Didi Amar

PhD. Student in Bioinformatics
School of Computer Science, Tel Aviv University
Advised by Prof. Ron Shamir
Member, Algorithms in Computational Genomics

Research Interests

I work on developing computational techniques for the analysis of high-throughput data sources, focusing on biological problems.
  • Expression profiles analysis (mRNA, methylation, miRNA)
  • Biological networks
  • Gene function prediction when data is limited (e.g., plants)
  • Biomarkers and classification
  • Computational complexity and algorithms

  • Teaching material

    Tools in bioinformatics

      For a full list including preprints check Google Scholar profile

      Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.
      D. Amar, R. Shamir, and D. Yekutieli. PLoS CB 2017

      A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action.
      S. Abadi, WX Yan, D. Amar, and I. Mayrose. PLoS CB 2017

      Analysis of blood-based gene expression in idiopathic Parkinson disease.
      R. Shamir*, C. Klein*, D. Amar.*, et al. Neurology 2017

      Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications.
      D. Amar, S. Izraeli, and R. Shamir. Oncogene 2017

      RichMind: A Tool for Improved Inference from Large-Scale Neuroimaging Results.
      A. Maron-Katz, D. Amar, T. Hendler, and R. Shamir. PLoS ONE 2016

      Enhancer methylation dynamics contribute to cancer plasticity and patient mortality.
      R. E. Bell, T. Golan, H. Malcov, D. Amar, A. Salamon, T. Liron, D. Sheinboim, S. Gelfman, Y. Gabet, R. Shamir, and C. Levy. Genome Research 2016

      Evidence of TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism.
      A. Domingo, D. Amar, K. Grutz, L. Lee, R. Rosales, N. Bruggemann, R. D. Jamora, E. Cutiongco dela-Paz, K. Lohmann, R. Shamir, C. Klein, A. Westenberger. Cellular and Molecular Life Sciences 2016

      Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets
      D. Amar, T. Hait, S. Izraeli, and R Shamir. Nucleic Acids Research 2015

      A hierarchical Bayesian model for flexible module discovery in three-way time series data
      D. Amar, A. Maron-Katz, D. Yekutieli, T. Hendler, and R Shamir. ISMB/ECCB 2015

      The MORPH-R web server and software tool for predicting missing genes in biological pathways
      D. Amar, I. Frades, D. Zaltzman, N. Ghatan, T. Diels, P. E Hedley, E. Alexandersson, O. Tzfadia, and R. Shamir. Physiologia Plantarum 2015

      Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case
      D. Amar, I. Frades, A. Danek, T. Goldberg, S. K Sharma, P. E Hedley, E. Proux-Wera, E., R. Shamir, O. Tzfadia, and E. Alexandersson. BMC Plant Biology 2014

      Constructing module maps for integrated analysis of heterogeneous biological networks
      D. Amar, and R. Shamir. Nucleic Acids Research 2014.

      Dissection of regulatory networks that are altered in disease via differential co-expression
      D. Amar, H. Safer. and R. Shamir. PLoS Computational Biology 2013

      The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana and Solanum lycopersicum pathways
      O. Tzfadia*, D. Amar*, L. Bradbury, E.T. Wurtzel, and R. Shamir. The Plant Cell 2012

      Transcriptional and Proteomic Analysis of the Aspergillus fumigatus DprtT Protease-Deficient Mutant
      S.Hagag, P. Kubitschek-Barreira, G. W. P. Neves, D. Amar, W. Nierman, I. Shalit, R. Shamir, L. Lopes-Bezerra, N. Osherov. PLoS One 2012

      PrtT-Regulated Proteins Secreted by Aspergillus fumigatus Activate MAPK Signaling in Exposed A549 Lung Cells Leading to Necrotic Cell Death
      H. Sharon, D. Amar, E. Levdansky, G. Mircus, Y. Shadkchan, R. Shamir, N. Osherov. PLoS One 2011

      (*) marks shared first co-authorship


    Email: davidama[at]post[dot]tau[dot]ac[dot]il
    Phone: 972-3-640-5394
    Adress: School of Computer Science, Schreiber Building
    Tel Aviv University
    Tel Aviv 69978, Israel