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When catastrophe strikes a cell

Jose M. C. Tubio, Xavier Estivill
2011 Nature  
Jose M. C.  ...  Tubio and Xavier Estivill are in the Genes and Disease Programme, Center for Genomic Regulation (CRG) and Pompeu Fabra University, Barcelona, Catalonia 08003, Spain. e-mail: xavier.estivill@crg.cat Figure  ... 
doi:10.1038/470476a pmid:21350479 fatcat:mh6pwqkbqrck3i75i4guwtnzc4

Somatic structural variation and cancer

Jose M. C. Tubio
2015 Briefings in Functional Genomics  
Jose Tubio is a 'Marie Curie' postdoctoral fellow at the Wellcome Trust Sanger Institute, and a member of the PanCancer initiative.  ...  Tubio et al. [51] analyzed the mechanism of L1 3 0 -transductions in whole-genome sequencing data from 244 cancer patients from 12 cancer types.  ...  Four chromosomes (A, B, C, D) are represented.  ... 
doi:10.1093/bfgp/elv016 pmid:25903743 fatcat:2k5n236vajetllt2pxv5ujyxhq

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

Xiaofang Jiang, Ashley Peery, A Hall, Atashi Sharma, Xiao-Guang Chen, Robert M Waterhouse, Aleksey Komissarov, Michelle M Riehl, Yogesh Shouche, Maria V Sharakhova, Dan Lawson, Nazzy Pakpour (+23 others)
2014 Genome Biology  
doi:10.1186/preaccept-1262842421127991 pmid:25244985 pmcid:PMC4195908 fatcat:oldmbrqdprg2rlo5jgxq66t5ri

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

Xiaofang Jiang, Ashley Peery, A Brantley Hall, Atashi Sharma, Xiao-Guang Chen, Robert M Waterhouse, Aleksey Komissarov, Michelle M Riehle, Yogesh Shouche, Maria V Sharakhova, Dan Lawson, Nazzy Pakpour (+23 others)
2014 Genome Biology  
Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range. Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was
more » ... duced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism. Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.
doi:10.1186/s13059-014-0459-2 pmid:25244985 pmcid:PMC4195908 fatcat:pkunw4fvwvf23mk5yp3bwaqone

PeSV-Fisher: Identification of Somatic and Non-Somatic Structural Variants Using Next Generation Sequencing Data

Geòrgia Escaramís, Cristian Tornador, Laia Bassaganyas, Raquel Rabionet, Jose M. C. Tubio, Alexander Martínez-Fundichely, Mario Cáceres, Marta Gut, Stephan Ossowski, Xavier Estivill, Jeong-Sun Seo
2013 PLoS ONE  
Third, a GC content normalization is applied to each window i based on the following adjustment: r à i~r i | m=m GC ð Þ , where m is the median of read-depth counts across all windows and m GC is the median  ...  To liken the data to a normal distribution, we further use the square-root transformation and use the global median as a shift parameter towards 0: r Ãà i~ffi ffiffiffi r à i p { ffiffiffiffi m p .  ... 
doi:10.1371/journal.pone.0063377 pmid:23704902 pmcid:PMC3660373 fatcat:c7andd5r75enbm36taqjc6op3u

Characterisation of the genomic landscape ofCRLF2-rearranged acute lymphoblastic leukemia

Lisa J. Russell, Lisa Jones, Amir Enshaei, Stefano Tonin, Sarra L. Ryan, Jeyanthy Eswaran, Sirintra Nakjang, Elli Papaemmanuil, Jose M. C. Tubio, Adele K. Fielding, Ajay Vora, Peter J. Campbell (+2 others)
2017 Genes, Chromosomes and Cancer  
V C 2017 Wiley Periodicals, Inc. genome and exome sequencing data are available using EGA accession numbers EGAD00001002007 and EGAD00001002008, respectively.  ...  mutations between IGH-and P2RY8-CRLF2 (17% vs. 19%, P 5 .46) or DS and non-DS patients (JAK2 Ex14, 44% vs. 35%, P 5 .613; JAK1 Ex14, 17% vs. 11%, P 5 1; Supporting Information Table 5 ; Figure 1B ,C)  ... 
doi:10.1002/gcc.22439 pmid:28033648 pmcid:PMC5396319 fatcat:qpyfmpdr4zaazbum7qk2mpzqwa

VAV2 signaling promotes regenerative proliferation in both cutaneous and head and neck squamous cell carcinoma

L Francisco Lorenzo-Martín, Natalia Fernández-Parejo, Mauricio Menacho-Márquez, Sonia Rodríguez-Fdez, Javier Robles-Valero, Sonia Zumalave, Salvatore Fabbiano, Gloria Pascual, Juana M García-Pedrero, Antonio Abad, María C García-Macías, Nazareno González (+10 others)
2020 Nature Communications  
This function, which is both catalysis- and RHO GTPase-dependent, is mediated by c-Myc- and YAP/TAZ-dependent transcriptomal programs associated with regenerative proliferation and cell undifferentiation  ...  Acknowledgements We thank M. Blázquez and CIC facilities' personnel for lab work and core unit technical assistance, respectively. X.R.B. is supported by grants from Worldwide Cancer Research (14-  ...  2 8 L + R h o A F 3 0 L + C d c 4 2 F 2 8 L + V a v 2 O n c + E 2 0 0 A + V a v 2 O n c + E 2 0 0 A M o c k + V a v 2 O n c + R a c 1 F 2 8 L + R a c 1 F 2 8 L + R h o A F 3 0 L + R h o A F 3 0 L + C d  ... 
doi:10.1038/s41467-020-18524-3 pmid:32963234 pmcid:PMC7508832 fatcat:bpjgefmtdvbrll6jokckgfnopu

Genomic landscape and chronological reconstruction of driver events in multiple myeloma

Francesco Maura, Niccoló Bolli, Nicos Angelopoulos, Kevin J. Dawson, Daniel Leongamornlert, Inigo Martincorena, Thomas J. Mitchell, Anthony Fullam, Santiago Gonzalez, Raphael Szalat, Federico Abascal, Bernardo Rodriguez-Martin (+16 others)
2019 Nature Communications  
46 C H IS T1 H 1E LT B A C TG 1 E G R 1 P R K D 2 FG FR 3 K LH L6 M A X IR F4 P A B P C 1 K M T2 B S P 14 0 P R D M 1 S E TD 2 C Y LD P IM 1 P TP N 11 S A  ...  M H D 1 C C N D 1 N FK B 2 R P L1 0 TC L1 A TR A F2 R FT N 1 TB C 1D 29 B TG 1 ZN F2 92 B C L7 A H IS T1 H 1B R B 1 B H LH E 41 N FK B IA T1 R P S 3A TG D S D TX 1 FU  ... 
doi:10.1038/s41467-019-11680-1 pmid:31444325 pmcid:PMC6707220 fatcat:cy27chxv5rchbis5t7ytwceo5u

A second transmissible cancer in Tasmanian devils

Ruth J. Pye, David Pemberton, Cesar Tovar, Jose M. C. Tubio, Karen A. Dun, Samantha Fox, Jocelyn Darby, Dane Hayes, Graeme W. Knowles, Alexandre Kreiss, Hannah V. T. Siddle, Kate Swift (+3 others)
2015 Proceedings of the National Academy of Sciences of the United States of America  
(B) Microsatellite genotypes at nine polymorphic microsatellite loci (L, E, D, N, C, M, J, F, and K).  ...  The lengths of the two (L, D, N, M, J, F, and K) or three (E and C) alleles found at each locus and their color codes are shown on the left, and their genotypes in DFT1 tumors, DFT2 tumors, DFT2 hosts,  ... 
doi:10.1073/pnas.1519691113 pmid:26711993 pmcid:PMC4720317 fatcat:xhbepr6mjvesjjmk2techcr4gq

The evolutionary history of lethal metastatic prostate cancer

Gunes Gundem, Peter Van Loo, Barbara Kremeyer, Ludmil B. Alexandrov, Jose M. C. Tubio, Elli Papaemmanuil, Daniel S. Brewer, Heini M. L. Kallio, Gunilla Högnäs, Matti Annala, Kati Kivinummi, Victoria Goody (+18 others)
2015 Nature  
C!are!annotated!in!the!2dUDP!plot!(j).!Numbers!of!substitutions!in! WGS! data! assigned! to! each! subclone! are! plotted! in! (c)! and! (k).! VAFs! from! WGS! and! ! FUNDING$ This!study!was!  ...  M.!carried!out!laboratory!analysis.!E.P.,!D.B.,!H.C.W.,!C.C.,!P.J.C.!and!all!authors! edited!the!paper.!D.B.,!Z.KUJ.,!H.C.W.,!G.G.!and!D.C.W.!coordinated!the!study.!H.M.L.K.!and! cluster! is!  ... 
doi:10.1038/nature14347 pmid:25830880 pmcid:PMC4413032 fatcat:sgurvcnsibappdqsqnw5gsq3oq

Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma

Patrick S Tarpey, Sam Behjati, Susanna L Cooke, Peter Van Loo, David C Wedge, Nischalan Pillay, John Marshall, Sarah O'Meara, Helen Davies, Serena Nik-Zainal, David Beare, Adam Butler (+22 others)
2013 Nature Genetics  
Chondrosarcoma (CHS) is a heterogeneous collection of malignant bone tumours and is the second most common primary malignancy of bone after osteosarcoma. Recent work has identified frequent, recurrent mutations in IDH1/2 in nearly half of central CHS. However, there has been little systematic genomic analysis of this tumour type and thus the contribution of other genes is unclear. Here we report comprehensive genomic analyses of 49 cases of CHS. We identified hypermutability of the major
more » ... ge collagen COL2A1 with insertions, deletions and rearrangements identified in 37% of cases. The patterns of mutation were consistent with selection for variants likely to impair normal collagen biosynthesis. In addition we identified mutations in IDH1/2 (59%), TP53 (20%), the RB1 pathway (33%) and hedgehog signaling (18%).
doi:10.1038/ng.2668 pmid:23770606 pmcid:PMC3743157 fatcat:6kwx35jiojgwhon2dotlltpezm

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

Grace Collord, Patrick Tarpey, Natalja Kurbatova, Inigo Martincorena, Sebastian Moran, Manuel Castro, Tibor Nagy, Graham Bignell, Francesco Maura, Matthew D. Young, Jorge Berna, Jose M. C. Tubio (+27 others)
2018 Scientific Reports  
The majority of the mutations were substitutions, 72% of which were C > T transitions.  ...  (c) Dendrogram obtained by unsupervised clustering annotated with clinical and genomic features.  ... 
doi:10.1038/s41598-018-31659-0 pmid:30202034 pmcid:PMC6131140 fatcat:ubns44u2dzfwhbcyfk25rj4opq

CDKN2A deletion is a frequent event associated with poor outcome in patients with peripheral T-cell lymphoma not otherwise specified (PTCL-NOS)

Francesco Maura, Anna Dodero, Cristiana Carniti, Niccolò Bolli, Martina Magni, Valentina Monti, Antonello Cabras, Daniel Leongamornlert, Federico Abascal, Benjamin Diamond, Bernardo Rodriguez-Martin, Jorge Zamora (+7 others)
2020 Haematologica  
B-C) Representative examples of CDKN2/p16 IHC results in cases with normal (B) and deleted (C) alleles.  ...  This difference was significant (p = 0.01, Student t-test)(Figure 3A-C).  ... 
doi:10.3324/haematol.2020.262659 pmid:33054126 pmcid:PMC8561277 fatcat:uudw2dowvjdy5nhyrjsy476nzu

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures [article]

Grace Collord, Patrick Tarpey, Natalja Kurbatova, Inigo Martincorena, Sebastian Moran, Manuel Castro, Tibor Nagy, Graham Bignell, Francesco Maura, Jorge Berna, Jose M. Tubio, Chris E. McMurran (+26 others)
2017 bioRxiv   pre-print
http://dx.doi.org/10.1101/146811 doi: bioRxiv preprint first posted online Jun. 6, 2017; 12 Tubio, J. M. et al. Mobile DNA in cancer.  ...  . & Georgescu, M. M. Overexpression of ezrin inactivates 576 NF2 tumor suppressor in glioblastoma. Neuro Oncol 12, 528-539, doi:10.1093/neuonc/nop060 Shaw, R. J. et al.  ... 
doi:10.1101/146811 fatcat:y46dx3faxjagbfanx7b2bjjbfu

The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

Maximilian R. Stammnitz, Tim H.H. Coorens, Kevin C. Gori, Dane Hayes, Beiyuan Fu, Jinhong Wang, Daniel E. Martin-Herranz, Ludmil B. Alexandrov, Adrian Baez-Ortega, Syd Barthorpe, Alexandra Beck, Francesca Giordano (+14 others)
2018 Cancer Cell  
N., Bai, S., Zhao, C., Wang, H., Wang, J., Xu, L., Sakabe, M., Zhou, W., Xin, M., et al. (2017) .  ...  Murchison, E.P., Tovar, C., Hsu, A., Bender, H.S., Kheradpour, P., Rebbeck, C.A., Obendorf, D., Conlan, C., Bahlo, M., Blizzard, C.A., et al. (2010).  ... 
doi:10.1016/j.ccell.2018.03.013 pmid:29634948 pmcid:PMC5896245 fatcat:gwntdfnmuffs3iiare7infri7m
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