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Portrait of Antonina Mitrofanova

Antonina Mitrofanova, PhD

My laboratory develops computational algorithms to elucidate genomic, transcriptomic, and epigenomic mechanisms of therapeutic resistance in oncology and to identify optimal treatment strategies for cancer patients. Our goal is to build a panel of markers to predict patients at risk of treatment resistance, with further advice on their optimal therapeutic course.

Sukanya Panja

PhD student, Pre-Doctoral Fellow

Nusrat Epsi

PhD student,  Graduate Assistant

Sarra Rahem

PhD Student

Zach Bohannan

PhD Student

Daniel Martingano, MD

PhD Student

Ahmed Mahmoud

PhD Student

Vincent Amoruccio

PhD Student

Contact us at

1. Epsi, N., Panja, S., Pine, Sh. and Mitrofanova, A.† (2019).
pathCHEMO, a generalizable computational framework uncovers molecular pathways of chemoresistance in lung adenocarcinoma.
Nature Communications Biology (accepted August 1st, 2019)
† Senior Corresponding author.

2. Bohannan, Z. and Mitrofanova, A.† (2019).
Calling variants in the clinic: Informed variant calling decisions based on biological, clinical, and laboratory variables.
Computational and Structural Biotechnology Journal (accepted April 3rd, 2019)
† Senior Corresponding author.

3. Panja, S., Hayati, S., Epsi, N.J., Parrott, J.S., and Mitrofanova, A.† (2018).
Integrative (epi) genomic analysis to predict response to androgen-deprivation therapy in prostate cancer.
EBioMedicine (collaboration between Cell Press and THE LANCET),
Volume 31, ppi: 110-121. PMID: 29685789.
† Senior Corresponding author.

4. Aytes, A.*, Giacobbe, A.*, Mitrofanova, A.*, Ruggero, K., Cyrta, J., Arriaga, J., Palomero, L., Farran-Matas, S., Rubin, M.A., Shen, M.M., Califano, A., and Abate-Shen, C. (2018).
NSD2 is a conserved driver of metastatic prostate cancer progression.
Nature Communications, 9(1):5201. PMID: 30518758.
*Co-first author.

5. LeMagnen, C., Virk, R., Dutta, A., Kim, J.Y., Panja, S., Lopez Bujanda, Z.A., Califano, A., Drakes, C., Mitrofanova, A.‡ , Abate-Shen, C. (2018).
Cooperation of loss of NKX3.1 and inflammation in prostate cancer initiation
Disease Models and Mechanisms, pii: dmm.035139. doi: 10.1242/dmm.035139, PMID: 30266798.
† Senior author.

6. Dillon L.W., Hayati, S., Roloff, G.W., Tunc, I., Pirooznia, M., Mitrofanova, A.‡ , Hourigan C.S. (2018).
Targeted RNA-Sequencing For The Quantification Of Measurable Residual Disease In Acute Myeloid Leukemia
Haematologica, pii: haematol.2018.203133. doi: 10.3324/haematol.2018.203133, PMID: 30171026.
† Senior author.

7. Chua, C.W., Epsi, N.J., Lei, M., Li, Bo., Bergren, S.K., Cardiff, R.D., Hibshoosh, H., Mitrofanova, A.‡ , and Shen, M.M. (2018).
Differential requirements of androgen receptor in luminal progenitors during prostate regeneration and tumor initiation.
eLIFE, 2018 Jan 15;7. PMID: 29334357.
‡ Senior author.

8. Dutta, A., Panja, S., Virk, R.V., Kim, J.Y., Zott, R., Cremers, S., Golombos, D.M., Liu, D., Mosquera, J.M., Mostaghel, E.A., Barbieri, C.E., Mitrofanova, A.† , and Abate-Shen, C.† (2017).
Co-clinical analysis of a genetically-engineered mouse model and human prostate cancer reveals significance of NKX3.1 expression for response to 5a-reductase inhibition.
European Urology, pii: S0302-2838(17)30252-X. PMID: 28385453.
† co-Senior co-Corresponding authors.

9. Hayati, Sh., Mitrofanova, A.† (2017).
Computational approaches to identify alternative splice variants as biomarkers of disease progression and drug resistance in Acute Myeloid Leukemia.
Keystone Symposia mRNA Processing and Human Disease; RECOMB 2017 (abstract)
† Senior Corresponding author.

10. Zou, M.*, Toivanen, R.*, Mitrofanova, A.# , Floch, N., Hayati, S., Sun, Y., Le Magnen, C., Chester, D., Mostaghel, E.A., Califano, A., Rubin, M.A., Shen, M.M., and Abate-Shen, C. (2017)
Transdifferentiation as a mechanism of treatment resistance in a mouse model of castration-resistant prostate cancer.
Cancer Discovery, DOI: 10.1158/2159-8290.CD-16-1174, PMID: 28411207
*Co-first authors. # Leading computational author.

11. Talos, F., Mitrofanova, A.#, Bergren, S.K., Califano, A., and Shen, M.M. (2017)
A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue.
Nature Communications, 8:14662. PMID: 28429718.
# Leading computational author.

12. Dutta, A.*, Le Magnen, C.*, Mitrofanova, A.#, Ouyang, X., Califano, A., and Abate-Shen, C. (2016).
Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.
Science, 352(6293): 1576-1580, PMID: 27339988
*Equal contributions.
# Leading computational author.

13. Mitrofanova, A.*, Aytes, A.*, Zou, M., Shen, M., Abate-Shen, C., and Califano, A. (2015).
Predicting drug response in human prostate cancer from preclinical analysis of in vivo mouse models.
Cell Reports, 12(12):2060-71 PMID: 26387954, PMCID: PMC4591242
*Equal contributions.

14. Aytes, A.*, Mitrofanova, A.*, Lefebvre, C.*, Alvarez, M. J., Castillo-Martin, M., Zheng, T., Eastham, J. A., Gopalan, A., Pienta, K. J., Shen, M. M., Califano, A., and Abate-Shen, C. (2014).
Cross-species analysis of genome-wide regulatory networks identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy.
Cancer Cell, 25(5):638-651, PMCID: PMC4051317.
*Equal contributions.

15. Aytes, A., Mitrofanova, A.#, Kinkade, C.W., Lefebvre, C., Lei, M., Phelan, V., Carl Le, H., Koutcher, J.A., Cardiff, R.D., Califano, A., Shen, M.M., and Abate-Shen, C. (2013).
ETV4 promotes metastasis in response to combined activation of PI3 kinase and RAS signaling in a mouse model of advanced prostate cancer,
Proceedings of the National Academy of Sciences (PNAS), 110(37):E3506-1, PMID: 23918374, PMCID: PMC3773788
# Leading computational author.

16. Wang, Z. A., Mitrofanova, A.#, Bergren, S. K., Cardiff, R. D., Abate-Shen, C., Califano, A., and Shen, M. M. (2013).
Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell of origin model for prostate cancer heterogeneity.
Nature Cell Biology, 15: 274-283. PMID: 23434823, PMCID: PMC3743266
# Leading computational author.

17. Wang, J., Kobayashi, T., Floch, N., Kinkade, C. W., Aytes, A., Dankort, D., Lefebvre, C., Mitrofanova, A., Cardiff, R. D., McMahon, M., Califano, A., Shen, M. M., and Abate-Shen, C. (2012).
B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer.
Cancer Research, 72: 4765-4776. PMID: 22836754, PMCID: PMC3445712

18. Floch, N., Kinkade, C. W., Kobayashi, T., Aytes, A., Lefebvre, C., Mitrofanova, A., Cardiff, R. D., Califano, A., Shen, M. M., and Abate-Shen C. (2012).
Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model.
Cancer Research, 72: 4483-4493. PMID: 22815528, PMCID: PMC3432676.

19. Mitrofanova, A., Pavlovic, V., and Mishra, B. (2010).
Prediction of protein functions with gene ontology and inter-species protein homology data.
Journal of IEEE/ACM Transactions on Computational Biology and Bioinformatics, ISSN 1545-5963. PMID: 21393654

20. Mitrofanova, A., Kleinberg, S., Carlton, J., Kasif, S., and Mishra, B. (2010).
Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle.
Artificial Intelligence in Medicine, 49: 167-176. PMID: 20580212

21. Mitrofanova, A., and Mishra, B. (2010).
On a novel coalescent model for genome-wide evolution of copy number variations.
International Journal of Data Mining and Bioinformatics, 4: 300-315. PMID: 20681481

22. Mitrofanova, A., Farach-Colton, M., and Mishra, B. (2009).
Efficient and robust prediction algorithms for protein complexes using Gomory-Hu trees.
Pacific Symposium on Biocomputing, 215-226. PMID: 19209703

23. Mitrofanova, A., and Mishra, B. (2008).
Population genetics of human copy number variations: models and simulation of their evolution along and across the genomes.
The Twenty-Third Annual ACM Symposium on Applied Computing, Bioinformatics track, 1309-1310. ISBN: 978-1-59593-753-7

24. Mitrofanova, A., Pavlovic, V., and Mishra, B. (2008).
Integrative protein function transfer using factor graphs and heterogeneous data sources.
IEEE International Conference on Bioinformatics and Biomedicine, ISBN: 978-0-7695-3452-7

25. Mitrofanova, A., Kleinberg, S., Carlton, J., Kasif, S., and Mishra, B. (2008).
Systems biology via redescription and ontologies (III): protein classification using malaria parasites temporal transcriptomic profiles.
IEEE International Conference on Bioinformatics and Biomedicine, ISBN: 978-0-7695-3452-7

PhD in Computer Science, New York University, Courant Institute of mathematical Sciences, 2009

PostDoctoral training, Columbia University Cancer Center, 2015

NSF Computing Innovation Fellow

PCF Young Investigator Award

Rutgers SHP Excellence in Research Award

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