Columbia University

Antonina Mitrofanova Antonina Mitrofanova

I am a Prostate Cancer Foundation (PCF) Young Investigator
at Columbia University, mentored by Dr Michael Shen
and co-advised by Dr Cory Abate-Shen and Dr Andrea Califano.

Previously I was a PostDoctoral Computing Innovation Fellow (NSF, CRA, CCC) at Columbia University, hosted by Professor Andrea Califano.

Research interests

My main research interests are in bioinformatics algorithms applied to protein and gene networks, transcriptional networks, cancer regulatory networks, and probabilistic models in biology.

My doctoral dissertation, Efficient and Robust Systems Biology Algorithms for Biological Networks over Mutiple Time-Scales: From Evolutionary to Regulatory Time, introduced a series of novel methods to address the problems commonly faced in noisy and poorly annotated protein and gene networks.

At Columbia, I am working on problems that arise in assembling and mining regulatory networks for prostate cancer and am affiliated with the Center for Computational Biology and Bioinformatics and Irving Cancer Research Center.


I received my Ph.D. in Computer and Information Science, Bioinformatics Group, from New York University, NYU,  in September, 2009. I was extremely lucky and privileged to be advised  by Professor Bud Mishra.

I was awarded Janet Fabri Award (for the dissertation determined to be the department's most outstanding) and Henning Biermann Prize (outstanding contributions to education or service to the department) by the Department of Computer Science, NYU.

From 1995 to 1999, I was a medical student at the National Medical University (Kiev, Ukraine), Division of General Medicine.

My academic honors and awards.

Get in touch

I am organizing meetings in Biological Networks at Columbia University. Please send me a note if you wish to attend or to be scheduled for a talk!

Email: antonina at
Email: antonina at

Office: 1130 St. Nicholas Ave. Room 909
New York NY 10032 USA


Refereed Journal Publications
  • Mitrofanova, A.*, Aytes, A.*, Zou, M., Shen, M., Abate-Shen, C., and Califano, A.
    Predicting drug response in human prostate cancer from preclinical analysis of in vivo mouse models.
    Cell Reports. September 2015.
    *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.
    Cross-species analysis of genome-wide regulatory networks identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy.
    Cancer Cell. Volume 25, Issue 5, p638-651, 12 May 2014.

    *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.
    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, September 2013.

    * Leading computational author.
  • Wang, Z. A., Mitrofanova*, A., Bergren, S. K., Cardiff, R. D., Abate-Shen, C., Califano, A., and Shen, M. M.
    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, February-March 2013.
    PMID: 23434823.

    * Leading computational author.
  • Jingqiang Wang, Takashi Kobayashi, Nicolas Floch, Carolyn Waugh Kinkade, Alvaro Aytes, David Dankort, Celine Lefebvre, Antonina Mitrofanova, Robert D. Cardiff, Martin McMahon, Andrea Califano, Michael M. Shen, and Cory Abate-Shen (2012)
    B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer,
    Cancer Research, 72: 4765-4776. September 2012.
    PMCID: PMC3445712
  • Nicolas Floch, Carolyn Waugh Kinkade, Takashi Kobayashi, Alvaro Aytes, Celine Lefebvre, Antonina Mitrofanova, Robert D. Cardiff, Andrea Califano, Michael M. Shen, Cory Abate-Shen (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. September 2012.
    PMCID: PMC3432676
  • Antonina Mitrofanova, Vladimir Pavlovic and Bud Mishra
    Prediction of Protein Functions with Gene Ontology and Protein Homology Data,
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE/ACM TCBB, Volume 8, Issue 3, pp 775-784, May-June 2011.
    PMID: 21393654
  • Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, and Bud Mishra, Predicting Malaria Interactome Classifications from Time-Course Transcriptomic Data along the Intra-Erythrocytic Developmental Cycle
    Artificial Intelligence in Medicine, AIIM, Volume 49, Issue 3, pp 167-176, July 2010.
    PMID: 20580212
  • Antonina Mitrofanova and Bud Mishra
    On a Novel Coalescent Model for Genome-Wide Evolution of Copy Number Variations, International Journal of Data Mining and Bioinformatics, IJDMB, Volume 4, Number 3, pp 300-15, June 2010.
    PMID: 20681481
Refereed Conference Publications
  • Antonina Mitrofanova, Martin Farach-Colton, and Bud Mishra
    Efficient and Robust Prediction Algorithms for Protein Complexes using Gomory-Hu Trees, Pacific Symposium on Biocomputing 2009, PMID: 19209703 , PSB 2009[pdf]
  • Antonina Mitrofanova, Vladimir Pavlovic, and Bud Mishra
    Integrative Protein Function Transfer using Factor Graphs and Heterogeneous Data Sources, IEEE International Conference on Bioinformatics and Biomedicine 2008, IEEE BIBM 2008 , ISBN: 978-0-7695-3452-7, [pdf]
  • Antonina Mitrofanova and Bud Mishra
    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, ACM SAC 2008, Bioinformatics track, ISBN: 978-0-7695-3452-7, [link]
  • Aggelos Kiayias and Antonina Mitrofanova
    Syntax-Driven Private Evaluation of Quantified Membership Queries
    Applied Cryptography and Network Security 2006, ISBN:3-540-34703-8 , ACNS 2006, [link]
  • Aggelos Kiayias and Antonina Mitrofanova
    Testing Disjointness of Private Datasets
    Financial Cryptography 2005, ISBN:3-540-26656-9 , FC 2005.
    , [link]