detection of minimal residual disease after chemoradiotherapy for localized esophageal cancer”, Gastroenterology, Volume 158, Issue 3, Pages 494-505, (2020).

18. Bloomstein J, von Eyben R, Chan A., Rankin E, Fregoso D, Wang-Chiang J, Lee L, Xie L-X., MacLaughlan David S., Stehr H., Esfahani MS, Giaccia A., Kidd E, “Validated limited gene predictor for cervical cancer lymph node metastases”, Oncotarget 11 24 2302-2309, (2020).

17. Newman AM, Steen CB, Liu CL, Gentles A , Chaudhuri AA, Scherer F, Khodadoust MS, Esfahani MS, Luca B, Steiner D, Diehn M and Alizadeh AA, “Determining cell-type abundance and expression from bulk tissues with digital cytometry”, Nature Biotechnology, 37, pages773–782, (2019).

16. Dudley JC, Schroers-Martin J, Lazzareschi DV, Shi WY, Chen SB, Esfahani MS, et al, Alizadeh AA & Diehn M, “Detection and surveillance of bladder cancer using urine tumor DNA”, Cancer Discovery, Vol 9, Issue 4, 500-509, (2019).

15. Kurtz DM, Scherer F, Jin M, Soo J, Craig A, Esfahani MS, et. al., Diehn M and Alizadeh AA, “Circulating tumor DNA measurements as early outcome predictors in Diffuse Large B-Cell Lymphoma”, Journal of Clinical Oncology, Vol 36, Issue 28, 2848-2853, (2018).

14. Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Khodadoust MS, Esfahani MS, et. al., Alizadeh AA, Diehn M, “Early detection of molecular residual disease in localized lung cancer by circulating tumor DNA profiling”, Cancer Discovery, 7.12, 1394-1403, (2017).

13. Chabon JJ, Simmons AD, Lovejoy A, Esfahani MS, et al, Alizadeh AA, Diehn M, “Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients”, Nature Communications Volume, 7, Issue 1, 1-15, (2016).

12. Scherer F, Kurtz DM, Newman AM, Craig A, Stehr H, Esfahani MS, et al., Diehn M, Alizadeh AA, “Distincts biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA”, Science Translational Medicine, 8, (2016).

11. Dehghannasiri R, Esfahani MS, Dougherty ER, “An experimental design framework for Markovian gene regulatory networks under stationary control policy”, BMC Systems Biology, Volume 12, Issue 8, (2018).

10. Dehghannasiri R, Esfahani MS, Dougherty ER, “Optimal Bayesian Kalman filtering with prior update”, IEEE Transactions on Signal Processing 66.8: 1982-1996, (2018).

9. Boluki S, Esfahani MS, Qian X, Dougherty ER, “Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors”, BMC Bioinformatics, 18 (14), (2017).

8. Boluki* S, Esfahani* MS, Qian X, Dougherty ER, “Constructing pathway-based priors within a Gaussian mixture model for Bayesian regression and classification”, IEEE/ACM Transaction on Computational Biology and Bioinformatics, vol. 16, no. 2, pp. 524-537, (2017).

7. Dehghannasiri R, Esfahani MS, Dougherty ER, “Intrinsically Bayesian robust Kalman filter: an innovation process approach”, IEEE Transactions on Signal Processing 65.10: 2531-2546, (2017).

6. Esfahani MS, and Dougherty ER, "An Optimization-based framework for the transformation of incomplete biological knowledge into a probabilistic structure and its application to the utilization of gene/protein signaling pathways in discrete phenotype classification", IEEE/ACM Transactions on Computational Biology and Bioinformatics 12.6: 1304-1321, (2015).

5. Broumand A, Esfahani MS, Yoon BJ, and Dougherty ER, "Discrete optimal Bayesian classification with error-conditioned sequential sampling", Pattern Recognition 48.11: 3766-3782, (2015)

4. Esfahani MS and Dougherty ER, "Incorporation of Biological pathway knowledge in the construction of priors for optimal Bayesian classification", IEEE/ACM Transactions on Comp. Biology and Bioinformatics 1.1: 202-218, (2014)

3. Esfahani MS, and Dougherty ER, "Effect of separate sampling on classification accuracy", Bioinformatics, Vol. 30, No. 2, 242-250, (2014).

2. Esfahani MS, Jason Knight, et al., Dougherty ER, "Classifier design given an uncertainty class of feature distributions via regularized maximum likelihood and the incorporation of biological pathway knowledge in steady-state phenotype classification", Pattern Recognition 46.10: 2783-279, (2013).

1. Esfahani MS, Yoon BJ, and Dougherty ER, "Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty", BMC Bioinformatics 12, no. Suppl 10: S9, (2011).