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  1. No Access

    Chapter and Conference Paper

    On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem

    A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals (aka inversions) and repeats. These biological findings are formalized h...

    Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter in Combinatorial Pattern Matching (2006)

  2. No Access

    Chapter and Conference Paper

    Sorting by Length-Weighted Reversals: Dealing with Signs and Circularity

    We consider the problem of sorting linear and circular permutations and 0/1 sequences by reversals in a length-sensitive cost model. We extend the results on sorting by length-weighted reversals in two directi...

    Firas Swidan, Michael A. Bender, Dongdong Ge, Simai He… in Combinatorial Pattern Matching (2004)

  3. No Access

    Chapter and Conference Paper

    On the Complexity of Protein Similarity Search under mRNA Structure Constraints

    This paper addresses the complexity of a new problem associated with RNA secondary structure prediction. The issue is to identify an mRNA which has the secondary structure (=set of bonds) of a given mRNA, and ...

    Rolf Backofen, N.S. Narayanaswamy, Firas Swidan in STACS 2002 (2002)