Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Faster and simpler algorithm for sorting signed permutations by reversals
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
The complexity of gene placement
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Gossip is synteny: incomplete gossip and an exact algorithm for syntenic distance
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Gossip is synteny: incomplete gossip and the syntenic distance between genomes
Journal of Algorithms
Reconstructing an ancestral genome using minimum segments duplications and reversals
Journal of Computer and System Sciences - Computational biology 2002
Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Evolutionary Puzzles: An Introduction to Genome Rearrangement
ICCS '01 Proceedings of the International Conference on Computational Science-Part II
Phylogenetic Inference from Mitochondrial Genome Arrangement Data
ICCS '01 Proceedings of the International Conference on Computational Science-Part II
Finding an Optimal Inversion Median: Experimental Results
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Discovering Poetic Allusion in Anthologies of Classical Japanese Poems
DS '99 Proceedings of the Second International Conference on Discovery Science
Hybridization and Genome Rearrangement
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Chromosomal breakpoint re-use in the inference of genome sequence rearrangement
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
An O(n2) algorithm for signed translocation
Journal of Computer and System Sciences - Special issue on bioinformatics II
Genome rearrangements: a correct algorithm for optimal capping
Information Processing Letters
Whole genome duplications, multi-break rearrangements, and genome halving problem
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Consensus Genetic Maps as Median Orders from Inconsistent Sources
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multi-break rearrangements and chromosomal evolution
Theoretical Computer Science
HP Distance Via Double Cut and Join Distance
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Genome Halving under DCJ Revisited
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
Transposition Distance Based on the Algebraic Formalism
BSB '08 Proceedings of the 3rd Brazilian symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Multichromosomal Genome Median and Halving Problems
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Hurdles Hardly Have to Be Heeded
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Polynomial-Time Algorithm for Sorting by Generalized Translocations
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
Swarming along the evolutionary branches sheds light on genome rearrangement scenarios
Proceedings of the 11th Annual conference on Genetic and evolutionary computation
Constraint Programming Models for Transposition Distance Problem
BSB '09 Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
A new linear time algorithm to compute the genomic distance via the double cut and join distance
Theoretical Computer Science
Counting All DCJ Sorting Scenarios
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Rearrangement Models and Single-Cut Operations
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
An improved algorithm for sorting by block-interchanges based on permutation groups
Information Processing Letters
On the similarity of sets of permutations and its applications to genome comparison
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Multi-break rearrangements: from circular to linear genomes
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Listing all sorting reversals in quadratic time
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Advances on genome duplication distances
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
On exploring genome rearrangement phylogenetic patterns
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Limited lifespan of fragile regions in mammalian evolution
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Weighted genomic distance can hardly impose a bound on the proportion of transpositions
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
A practical algorithm for ancestral rearrangement reconstruction
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
An O(n3/2log(n)) algorithm for sorting by reciprocal translocations
Journal of Discrete Algorithms
Maximizing synteny blocks to identify ancestral homologs
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
A unifying view of genome rearrangements
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
An O(n3/2√log(n)) algorithm for sorting by reciprocal translocations
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Genome rearrangements with partially ordered chromosomes
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Sorting by translocations via reversals theory
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Estimators of translocations and inversions in comparative maps
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
A parsimony approach to genome-wide ortholog assignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Evolution of genome organization by duplication and loss: an alignment approach
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
DCJ-indel distance with distinct operation costs
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Heuristics for the Sorting by Length-Weighted Inversion Problem
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Listing Sorting Sequences of Reversals and Translocations
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Sorting genomes by generalized translocations
Theoretical Computer Science
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Many people believe that transformations of humans into mice happen only in fairy tales. However, despite some differences in appearance and habits, men and mice are genetically very similar. In the pioneering paper, J.H. Nadeau and B.A. Taylor (1984) estimated that surprisingly few genomic rearrangements (178/spl plusmn/39) happened since the divergence of human and mouse 80 million years ago. However, their analysis is nonconstructive and no rearrangement scenario for human-mouse evolution has been suggested yet. The problem is complicated by the fact that rearrangements in multi chromosomal genomes include inversions, translocations, fusions and fissions of chromosomes, a rather complex set of operations. As a result, at first glance, a polynomial algorithm for the genomic distance problem with all these operations looks almost as improbable as the transformation of a (real) man into a (real) mouse. We prove a duality theorem which expresses the genomic distance in terms of easily computable parameters reflecting different combinatorial properties of sets of strings. This theorem leads to a polynomial time algorithm for computing most parsimonious rearrangement scenarios. Based on this result and the latest comparative physical mapping data we have constructed a scenario of human-mouse evolution with 131 reversals/translocaitons/fusions/fissions. A combination of the genome rearrangement algorithm with the recently proposed experimental technique called ZOO FISH suggests a new constructive approach to the 100 year old problem of reconstructing mammalian evolution.