PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees-Reference-Cited by-同舟云学术

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PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees

Published:2014-08-08 Issue:1 Volume:15 Page:
ISSN:1471-2105
Container-title:BMC Bioinformatics
language:en
Short-container-title:BMC Bioinformatics

Author:

Lucas Joseph MEX,Muffato Matthieu,Roest Crollius Hugues

Publisher

Springer Science and Business Media LLC

Subject

Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology

Link

https://link.springer.com/content/pdf/10.1186/1471-2105-15-268.pdf

Reference39 articles.

1. Murphy WJ, Larkin DM, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O’brien SJ, Everts-van der Wind A: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 2005, 309 (5734): 613-7. doi:10.1126/science.1111387,

2. Chauve C, Tannier E: A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput Biol. 2008, 4 (11): 1000234-10.1371/journal.pcbi.1000234. doi:10.1371/journal.pcbi.1000234. PMID:19043541,

3. Darai-Ramqvist E, Sandlund A, Müller S, Klein G, Imreh S, Kost-Alimova M: Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions. Genome Res. 2008, 18 (3): 370-9. doi:10.1101/gr.7010208,

4. Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Pezeron G, Mourrain P, Ellingsen S, Oates A. C, Thisse C, Thisse B, Foucher I, Adolf B, Geling A, Lenhard B, Becker TS: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 2007, 17 (5): 545-55. doi:10.1101/gr.6086307,

5. Irimia M, Tena JJ, Alexis M. S, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB: Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res. 2012, 22 (12): 2356-67. doi:10.1101/gr.139725.112,

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3. An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice;Genes;2020-09-04

4. Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications;Molecular Biology and Evolution;2020-06-18

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