Search Results - (Author, Cooperation:D. Sankoff)
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1Latest Papers from Table of Contents or Articles in PressF. Denoeud ; L. Carretero-Paulet ; A. Dereeper ; G. Droc ; R. Guyot ; M. Pietrella ; C. Zheng ; A. Alberti ; F. Anthony ; G. Aprea ; J. M. Aury ; P. Bento ; M. Bernard ; S. Bocs ; C. Campa ; A. Cenci ; M. C. Combes ; D. Crouzillat ; C. Da Silva ; L. Daddiego ; F. De Bellis ; S. Dussert ; O. Garsmeur ; T. Gayraud ; V. Guignon ; K. Jahn ; V. Jamilloux ; T. Joet ; K. Labadie ; T. Lan ; J. Leclercq ; M. Lepelley ; T. Leroy ; L. T. Li ; P. Librado ; L. Lopez ; A. Munoz ; B. Noel ; A. Pallavicini ; G. Perrotta ; V. Poncet ; D. Pot ; Priyono ; M. Rigoreau ; M. Rouard ; J. Rozas ; C. Tranchant-Dubreuil ; R. VanBuren ; Q. Zhang ; A. C. Andrade ; X. Argout ; B. Bertrand ; A. de Kochko ; G. Graziosi ; R. J. Henry ; Jayarama ; R. Ming ; C. Nagai ; S. Rounsley ; D. Sankoff ; G. Giuliano ; V. A. Albert ; P. Wincker ; P. Lashermes
American Association for the Advancement of Science (AAAS)
Published 2014Staff ViewPublication Date: 2014-09-06Publisher: American Association for the Advancement of Science (AAAS)Print ISSN: 0036-8075Electronic ISSN: 1095-9203Topics: BiologyChemistry and PharmacologyComputer ScienceMedicineNatural Sciences in GeneralPhysicsKeywords: Caffeine/biosynthesis/*genetics ; Coffea/classification/*genetics ; *Evolution, Molecular ; *Genome, Plant ; Methyltransferases/genetics/*physiology ; Phylogeny ; Plant Proteins/genetics/*physiologyPublished by: -
2Articles: DFG German National LicensesStaff View
ISSN: 0006-291XSource: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyChemistry and PharmacologyPhysicsType of Medium: Electronic ResourceURL: -
3Articles: DFG German National LicensesStaff View
ISSN: 0378-2166Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: Linguistics and Literary StudiesType of Medium: Electronic ResourceURL: -
4Articles: DFG German National LicensesStaff View
ISSN: 0024-3841Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: Linguistics and Literary StudiesType of Medium: Electronic ResourceURL: -
5Articles: DFG German National LicensesStaff View
ISSN: 0022-5193Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyType of Medium: Electronic ResourceURL: -
6Articles: DFG German National LicensesStaff View
ISSN: 0022-5193Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyType of Medium: Electronic ResourceURL: -
7Articles: DFG German National LicensesStaff View
ISSN: 0022-5193Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyType of Medium: Electronic ResourceURL: -
8Articles: DFG German National LicensesStaff View
ISSN: 0006-291XSource: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyChemistry and PharmacologyPhysicsType of Medium: Electronic ResourceURL: -
9Articles: DFG German National LicensesStaff View
ISSN: 0300-9084Keywords: chromosome inversion ; genome shuffling ; molecular evolution ; phylogenetic invariantsSource: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyChemistry and PharmacologyType of Medium: Electronic ResourceURL: -
10Articles: DFG German National LicensesStaff View
ISSN: 1432-1432Keywords: Phenylalanine tRNA ; Methionine initiator tRNA ; Evolution ; Mutations ; ConformationSource: Springer Online Journal Archives 1860-2000Topics: BiologyNotes: Summary Sequence data from methionine initiator and phenylalanine transfer RNAs were used to construct phylogenetic trees by the maximum parsimony method. Although eukaryotes, prokaryotes and chloroplasts appear related to a common ancestor, no firm conclusion can be drawn at this time about mitochondrial-coded transfer RNAs. tRNA evolution is not appropriately described by random hit models, since the various regions of the molecule differ sharply in their mutational fixation rates. ‘Hot’ mutational spots are identified in the TψC, the amino acceptor and the upper anticodon stems; the D arm and the loop areas on the other hand are highly conserved. Crucial tertiary interactions are thus essentially preserved while most of the double helical domain undergoes base pair interchange. Transitions are about half as costly as transversions, suggesting that base pair interchanges proceed mostly through G-U and A -C intermediates. There is a preponderance of replacements starting from G and C but this bias appears to follow the high G + C content of the easily mutated base paired regions.Type of Medium: Electronic ResourceURL: -
11Articles: DFG German National LicensesStaff View
ISSN: 0092-8240Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyMathematicsType of Medium: Electronic ResourceURL: -
12Articles: DFG German National LicensesStaff View
ISSN: 0092-8240Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyMathematicsType of Medium: Electronic ResourceURL: -
13Articles: DFG German National LicensesStaff View
ISSN: 0092-8240Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyMathematicsType of Medium: Electronic ResourceURL: -
14Articles: DFG German National LicensesStaff View
ISSN: 0092-8240Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyMathematicsType of Medium: Electronic ResourceURL: -
15Articles: DFG German National LicensesStaff View
ISSN: 0092-8240Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyMathematicsType of Medium: Electronic ResourceURL: -
16Articles: DFG German National LicensesStaff View
ISSN: 0092-8240Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002Topics: BiologyMathematicsType of Medium: Electronic ResourceURL: -
17Articles: DFG German National LicensesStaff View
ISSN: 1432-0541Keywords: Computational biology ; Approximation algorithms ; Branch- and-bound algorithms ; Experimental analysis of algorithms ; Edit distance ; Permutations ; Sorting by reversals ; Chromosome inversions ; Genome rearrangementsSource: Springer Online Journal Archives 1860-2000Topics: Computer ScienceMathematicsNotes: Abstract Motivated by the problem in computational biology of reconstructing the series of chromosome inversions by which one organism evolved from another, we consider the problem of computing the shortest series of reversals that transform one permutation to another. The permutations describe the order of genes on corresponding chromosomes, and areversal takes an arbitrary substring of elements, and reverses their order. For this problem, we develop two algorithms: a greedy approximation algorithm, that finds a solution provably close to optimal inO(n 2) time and0(n) space forn-element permutations, and a branch- and-bound exact algorithm, that finds an optimal solution in0(mL(n, n)) time and0(n 2) space, wherem is the size of the branch- and-bound search tree, andL(n, n) is the time to solve a linear program ofn variables andn constraints. The greedy algorithm is the first to come within a constant factor of the optimum; it guarantees a solution that uses no more than twice the minimum number of reversals. The lower and upper bounds of the branch- and-bound algorithm are a novel application of maximum-weight matchings, shortest paths, and linear programming. In a series of experiments, we study the performance of an implementation on random permutations, and permutations generated by random reversals. For permutations differing byk random reversals, we find that the average upper bound on reversal distance estimatesk to within one reversal fork〈1/2n andn〈100. For the difficult case of random permutations, we find that the average difference between the upper and lower bounds is less than three reversals forn〈50. Due to the tightness of these bounds, we can solve, to optimality, problems on 30 elements in a few minutes of computer time. This approaches the scale of mitochondrial genomes.Type of Medium: Electronic ResourceURL: