Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state.
Cerezo-Wallis D, Contreras-Alcalde M, Troulé K, Catena X, Mucientes Cynthia, G. Calvo T, Cañón E, Tejedo, C, Pennacchi C. P, Hogan S, Kölblinger P, Tejero H, Chen X.A, Ibarz N, Graña-Castro O, Martinez L, Muñoz J, Ortiz-Romero P, Rodriguez-Peralto JL, Gómez-López G, Al-Shahrour F, Rabadán R, Levesque MP, Olmeda D, S.Soengas M.
Nat Med. 2020. Oct. 19. doi: 10.1038/s41591-020-1073-3.
PMID: 33077955
An analysis of tissue-specific alternative splicing at the protein level.
Rodriguez JM, Pozo F, Di Domenico T, Vazquez J, Tress L.M.
PLoS Comput Biol. 2020 Oct 5. Online ahead of print. doi: 10.1371/journal.pcbi.1008287.
PMID: 33017396
Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases.
Lynch J C, Bernard R, Martínez-Val A, Shahbazi N. M, Nóbrega-Pereira S, Calvo I, Blanco-Aparicio C, Tarantino C, Garreta E, Richart-Ginés L, Alcazar N, Graña-Castro O, Gómez-López G, Aksoy I, Muñoz-Martín M, Martínez S, Ortega S, Prieto S, Simboeck E, Camasses A, Attolini Stephan-Otto C, Fernandez F.A, Sierra I.M, Fraga F.M, Pastor J, Fisher D, Montserrat N, Savatier P, Muñoz J, Zernicka-Goetz M, Serrano M.
Nat Cell Biol. 2020 Sep 28. Online ahead of print. doi: 10.1038/s41556-020-0573-1.
PMID: 32989249
MicroRNA expression profiles in molecular subtypes of clear-cell renal cell carcinoma are associated with clinical outcome and repression of specific mRNA targets.
Verbiest A, Van Hoef V, Rodriguez-Antona C, García-Donas J, Graña-Castro O, Albersen M, Baldewijns M, Laenen A, Roussel E, Schöffski P, Wozniak A, Caruso S, Couchy G, Zucman-Rossi J, Beuselinck B.
PLoS One. 2020 Sep 11;15(9):e0238809. doi: 10.1371/journal.pone.0238809.
PMID: 32915890
Tumor regression and resistance mechanisms upon CDK4 and RAF1 inactivation in KRAS/P53 mutant lung adenocarcinomas.
Esteban-Burgos L, Wang H, Nieto P, Zheng J, Blanco-Aparicio C, Varela C, Gómez-López G, Fernández-García F, Sanclemente M, Guerra C, Drosten M, Galán J, Caleiras E, Martínez-Torrecuadrada J, Fajas L, Peng S-B, Santamaría D, Musteanu M, Barbacid M.
PNAS. 2020 Sept. 10. Online ahead of print. doi: 10.1073/pnas.2002520117.
PMID: 32913049
DREIMT: a drug repositioning database and prioritization tool for immunomodulation.
Troulé K, López-Fernández H, García-Martín S, Reboiro-Jato M, Carretero-Puche C, Martorell-Marugán J, Martín-Serrano G, Carmona-Sáez P, González-Peña D, Al-Shahrour F, Gómez-López G.
Bioinformatics. 2020 Aug 20. Online ahead of print. doi: 10.1093/bioinformatics/btaa727.
PMID: 32818254
TGF-β induced IGFBP-3 is a key paracrine factor from activated pericytes that promotes colorectal cancer cell migration and invasion.
Navarro R, Tapia-Galiseo A, Martín-García L, Tarín C, Corbacho C, Gómez-López G, Sánchez-Tirado E, Campuzano S, González-Cortés A, Yáñez-Sedeño P, Compte M, Álvarez-Vallina L, Sanz L.
Mol Oncol. 2020 Aug 7. Online ahead of print. doi: 10.1002/1878-0261.12779.
PMID: 32767843
Perspectives on ENCODE.
ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM.
Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29. Erratum in: Nature. 2022 May;605(7909):E4.
PMID: 32728248
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z.
Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. Erratum in: Nature. 2022 May;605(7909):E3.
PMID: 32728249
A user guide for the online exploration and visualization of PCAWG data.
Goldman M.J, Zhan J, A.Fonseca N, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, D. O’Connor B, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Fülgrabe A, Al-Shahrour F, Keays M, Haussler D, N.Weinstein J, Huber W, Valencia A, J. Park P, Papatheodorou I, Zhu J, Ferretti V, Vazquez M.
Nat. Comm. 2020 Jul 7; 11, 3400. doi: 10.1038/s41467-020-16785-6.
PMID: 32636365
Transient exposure to miR-203 enhances the differentiation capacity of established pluripotent stem cells.
Salazar-Roa M, Trakala M, Álvarez-Fernandez M, Valdés-Mora F, Zhong C, Muñoz J, Yu Y, J Peters T, Graña-Castro O, Serrano R, Zapatero-Solana E, Abad M, Bueno M.J, Gómez de Cedrón M, Fernández-Piqueras J, Serrano M, Blasco M.A, Wang D-Z, J Clark S, Izpisua-Belmonte JC, Ortega S, Malumbres
M. Embo J. 2020 Jul 2; Online ahead of print. doi: 10.15252/embj.2019104324.
PMID: 32614092
The GATA3 X308_Splice breast cancer mutation is a hormone context-dependent oncogenic driver.
Hruschka N, Kalisz M, Subijana M, Graña-Castro O, Del Cano-Ochoa F, Paré Brunet L, Chernukhin I, Sagrera A, De Reynies A, Kloesch B, Chin S-F, Burgués O, Andreu D, Bermejo B, Cejalvo JM, Sutton J, Caldas C, Ramón-Maiques S, S Carroll J, Prat A, X Real F, Martinelli P.
Oncogene. 2020 Jun 25; Online ahead of print. doi: 10.1038/s41388-020-1376-3.
PMID: 32587399
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships.
Sánchez-Valle J, Tejero H, Fernández JM, Juan D, Urda-García B, Capella-Gutiérrez S, Al-Shahrour F, Tabarés-Seisdedos R, Baudot A, Pancaldi V, Valencia A.
Nat Commun. 2020 Jun 5;11(1):2854. doi: 10.1038/s41467-020-16540-x.
PMID: 32504002
Discovery of new targets to control metastasis in pancreatic cancer by single cell transcriptomics analysis of circulating tumor cells.
Dimitrov-Markov S, Perales-Patón J, Bockorny B, Dopazo A, Muñoz M, Baños N, Bonilla V, Menendez C, Duran Y, Huang L, Perea S, Muthuswamy SK, Al-Shahrour F, Lopez-Casas PP, Hidalgo M.
Mol Cancer Ther. 2020 Jun 4:molcanther.1166.2020. doi: 10.1158/1535-7163.MCT-19-1166. Online ahead of print.
PMID: 32499301
Autocrine CCL5 effect mediates trastuzumab resistance by ERK pathway activation in HER2-positive breast cancer.
Zazo S, González-Alonso P, Martin-Aparicio E, Chamizo C, Luque M, Sanz-Alvarez M, Mínguez P, Gómez-López G, Cristobal I, Caramés C, García-Foncillas J, Eroles P, Lluch A, Arpí O, Rovira A, Albanell J, Madoz-Gúrpide J, Rojo F.
Mol Cancer Ther. 2020 May 13. pii: molcanther.1172.2019.
PMID: 32404410
How can bioinformatics contribute to the routine application of personalized precision medicine?
Carretero-Puche C, García-Martín S, García-Carbonero R, Gómez-López G, Al-Shahrour, F.
Expert Rev Precis Med. 2020 May 7. doi:10.1080/23808993.2020.1758062. Link
Metatax: Metataxonomics with a Compi-Based Pipeline for Precision Medicine.
Osvaldo Graña-Castro, Hugo López-Fernández, Alba Nogueira-Rodríguez, Florentino Fdez-Riverola, Fátima Al-Shahrour, Daniel Glez-Peña.
Interdiscip Sci Comput Life Sci. 2020 Apr 30; doi:10.1007/s12539-020-00368-6.
PMID: 32350726
The Hippo Pathway Transducers YAP1/TEAD Induce Acquired Resistance to Trastuzumab in HER2-Positive Breast Cancer.
González-Alonso P, Zazo S, Martín-Aparicio E, Luque M, Chamizo C, Sanz-Álvarez M, Minguez P, Gómez-López G, Cristóbal I, Caramés C, García-Foncillas J, Eroles P, Lluch A, Arpí O, Rovira A, Albanell J, Piersma SR, Jimenez CR, Madoz-Gúrpide J, Rojo F.
Cancers 2020, 12(5), 1108.
PMID: 32365528
CDK4/6 Inhibitors Impair Recovery from Cytotoxic Chemotherapy in Pancreatic Adenocarcinoma.
Salvador-Barbero, B., Álvarez-Fernández, M., Zapatero-Solana, E., El Bakkali, A., Menéndez, M. del C., López-Casas, P.P., Di Domenico, T., Xie, T., VanArsdale, T., Shields, D.J., Hidalgom M, Malumbres, M.
Cancer Cell. 2020 Feb. doi: 10.1016/j.ccell.2020.01.007.
PMID: 32109375
The mTOR Pathway Is Necessary for Survival of Mice With Short Telomeres.
Iole Ferrara-Romeo, Paula Martinez, Sarita Saraswati, Kurt Whittemore, Osvaldo Graña-Castro, Lydia Thelma Poluha, Rosa Serrano, Elena Hernandez-Encinas, Carmen Blanco-Aparicio, Juana Maria Flores, Maria A Blasco.
Nature Communications. 2020 Mar 3; 11 (1), 1168. doi: 10.1038/s41467-020-14962-1.
PMID: 32127537
Pan-cancer analysis of whole genomes.
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
Nature 2020; 578, 82–93. doi: 10.1038/s41586-020-1969-6.
PMID: 32025007
Few SINEs of Life: Alu Elements Have Little Evidence For Biological Relevance Despite Elevated Translation.
Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M, Mudge JM, Tress ML.
NAR Genom Bioinform. 2020 Mar;2(1):lqz023.
PMID: 31886458
