Selected publications

  • Markin, A., Wagle, S., Anderson, T.K. and Eulenstein, O., 2022. RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks. Bioinformatics.
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  • Markin, A. and Eulenstein, O., 2021. Quartet-Based Inference is Statistically Consistent Under the Unified Duplication-Loss-Coalescence Model. Bioinformatics.
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  • Markin, A., 2020. On the Extremal Maximum Agreement Subtree Problem. Descrete Applied Mathematics, Elsevier.
    Solving problem NC3 from Mike Steel's list of phylogenetic challenges.
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Journal papers

  • Markin, A., Wagle, S., Anderson, T.K., and Eulenstein, O., 2022. RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks. Bioinformatics.
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  • Paszek, J., Markin, A., Gorecki, P., and Eulenstein, O., 2021 Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming. Jounral of Computational Biology.
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  • Markin, A. and Eulenstein, O., 2021 Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model. Bioinformatics.
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  • Markin, A., 2020. On the Extremal Maximum Agreement Subtree Problem. Descrete Applied Mathematics, Elsevier.
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  • Górecki, P., Markin, A. and Eulenstein, O., 2020. Exact median-tree inference for unrooted reconciliation costs. BMC Evolutionary Biology, 20(1), pp.1-15.
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  • Markin, A. and Eulenstein, O., 2018. Cophenetic Median Trees. IEEE/ACM Transaction on Computational Biology and Bioinformatics (invited paper).
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  • Markin, A. and Eulenstein, O, 2017. Efficient Local Search for Euclidean Path-Difference Median Trees. Accepted in IEEE/ACM Transaction on Computational Biology and Bioinformatics (invited paper).
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  • Markin, A. and Eulenstein, O., 2017. Computing Manhattan Path-Difference Median Trees: a Practical Local Search Approach. IEEE/ACM Transaction on Computational Biology and Bioinformatics (invited paper).
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Conference papers

  • Nguyen, HN. Markin, A., Friedberg, I., and Eulenstein, O., 2020. Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it. Bioinformatics (ECCB'20 proceedings).
  • Ansarifar, J., Markin, A., Górecki, P. and Eulenstein, O., 2020. Integer Linear Programming Formulation for the Unified Duplication-Loss-Coalescence Model. In International Symposium on Bioinformatics Research and Applications (pp. 229-242). Springer, Cham.
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  • Markin, A. and Eulenstein, O., 2019. Consensus Clusters in Robinson-Foulds Reticulation Networks. Workshop on Algorithms in Bioinformatics (WABI'2019) proceedings.
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  • Markin, A., Anderson, T.K., Vadali, V.S.K.T. and Eulenstein, O., 2019. Robinson-Foulds Reticulation Networks. ACM-BCB'2019 proceedings.
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  • Górecki, P., Markin, A. and Eulenstein, O., 2019. Feasibility Algorithms for the Duplication-Loss Cost. In International Computing and Combinatorics Conference (COCOON'2019), pp. 206-218. Springer, Cham.
  • Markin, A., Vadali, V.S.K.T. and Eulenstein, O., 2018. Solving the Gene Duplication Feasibility Problem in Linear Time. In International Computing and Combinatorics Conference (COCOON'2018), pp. 378-390. Springer, Cham.
  • Górecki, P., Markin, A. and Eulenstein, O., 2018. Cophenetic Distances: A Near-Linear Time Algorithmic Framework. In International Computing and Combinatorics Conference (COCOON'2018), pp. 168-179. Springer, Cham.
  • Markin, A. and Eulenstein, O., 2017. Cophenetic Median Trees Under the Manhattan Distance. ACM-BCB'2017 proceedings.
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  • Gorecki, P., Markin, A. Mykowiecka, A., Paszek, J., and Eulenstein, O., 2017. Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees. In International Symposium on Bioinformatics Research and Applications, pp. 234-245. Springer, Cham.
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  • Markin, A. and Eulenstein, O., 2016. Manhattan Path-Difference Median Trees. ACM-BCB'2016 proceedings.
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  • Markin, A. and Eulenstein, O., 2016. Path-Difference Median Trees. Bioinformatics Research and Applications: 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016. Springer International Publishing, Cham.
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