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- Michael A. Bender, Dongdong Ge, +4 authors Firas Swidan
- SODA
- 2004

We study the problem of sorting integer sequences and permutations by length-weighted reversals. We consider a wide class of cost functions, namely <i>f(l)</i> = <i>l</i><sup>α</sup> for all α ≥ 0, where <i>l</i> is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worst-case cost of… (More)

- Firas Swidan, Eduardo P. C. Rocha, Michael Shmoish, Ron Y. Pinter
- PLoS Computational Biology
- 2006

We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying "maximal similar segments," and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating… (More)

- Rolf Backofen, N. S. Narayanaswamy, Firas Swidan
- STACS
- 2002

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 directions: we consider the signed case for linear sequences and also the signed and unsigned cases for circular sequences. We give lower and upper bounds as… (More)

- Michael A. Bender, Dongdong Ge, +4 authors Firas Swidan
- J. Comput. Syst. Sci.
- 2008

We study the problem of sorting binary sequences and permutations by length-weighted reversals. We consider a wide class of cost functions, namely f(`) = ` for all α ≥ 0, where ` is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worst-case cost of sorting by reversals. Then we develop algorithms to… (More)

- Rolf Backofen, N S Narayanaswamy, Firas Swidan
- In silico biology
- 2002

Selenocysteine is the 21th amino acid, which occurs in all kingdoms of life. Selenocysteine is encoded by the STOP-codon UGA. For its insertion, it requires a specific mRNA sequence downstream the UGA-codon that forms a hairpin like structure (called Sec insertion sequence (SECIS)). We consider the computational problem of generating new amino acid… (More)

- Michael Gutkin, Gideon Dror, +8 authors Panos Giannopoulos
- 2008

- Firas Swidan, Ron Shamir
- Adv. Bioinformatics
- 2009

Comparing genomes is an essential preliminary step to solve many problems in biology. Matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. Though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. Here,… (More)

- Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter
- Journal of Computational Biology
- 2006

A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals (i.e., inversions) and repeats. These biological findings are formalized here in a new mathematical model, called repeat-annotated phylogenetic trees (RAPT). We show that, under RAPT, the evolutionary process--including… (More)

- Rolf Backofen, N. S. Narayanaswamy, Firas Swidan
- German Conference on Bioinformatics
- 2001