01876nas a2200181   4500008004100000022001400041245005400055210004800109260001600157300001000173490000600183520137000189100002101559700001701580700003101597700002101628856004501649       2016                        eng d  a2045-232200aThe pan-cancer pathological regulatory landscape.0 apancancer pathological regulatory landscape  c2016 Dec 21  a397090 v63 aDysregulation of the normal gene expression program is the cause of a broad range of diseases, including cancer. Detecting the specific perturbed regulators that have an effect on the generation and the development of the disease is crucial for understanding the disease mechanism and for taking decisions on efficient preventive and curative therapies. Moreover, detecting such perturbations at the patient level is even more important from the perspective of personalized medicine. We applied the Transcription Factor Target Enrichment Analysis, a method that detects the activity of transcription factors based on the quantification of the collective transcriptional activation of their targets, to a large collection of 5607 cancer samples covering eleven cancer types. We produced for the first time a comprehensive catalogue of altered transcription factor activities in cancer, a considerable number of them significantly associated to patient’s survival. Moreover, we described several interesting TFs whose activity do not change substantially in the cancer with respect to the normal tissue but ultimately play an important role in patient prognostic determination, which suggest they might be promising therapeutic targets. An additional advantage of this method is that it allows obtaining personalized TF activity estimations for individual patients.1 aFalco, Matias, M1 aBleda, Marta1 aCarbonell-Caballero, José1 aDopazo, Joaquín  uhttp://www.nature.com/articles/srep3970900573nas a2200145   4500008004100000245005300041210004800094260001600142490000600158100002200164700001700186700003100203700002000234856017300254       2016                        eng d00aThe pan-cancer pathological regulatory landscape0 apancancer pathological regulatory landscape  cJan-12-20160 v61 aFalco, Matias, M.1 aBleda, Marta1 aCarbonell-Caballero, José1 aDopazo, Joaquin  uhttp://www.nature.com/articles/srep39709http://www.nature.com/articles/srep39709.pdfhttp://www.nature.com/articles/srep39709.pdfhttp://www.nature.com/articles/srep3970902086nas a2200253   4500008004100000022001400041245014200055210006900197260001600266300001400282490000700296520127300303653001601576653001101592653001401603653000801617100003101625700002001656700002201676700001801698700001801716700002001734856007801754       2015                        eng d  a1537-171900aA phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus Citrus.0 aphylogenetic analysis of 34 chloroplast genomes elucidates the r  c2015 Apr 14  a2015-20350 v323 aCitrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because of its commercial relevance, the origin of cultivated citrus species and the history of its domestication still remain an open question. Here we present a phylogenetic analysis of the chloroplast genomes of 34 citrus genotypes which constitutes the most comprehensive and detailed study to date on the evolution and variability of the genus Citrus. A statistical model was used to estimate divergence times between the major citrus groups. Additionally, a complete map of the variability across the genome of different citrus species was produced, including single nucleotide variants, heteroplasmic positions, indels and large structural variants. The distribution of all these variants provided further independent support to the phylogeny obtained. An unexpected finding was the high level of heteroplasmy found in several of the analysed genomes. The use of the complete chloroplast DNA not only paves the way for a better understanding of the phylogenetic relationships within the Citrus genus, but also provides original insights into other elusive evolutionary processes such as chloroplast inheritance, heteroplasmy and gene selection.10achloroplast10acitrus10aPhylogeny10aWGS1 aCarbonell-Caballero, José1 aAlonso, Roberto1 aIbañez, Victoria1 aTerol, Javier1 aTalon, Manuel1 aDopazo, Joaquin  uhttp://mbe.oxfordjournals.org/content/early/2015/04/27/molbev.msv082.full