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  1. Article

    Open Access

    Characterizing compatibility and agreement of unrooted trees via cuts in graphs

    Deciding whether there is a single tree —a supertree— that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this ...

    Sudheer Vakati, David Fernández-Baca in Algorithms for Molecular Biology (2014)

  2. Article

    Open Access

    Incompatible quartets, triplets, and characters

    We study a long standing conjecture on the necessary and sufficient conditions for the compatibility of multi-state characters: There exists a function f(r) such that, for any set C of r-state characters, C is co...

    Brad Shutters, Sudheer Vakati, David Fernández-Baca in Algorithms for Molecular Biology (2013)

  3. Article

    Open Access

    Exploring biological interaction networks with tailored weighted quasi-bicliques

    Biological networks provide fundamental insights into the functional characterization of genes and their products, the characterization of DNA-protein interactions, the identification of regulatory mechanisms,...

    Wen-Chieh Chang, Sudheer Vakati, Roland Krause, Oliver Eulenstein in BMC Bioinformatics (2012)