@article {563,
	title = {Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation},
	journal = {BMC Genomics},
	volume = {16},
	year = {2015},
	month = {Feb},
	pages = {69},
	abstract = {Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored.},
	issn = {1471-2164},
	doi = {10.1186/s12864-015-1280-3},
	url = {https://doi.org/10.1186/s12864-015-1280-3},
	author = {Terol, Javier and Iba{\~n}ez, Victoria and Carbonell, Jos{\'e} and Alonso, Roberto and Estornell, Leandro H. and Licciardello, Concetta and Gut, Ivo G. and Dopazo, Joaquin and Talon, Manuel}
}
@article {1115,
	title = {Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation.},
	journal = {BMC genomics},
	volume = {16},
	year = {2015},
	month = {2015 Feb 13},
	pages = {69},
	abstract = {BACKGROUND: Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored. RESULTS: Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5{\textquoteright} end of the deletion. The Arrufatina Mule displayed "dissimilar" 9-bp target site duplications separated by 2 Mb. Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome. CONCLUSIONS: Taken together, this information is compatible with the proposal that in both mutants, the TTC-repeat motif formed a triplex DNA structure generating a loop that brought in close proximity the originally distinct reactive ends. In Arrufatina, the loop brought the Mule ends nearby the 2 distinct insertion target sites and the inverted insertion of the transposable element between these target sites provoked the release of the in-between fragment. This proposal requires the involvement of a unique transposon and sheds light on the unresolved question of how two distinct sites become located in close proximity. These observations confer a crucial role to the TTC-repeats in fundamental plant processes as meiotic recombination and chromosomal rearrangements.},
	issn = {1471-2164},
	doi = {10.1186/s12864-015-1280-3},
	url = {http://www.biomedcentral.com/1471-2164/16/69},
	author = {Terol, Javier and Iba{\~n}ez, Victoria and Carbonell, Jos{\'e} and Alonso, Roberto and Estornell, Leandro H and Licciardello, Concetta and Gut, Ivo G and Joaqu{\'\i}n Dopazo and Talon, Manuel}
}
@article {500,
	title = {Inferring the functional effect of gene expression changes in signaling pathways.},
	journal = {Nucleic Acids Res},
	volume = {41},
	year = {2013},
	month = {2013 Jul},
	pages = {W213-7},
	abstract = {<p>Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few methods aimed to identify the signaling circuits, within a pathway, associated to the biological problem studied exist and none of them provide a convenient graphical web interface. We present PATHiWAYS, a web-based signaling pathway visualization system that infers changes in signaling that affect cell functionality from the measurements of gene expression values in typical expression microarray case-control experiments. A simple probabilistic model of the pathway is used to estimate the probabilities for signal transmission from any receptor to any final effector molecule (taking into account the pathway topology) using for this the individual probabilities of gene product presence/absence inferred from gene expression values. Significant changes in these probabilities allow linking different cell functionalities triggered by the pathway to the biological problem studied. PATHiWAYS is available at: http://pathiways.babelomics.org/. </p>},
	keywords = {Animals, Humans, Internet, Mice, Models, Statistical, Receptors, Cell Surface, Signal Transduction, Software, Transcriptome},
	issn = {1362-4962},
	doi = {10.1093/nar/gkt451},
	author = {Sebasti{\'a}n-Leon, Patricia and Carbonell, Jos{\'e} and Salavert, Francisco and S{\'a}nchez, Rub{\'e}n and Medina, Ignacio and Dopazo, Joaquin}
}
