Zobrazeno 1 - 9
of 9
pro vyhledávání: '"Qiaoji Xu"'
Publikováno v:
Scientific Reports, Vol 13, Iss 1, Pp 1-16 (2023)
Abstract To reconstruct the ancestral genome of a set of phylogenetically related descendant species, we use the raccroche pipeline for organizing a large number of generalized gene adjacencies into contigs and then into chromosomes. Separate reconst
Externí odkaz:
https://doaj.org/article/8f63da73a1b04a41877db1ad2b8481f0
Autor:
Andre S. Chanderbali, Lingling Jin, Qiaoji Xu, Yue Zhang, Jingbo Zhang, Shuguang Jian, Emily Carroll, David Sankoff, Victor A. Albert, Dianella G. Howarth, Douglas E. Soltis, Pamela S. Soltis
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-10 (2022)
Gamma triplication arises via two whole-genome duplications early in eudicot history, but the relative timing of these is unclear. Here, the authors report the genomes of Buxales and Trochodendrales and reject the hypothesis of gamma arising via inte
Externí odkaz:
https://doaj.org/article/a94ebca4c2fe4396ba7e2cb101783b23
Publikováno v:
Algorithms, Vol 14, Iss 6, p 160 (2021)
The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogeneticall
Externí odkaz:
https://doaj.org/article/41b78ccdac4d4fc1bd7c1725bb2f7fde
Autor:
Yue Zhang, David Sankoff, Lingling Jin, Chunfang Zheng, Qiaoji Xu, Jim Leebens-Mack, Xiaomeng Zhang
Publikováno v:
Journal of Computational Biology. 28:1156-1179
Recurrent whole genome duplication and the ensuing loss of redundant genes-fractionation-complicate efforts to reconstruct the gene orders and chromosomes of the ancestors associated with the nodes of a phylogeny. Loss of genes disrupts the gene adja
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1758da6907db7113425b1a7f0f9d981c
https://doi.org/10.1089/cmb.2021.0340
https://doi.org/10.1089/cmb.2021.0340
To reconstruct the ancestral genome of a set of phylogenetically related descendant species, we use the raccroche pipeline for organizing a large number of generalized gene adjacencies into contigs and then into chromosomes. Separate reconstructions
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5644396d4f260bda62d38fa4984bd123
https://doi.org/10.1101/2022.09.28.509880
https://doi.org/10.1101/2022.09.28.509880
Autor:
Xiaomeng Zhang, Lingling Jin, Jim Leebens-Mack, David Sankoff, Chunfang Zheng, Yue Zhang, Qiaoji Xu
Publikováno v:
Journal of bioinformatics and computational biology. 19(6)
Using RACCROCHE, a method for reconstructing gene content and order of ancestral chromosomes from a phylogeny of extant genomes represented by the gene orders on their chromosomes, we study the evolution of three orders of woody plants. The method re
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::088250fccdf2bb441c928c027ba18c85
https://pubmed.ncbi.nlm.nih.gov/34806950
https://pubmed.ncbi.nlm.nih.gov/34806950
Autor:
Andre S, Chanderbali, Lingling, Jin, Qiaoji, Xu, Yue, Zhang, Jingbo, Zhang, Shuguang, Jian, Emily, Carroll, David, Sankoff, Victor A, Albert, Dianella G, Howarth, Douglas E, Soltis, Pamela S, Soltis
Publikováno v:
Nature communications. 13(1)
Ancient whole-genome duplications (WGDs) characterize many large angiosperm lineages, including angiosperms themselves. Prominently, the core eudicot lineage accommodates 70% of all angiosperms and shares ancestral hexaploidy, termed gamma. Gamma aro
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::2b544c773b430b32ae1ae0ecacd60f0c
https://pubmed.ncbi.nlm.nih.gov/35110570
https://pubmed.ncbi.nlm.nih.gov/35110570
Publikováno v:
Algorithms, Vol 14, Iss 160, p 160 (2021)
Algorithms
Volume 14
Issue 6
Algorithms
Volume 14
Issue 6
The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogeneticall
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a55f6eb2d1bc068165752e1f837b20b
https://www.mdpi.com/1999-4893/14/6/160
https://www.mdpi.com/1999-4893/14/6/160
Publikováno v:
Computational Advances in Bio and Medical Sciences ISBN: 9783030792893
ICCABS
ICCABS
Given the phylogenetic relationships of several extant species, the reconstruction of their ancestral genomes at the gene and chromosome level is made difficult by the cycles of whole genome doubling followed by fractionation in plant lineages. Fract
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::86ae4e9711d884a24449e71963cf29a5
https://doi.org/10.1007/978-3-030-79290-9_9
https://doi.org/10.1007/978-3-030-79290-9_9