Antonina Mitrofanova lab
Computational Medicine and Therapeutics
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    Selected peer-reviewed publications: (PubMed link to full publication list).

    I. Cancer-related publications:

  • Panja, S.*, Truica, M.I.*, Yu, Ch.Y., Saggurthi, V., Craige, M.W., Whitehead, K., Tuiche, M.V., Al-Saadi, A., Vyas, R., Ganesan, Sh., Gohel, S., Coffman, F., Parrott, J.S., Jha, Sh., Kim, I., Schaeffer, E., Kothari, V.†, Abdulkadir, S.A.†, Mitrofanova, A.† (2024).
    Mechanism-centric regulatory network identifies NME2 and MYC programs as markers of Enzalutamide resistance in CRPC.
    Nature Communications, 15(1):352. PMID: 38191557.
    * Co-first authors
    † Senior Corresponding authors.

  • Ramakrishnan, A.*, Datta, I.*, Panja, S.*, Patel, H., Liu, Y., Craige, M.W., Chu, C., Jean-Marie, G., Oladoja, A-R.,
    Kim, I.Y., and Mitrofanova, A.† (2023).
    Tissue-specific biological aging predicts progression in prostate cancer and acute myeloid leukemia.
    Frontiers in Oncology, 6:13:1222168. PMID: 37746266.
    * Co-first authors
    † Senior Corresponding author.

  • Bohannan, Z., Coffman, F., and Mitrofanova, A.† (2022).
    Random survival forest model identifies novel biomarkers of event-free survival in high-risk pediatric acute lymphoblastic leukemia.
    Computational and Structural Biotechnology Journal, 20: 583-597. PMID: 35116134.
    † Senior Corresponding author.

  • Yu, Ch., Mitrofanova, A.† (2021).
    Mechanism-centric approaches for biomarker detection and precision therapeutics in cancer.
    Frontiers in Genetics, 12: 687813. PMID: 34408770.
    † Senior Corresponding author.

  • Panja, S., Rahem, S., Chua, C.J, Mitrofanova, A.† (2020).
    Big Data to Knowledge: application of machine learning to predictive modeling of therapeutic response in cancer.
    Current Genomics, 22(4):244-266, PMID: 35273457.
    † Senior Corresponding author.

  • Rahem, S.M., Epsi, N.J., Coffman, F.D., Mitrofanova, A.† (2020).
    Genome-wide analysis of therapeutic response uncovers molecular pathways governing tamoxifen resistance in ER+ breast cancer.
    EBioMedicine (published by THE LANCET), 61:103047, PMID: 33099086.
    † Senior Corresponding author.

  • Shibata, M., Epsi, N.J, Xuan, Sh., Mitrofanova, A. , Shen, M.M (2020).
    Bipotent progenitors do not require androgen receptor for luminal specification during prostate organogenesis.
    Stem Cell Reports, 15(5):1026-1036, PMID: 33176121.

  • Arriaga, J., Panja, S., Alshalalfa, M., Zhao, J., Zou, M., Giacobbe, A., Madubata4, C.J., Kim, J.Y.,
    Rodriguez, A., Coleman, I., Virk, R.K., Hibshoosh, H., Ertunc, O., Ozbek, B., Fountain, J., Karnes, R.J.,
    Luo, J., Antonarakis, E.S., Nelson, P.S., Feng, F.Y., Rubin, M.A., De Marzo, A.M., Rabadan, R., Sims, P.A.,
    Mitrofanova, A.†, Abate-Shen, C †(2020).
    A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance.
    Nature Cancer, 1(11):1082-1096, PMID: 34085047.
    † Co-Senior Co-Corresponding authors.

  • Epsi, N.J.*, Panja, S.*, Mitrofanova, A.† (2020).
    Big Data and its emerging role in precision medicine and therapeutic response (book chapter).
    Detection Methods in Precision Medicine, Royal Society of Chemistry.
    * Co-first authors
    † Senior Corresponding author.

  • 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, 2:334, PMID: 31508508.
    † Senior Corresponding author.

  • 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, 17:561-569. PMID: 31049166.
    † Senior Corresponding author.

  • 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 (published by THE LANCET),
    Volume 31, ppi: 110-121. PMID: 29685789.
    † Senior Corresponding author.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.


    • II. Publications related to other diseases:

  • Martingano, D., Nguyen, A., Nkeih, C., Singh, Sh., and Mitrofanova, A. † (2020).
    Clarithromycin use for adjunct surgical prophylaxis before non-elective cesarean deliveries to adapt to azithromycin shortages in COVID-19 pandemic.
    PLOS ONE, 15(12):e0244266, PMID: 33347510
    † Senior Corresponding author

  • Martingano D, Singh S, Mitrofanova, A. † (2020).
    Azithromycin in the Treatment of Preterm Prelabor Rupture of Membranes Demonstrates a Lower Risk of Chorioamnionitis and Postpartum Endometritis with an Equivalent Latency Period Compared with Erythromycin Antibiotic Regimens.
    Infect Dis Obstet Gynecol 2020:2093530. PMID: 32694907
    † Senior Corresponding author

  • Pastore, R.L., Murray, J.A., Coffman, F.D., Mitrofanova, A., Srinivasan, S. (2019).
    Physician Review of a Celiac Disease Risk Estimation and Decision-Making Expert System.
    J Am Coll Nutr. 38(8):722-728. PMID: 31063433

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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