Double Cut and Join with Insertions and Deletions

Dias Vieira Braga, Marília; Willing, Eyla; Stoye, Jens

Double Cut and Join with Insertions and Deletions

Dias Vieira Braga M, Willing E, Stoye J (2011)
Journal of Computational Biology 18(9): 1167-1184.

Zeitschriftenaufsatz | Veröffentlicht | Englisch

Download

Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!

DOI

https://doi.org/10.1089/cmb.2011.0118

Autor*in

Dias Vieira Braga, Marília^UniBi; Willing, Eyla^UniBi; Stoye, Jens^UniBi

Einrichtung

Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye

Erscheinungsjahr

2011

Zeitschriftentitel

Journal of Computational Biology

Band

18

Ausgabe

9

Seite(n)

1167-1184

ISSN

1066-5277

eISSN

1557-8666

Page URI

https://pub.uni-bielefeld.de/record/2091794

Zitieren

Dias Vieira Braga M, Willing E, Stoye J. Double Cut and Join with Insertions and Deletions. Journal of Computational Biology. 2011;18(9):1167-1184.

Dias Vieira Braga, M., Willing, E., & Stoye, J. (2011). Double Cut and Join with Insertions and Deletions. Journal of Computational Biology, 18(9), 1167-1184. https://doi.org/10.1089/cmb.2011.0118

Dias Vieira Braga, Marília, Willing, Eyla, and Stoye, Jens. 2011. “Double Cut and Join with Insertions and Deletions”. Journal of Computational Biology 18 (9): 1167-1184.

Dias Vieira Braga, M., Willing, E., and Stoye, J. (2011). Double Cut and Join with Insertions and Deletions. Journal of Computational Biology 18, 1167-1184.

Dias Vieira Braga, M., Willing, E., & Stoye, J., 2011. Double Cut and Join with Insertions and Deletions. Journal of Computational Biology, 18(9), p 1167-1184.

M. Dias Vieira Braga, E. Willing, and J. Stoye, “Double Cut and Join with Insertions and Deletions”, Journal of Computational Biology, vol. 18, 2011, pp. 1167-1184.

Dias Vieira Braga, M., Willing, E., Stoye, J.: Double Cut and Join with Insertions and Deletions. Journal of Computational Biology. 18, 1167-1184 (2011).

Dias Vieira Braga, Marília, Willing, Eyla, and Stoye, Jens. “Double Cut and Join with Insertions and Deletions”. Journal of Computational Biology 18.9 (2011): 1167-1184.

23 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Computing the family-free DCJ similarity.
Rubert DP, Hoshino EA, Braga MDV, Stoye J, Martinez FV., BMC Bioinformatics 19(suppl 6), 2018
PMID: 29745861

Genomic Distance with High Indel Costs.
da Silva PH, Machado R, Dantas S, Braga MDV., IEEE/ACM Trans Comput Biol Bioinform 14(3), 2017
PMID: 28113562

Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis.
Cai C, Wang L, Zhou L, He P, Jiao B., PLoS One 12(9), 2017
PMID: 28863197

Reconstructing cancer karyotypes from short read data: the half empty and half full glass.
Eitan R, Shamir R., BMC Bioinformatics 18(1), 2017
PMID: 29141589

Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming.
Lyubetsky V, Gershgorin R, Gorbunov K., BMC Bioinformatics 18(1), 2017
PMID: 29212445

Algorithms for reconstruction of chromosomal structures.
Lyubetsky V, Gershgorin R, Seliverstov A, Gorbunov K., BMC Bioinformatics 17(), 2016
PMID: 26780836

Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss.
Avdeyev P, Jiang S, Aganezov S, Hu F, Alekseyev MA., J Comput Biol 23(3), 2016
PMID: 26885568

eSTGt: a programming and simulation environment for population dynamics.
Spiro A, Shapiro E., BMC Bioinformatics 17(1), 2016
PMID: 27117841

A novel procedure on next generation sequencing data analysis using text mining algorithm.
Zhao W, Chen JJ, Perkins R, Wang Y, Liu Z, Hong H, Tong W, Zou W., BMC Bioinformatics 17(1), 2016
PMID: 27177941

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.
Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D., BMC Bioinformatics 17(1), 2016
PMID: 27687569

Comparative genomics meets topology: a novel view on genome median and halving problems.
Alexeev N, Avdeyev P, Alekseyev MA., BMC Bioinformatics 17(suppl 14), 2016
PMID: 28185564

Fast ancestral gene order reconstruction of genomes with unequal gene content.
Feijão P, Araujo E., BMC Bioinformatics 17(suppl 14), 2016
PMID: 28185578

The complete chloroplast and mitochondrial genomes of the green macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta).
Melton JT, Leliaert F, Tronholm A, Lopez-Bautista JM., PLoS One 10(4), 2015
PMID: 25849557

Sorting Linear Genomes with Rearrangements and Indels.
Braga MD, Stoye J., IEEE/ACM Trans Comput Biol Bioinform 12(3), 2015
PMID: 26357261

Comparing genomes with rearrangements and segmental duplications.
Shao M, Moret BM., Bioinformatics 31(12), 2015
PMID: 26072500

Reconstruction of ancestral gene orders using intermediate genomes.
Feijão P., BMC Bioinformatics 16 Suppl 14(), 2015
PMID: 26451811

A unifying model of genome evolution under parsimony.
Paten B, Zerbino DR, Hickey G, Haussler D., BMC Bioinformatics 15(), 2014
PMID: 24946830

DCJ-indel and DCJ-substitution distances with distinct operation costs.
da Silva PH, Machado R, Dantas S, Braga MD., Algorithms Mol Biol 8(1), 2013
PMID: 23879938

On the inversion-indel distance.
Willing E, Zaccaria S, Braga MD, Stoye J., BMC Bioinformatics 14 Suppl 15(), 2013
PMID: 24564182

Restricted DCJ-indel model: sorting linear genomes with DCJ and indels.
da Silva PH, Machado R, Dantas S, Braga MD., BMC Bioinformatics 13 Suppl 19(), 2012
PMID: 23281630

Promoting ranking diversity for genomics search with relevance-novelty combined model.
Yin X, Li Z, Huang JX, Hu X., BMC Bioinformatics 12 Suppl 5(), 2011
PMID: 21989180

Genomic distance under gene substitutions.
Braga MD, Machado R, Ribeiro LC, Stoye J., BMC Bioinformatics 12 Suppl 9(), 2011
PMID: 22151231

On the weight of indels in genomic distances.
Braga MD, Machado R, Ribeiro LC, Stoye J., BMC Bioinformatics 12 Suppl 9(), 2011
PMID: 22151784

14 References

Daten bereitgestellt von Europe PubMed Central.

Reductive evolution of resident genomes.
Andersson SG, Kurland CG., Trends Microbiol. 6(7), 1998
PMID: 9717214

Genome rearrangements with duplications.
Bader M., BMC Bioinformatics 11 Suppl 1(), 2010
PMID: 20122199

AUTHOR UNKNOWN, 0

Reductive genome evolution from the mother of Rickettsia.
Blanc G, Ogata H, Robert C, Audic S, Suhre K, Vestris G, Claverie JM, Raoult D., PLoS Genet. 3(1), 2007
PMID: 17238289

Braga, Lect. Notes Bioinform. 6398(), 2010

The solution space of sorting by DCJ.
Braga MD, Stoye J., J. Comput. Biol. 17(9), 2010
PMID: 20874401

Braga, Lect. Notes Bioinform. 6293(), 2010

Bryant, 2001

El-Mabrouk, J Discrete Algorithms 1(), 2001

Hannenhalli, Proc. FOCS 1995(), 1995

AUTHOR UNKNOWN, 0

Genome rearrangement with gene families.
Sankoff D., Bioinformatics 15(11), 1999
PMID: 10743557

DCJ path formulation for genome transformations which include insertions, deletions, and duplications.
Yancopoulos S, Friedberg R., J. Comput. Biol. 16(10), 2009
PMID: 19803734

Efficient sorting of genomic permutations by translocation, inversion and block interchange.
Yancopoulos S, Attie O, Friedberg R., Bioinformatics 21(16), 2005
PMID: 15951307

Export

Markieren/ Markierung löschen
Markierte Publikationen