“Este contenido se encuentra unicamente en inglés”

Fátima Al-Shahrour Jefe de Grupo
T +34 917 328 000 (Ext 2940)
falshahrour@cnio.es

Bioinformatics is a key discipline for understanding the cancer genome and for the future of cancer therapeutics. Bioinformatics- based approaches have the ability to transform the huge amount of biological data into comprehensive models that provide an in-depth understanding of cancer disease and the complex relationships among genotype and phenotype that are needed to identify cancer driver molecular alterations and new therapeutic targets.

The CNIO Bioinformatics Unit (BU) has several goals:

• To develop new computational methodologies and bioinformatics tools to enable the integration of biological and clinical data.
• To achieve genome analysis in cancer patients’ data to identify new biomarkers and mechanisms of drug response.
• To provide bioinformatics support with data analysis and interpretation using computational and statistical methods.
• To maintain the scientific computing facilities at the CNIO and to provide training in bioinformatics tools and methods.

Publicaciones

• Somatic genome editing with the RCAS-TVA-CRISPR-Cas9 system for precision tumor modeling.(2018)
  Oldrini B, Curiel-García Á, Marques C, Matia V, Uluçkan Ö, Graña-Castro O, Torres-Ruiz R, Rodriguez-Perales S, Huse JT, Squatrito M
  Nat Commun 9, 1466-.
• Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors.(2018)
  Djurec M, Graña O, Lee A, Troulé K, Espinet E, Cabras L, Navas C, Blasco MT, Martín-Díaz L, Burdiel M, Li J, Liu Z, Vallespinós M, Sanchez-Bueno F, Sprick MR, Trumpp A, Sainz B Jr., Al-Shahrour F, Rabadan R, Guerra C, Barbacid M.
  Proc Natl Acad Sci USA 115, E1147-E1156.
• In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer.(2018)
  Zagorac I, Fernandez-Gaitero S, Penning R, Post H, Bueno MJ, Mouron S, Manso L, Morente MM, Alonso S, Serra V, Muñoz J, Gómez-López G, Lopez-Acosta JF, Jimenez-Renard V, Gris-Oliver A, Al-Shahrour F, Piñeiro-Yañez E, Montoya-Suarez JL, Apala JV, Moreno-Torres A, Colomer R, Dopazo A, Heck AJR, Altelaar M, Quintela-Fandino M
  Nat Commun 9, 3501-.
• Terminal uridylyltransferases target RNA viruses as part of the innate immune system.(2018)
  Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosalka J, Leung C, Morgan M, Much C, Rudolph KLM, Enright AJ, O'Carroll D, Wang D, Miska EA.
  Nat Struct Mol Biol (in press).
• GENCODE reference annotation for the human and mouse genomes.(2018)
  Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P.
  Nucleic Acids Res (in press).
• APPRIS 2017: principal isoforms for multiple gene sets.(2018)
  Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML
  Nucleic Acids Res 46, D213-D217.
• PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data.(2018)
  Piñeiro-Yáñez E, Reboiro-Jato M, Gómez-López G, Perales-Patón J, Troulé K, Rodríguez JM, Tejero H, Shimamura T, López-Casas PP, Carretero J, Valencia A, Hidalgo M, Glez-Peña D, Al-Shahrour F.
  Genome Med 10, 41-.
• Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.(2018)
  Grassi L, Pourfarzad F, Ullrich S, Merkel A, Were F, Carrillo-de-Santa-Pau E, Yi G, Hiemstra IH, Tool ATJ, Mul E, Perner J, Janssen-Megens E, Berentsen K, Kerstens H, Habibi E, Gut M, Yaspo ML, Linser M, Lowy E, Datta A, Clarke L, Flicek P, Vingron M, Roos D, van den Berg TK, Heath S, Rico D, Frontini M, Kostadima M, Gut I, Valencia A, Ouwehand WH, Stunnenberg HG, Martens JHA, Kuijpers TW.
  Cell Reports 24, 2784-2794.
• CXCL5 as regulator of neutrophil function in cutaneous melanoma.(2018)
  Forsthuber A, Lipp K, Andersen L, Ebersberger S, Graña-Castro O, Ellmeier W, Petzelbauer P, Lichtenberger BM, Loewe R
  J Invest Dermatol (in press).
• Immunophenotype and Transcriptome Profile of Patients With Multiple Sclerosis Treated With Fingolimod: Setting Up a Model for Prediction of Response in a 2-Year Translational Study.(2018)
  Moreno-Torres I, González-García C, Marconi M, García-Grande A, Rodríguez-Esparragoza L, Elvira V, Ramil E, Campos-Ruíz L, García-Hernández R, Al-Shahrour F, Fustero-Torre C, Sánchez-Sanz A, García-Merino A, Sánchez López AJ.
  Front Inmmunol 9, 1963-.
• bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.(2018)
  Graña O, López-Fernández H, Fdez-Riverola F, González Pisano D, Glez-Peña D
  Bioinformatics 34, 1414-1415.
• CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation.(2018)
  Garcia-Carpizo V, Ruiz-Llorente S, Sarmentero J, Graña-Castro O, Pisano DG, Barrero MJ.
  Epigenetics & Chromatin 11, 30-.
• Loose ends: almost one in five human genes still have unresolved coding status.(2018)
  Abascal F, Juan D, Jungreis I, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML
  Nucleic Acids Res 46, 7070-7084.
• Targeted sequencing reveals low-frequency variants in EPHA genes as markers of paclitaxel-induced peripheral neuropathy.(2017)
  Apellániz-Ruiz M, Tejero H, Inglada-Pérez L, Sánchez-Barroso L, Gutiérrez-Gutiérrez G, Calvo I, Castelo B, Redondo A, García-Donás J, Romero-Laorden N, Sereno M, Merino M, Currás-Freixes M, Montero-Conde C, Mancikova V, Åvall-Lundqvist E, Green H, Al-Shahrour F, Cascon A, Robledo M, Rodriguez-Antona C
  Clin Cancer Res 23, 1227-1235.
• PheoSeq: A Targeted Next-Generation Sequencing Assay for Pheochromocytoma and Paraganglioma Diagnostics.(2017)
  Currás-Freixes M, Piñeiro-Yañez E, Montero-Conde C, Apellániz-Ruiz M, Calsina B, Mancikova V, Remacha L, Richter S, Ercolino T, Rogowski-Lehmann N, Deutschbein T, Calatayud M, Guadalix S, Álvarez-Escolá C, Lamas C, Aller J, Sastre-Marcos J, Lázaro C, Galofré JC, Patiño-García A, Meoro-Avilés A, Balmaña-Gelpi J, De Miguel-Novoa P, Balbín M, Matías-Guiu X, Letón R, Inglada-Pérez L, Torres-Pérez R, Roldán-Romero JM, Rodríguez-Antona C, Fliedner SMJ, Opocher G, Pacak K, Korpershoek E, de Krijger RR, Vroonen L, Mannelli M, Fassnacht M, Beuschlein F, Eisenhofer G, Cascón A, Al-Shahrour F, Robledo M
  J Mol Diagn 9, 575-588.
• Information Retrieval and Text Mining Technologies for Chemistry.(2017)
  Krallinger M, Rabal O, Lourenço A, Oyarzabal J, Valencia A
  Chem Rev 117, 7673-7761.
• Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells.(2017)
  Vu LP, Prieto C, Amin EM, Chhangawala S, Krivtsov A, Calvo-Vidal MN, Chou T, Chow A, Minuesa G, Park SM, Barlowe TS, Taggart J, Tivnan P, Deering RP, Chu LP, Kwon JA, Meydan C, Perales-Paton J, Arshi A, Gönen M, Famulare C, Patel M, Paietta E, Tallman MS, Lu Y, Glass J, Garret-Bakelman FE, Melnick A, Levine R, Al-Shahrour F, Järås M, Hacohen N, Hwang A, Garippa R, Lengner CJ, Armstrong SA, Cerchietti L, Cowley GS, Root D, Doench J, Leslie C, Ebert BL, Kharas MG.
  Nat Genet 49, 866-875.
• Somatic BRCA2 bi-allelic loss in the primary prostate cancer was associated to objective response to PARPi in a sporadic CRPC patient.(2017)
  Romero-Laorden N, Piñeiro-Yañez E, Gutierrez-Pecharroman A, Pacheco MI, Calvo E, Al-Shahrour F, Castro E, Olmos D
  Ann Oncol 28, 1158-1159.
• Most Alternative Isoforms Are Not Functionally Important.(2017)
  Tress ML, Abascal F, Valencia A
  Trends Biochem Sci 42, 408-410.
• Precision medicine needs pioneering clinical bioinformaticians.(2017)
  Gómez-López G, Dopazo J, Cigudosa JC, Valencia A, Al-Shahrour F
  Brief Bioinform (in press).
• Automatic identification of informative regions with epigenomic changes associated to hematopoiesis.(2017)
  Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A
  Nucleic Acids Res 45, 9244-9259.
• ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.(2017)
  Frenkel-Morgenstern M, Gorohovski A, Tagore S, Sekar V, Vazquez M, Valencia A.
  Nucleic Acids Res 45, 7094-7105.
• MIB2 variants altering NOTCH signalling result in left ventricle hypertrabeculation/non-compaction and are associated with Ménétrier-like gastropathy.(2017)
  Piccolo P, Attanasio S, Secco I, Sangermano R, Strisciuglio C, Limongelli G, Miele E, Mutarelli M, Banfi S, Nigro V, Pons T, Valencia A, Zentilin L, Campione S, Nardone G, Lynnes TC, Celestino-Soper PB, Spoonamore KG, D'Armiento FP, Giacca M, Staiano A, Vatta M, Collesi C, Brunetti-Pierri N
  Hum Mol Genet 26, 33-43.
• Genomic and molecular screenings identify different mechanisms for acquired resistance to MET inhibitors in lung cancer cells.(2017)
  Gimenez-Xavier P, Pros E, Bonastre E, Moran S, Aza A, Graña O, Gómez-López G, Derdak S, Dabad M, Esteve-Codina A, Hernandez Mora JR, Salinas-Chaparro D, Esteller M, Pisano D, Sanchez-Cespedes M
  Mol Cancer Ther 16, 1366-1376.
• CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.(2017)
  Flobak Å, Vazquez M, Lægreid A, Valencia A
  Bioinformatics 33, 2410-2412.
• Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis.(2017)
  Vargas-Parra GM, González-Acosta M, Thompson BA, Gómez C, Fernández A, Dámaso E, Pons T, Morak M, Del Valle J, Iglesias S, Velasco À, Solanes A, Sanjuan X, Padilla N, de la Cruz X, Valencia A, Holinski-Feder E, Brunet J, Feliubadaló L, Lázaro C, Navarro M, Pineda M, Capellá G
  Int J Cancer 141, 1365-1380.
• Pancreas cancer precision treatment using avatar mice from a Bioinformatics Perspective.(2017)
  Perales-Patón J, Piñeiro-Yañez E, Tejero H, López-Casas PP, Hidalgo M, Gómez-López G, Al-Shahrour F
  Public Health Genomics 20, 81-91.
• RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data.(2017)
  Rubio-Camarillo M, López-Fernández H, Gómez-López G, Carro Á, Fernández JM, Torre CF, Fdez-Riverola F, Glez-Peña D
  Comput Meth Prog Bio 138, 73-81.
• Prediction of miRNA-mRNA Interactions Using miRGate.(2017)
  Andrés-León E, Gómez-López G, Pisano DG.
  Methods Mol Biol 1580, 225-237.
• Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of observational studies.(2017)
  Catalá-López F, Hutton B, Driver JA, Page MJ, Ridao M, Valderas JM, Alonso-Arroyo A, Forés-Martos J, Martínez S, Gènova-Maleras R, Macías-Saint-Gerons D, Crespo-Facorro B, Vieta E, Valencia A, Tabarés-Seisdedos R
  Syst Rev 6, 69-.
• Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies.(2017)
  Catalá-López F, Hutton B, Driver JA, Ridao M, Valderas JM, Gènova-Maleras R, Forés-Martos J, Alonso-Arroyo A, Saint-Gerons DM, Vieta E, Valencia A, Tabarés-Seisdedos R.
  Syst Rev 6, 137-.
• Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity disorder and their first-degree relatives: a protocol for a systematic review and meta-analysis of observational studies.(2017)
  Catalá-López F, Hutton B, Page MJ, Ridao M, Driver JA, Alonso-Arroyo A, Forés-Martos J, Macías Saint-Gerons D, Vieta E, Valencia A, Tabarés-Seisdedos R
  Syst Rev 6, 189-.
• A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer.(2017)
  Sánchez-Valle J, Tejero H, Ibáñez K, Portero JL, Krallinger M, Al-Shahrour F, Tabarés-Seisdedos R, Baudot A, Valencia A
  Sci Rep 7, 4474-.
• Targeting Tumor Mitochondrial Metabolism Overcomes Resistance to Antiangiogenics.(2016)
  Navarro P, Bueno MJ, Zagorac I, Mondejar T, Sanchez J, Mourón S, Muñoz J, Gómez-López G, Jimenez-Renard V, Mulero F, Chandel NS, Quintela-Fandino M
  Cell Reports 15, 2705-2718.
• Chronic skin inflammation leads to bone loss by IL-17-mediated inhibition of Wnt signaling in osteoblasts.(2016)
  Uluçkan Ö, Jimenez M, Karbach S, Jeschke A, Graña O, Keller J, Busse B, Croxford AL, Finzel S, Koenders M, van den Berg W, Schinke T, Amling M, Waisman A, Schett G, Wagner EF
  Sci Transl Med 8, 330ra37-.
• Tissue damage and senescence provide critical signals for cellular reprogramming in vivo.(2016)
  Mosteiro LL, Pantoja C, Alcazar N, Marión RM, Chondronasiou D, Rovira M, Fernandez-Marcos PJ, Muñoz-Martin M, Blanco-Aparicio C, Pastor J, Gómez-López G, de Martino A, Blasco MA, Abad M, Serrano M
  Science 354, pii: aaf4445.-0.
• Telomeric RNAs are essential to maintain telomeres.(2016)
  Montero JJ, López de Silanes I, Graña O, Blasco MA
  Nat Communications 7, 12534-.
• Combined inhibition of DDR1 and Notch signaling is a therapeutic strategy for KRAS-driven lung adenocarcinoma.(2016)
  Ambrogio C, Gómez-López G, Falcone M, Vidal A, Nadal E, Crosetto N, Blasco RB, Fernández-Marcos PJ, Sánchez-Céspedes M, Ren X, Wang Z, Ding K, Hidalgo M, Serrano M, Villanueva A, Santamaría D, Barbacid M
  Nat Med 22, 270-277.
• Somatic embryonic FGFR2 mutations in keratinocytic epidermal nevi.(2016)
  Toll A, Fernández LC, Pons T, Groesser L, Sagrera A, Carrillo-de Santa Pau E, Vicente A, Baselga E, Vázquez M, Beltrán S, Pisano DG, Rueda D, Gut M, Pujol RM, Hafner C, Gut I, Valencia A, Real FX
  J Invest Dermatol 136, 1718-1721.
• Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance.(2016)
  Manso L, Mourón S, Tress M, Gómez-López G, Morente M, Ciruelos E, Rubio-Camarillo M, Rodriguez-Peralto JL, Pujana MA, Pisano DG, Quintela-Fandino M
  PLoS ONE 11, e0155840-.
• Deep sequencing reveals microRNAs predictive of antiangiogenic drug response.(2016)
  García-Donas J, Beuselinck B, Inglada-Pérez L, Graña O, Schöffski P, Wozniak A, Bechter O, Apellániz-Ruiz M, Leandro-García LJ, Esteban E, Castellano DE, González Del Alba A, Climent MA, Hernando S, Arranz JA, Morente M, Pisano DG, Robledo M, Rodriguez-Antona C.
  JCI Insight 7, e86051-.
• Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers.(2016)
  Pérez-Guijarro E, Karras P, Cifdaloz M, Martínez-Herranz R, Cañón E, Graña O, Horcajada-Reales C, Alonso-Curbelo D, Calvo TG, Gómez-López G, Bellora N, Riveiro-Falkenbach E, Ortiz-Romero PL, Rodríguez-Peralto JL, Maestre L, Roncador G, de Agustín Asensio JC, Goding CR, Eyras E, Megías D, Méndez R, Soengas MS
  Nat Communications 7, 13418-.
• p21Cip1 plays a critical role in the physiological adaptation to fasting through activation of PPARa.(2016)
  López-Guadamillas E, Fernández-Marcos PJ, Pantoja C, Muñoz-Martin M, Martínez D, Gómez-López G, Campos-Olivas R, Valverde AM, Serrano M
  Sci Rep 6, 34542-.
• Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML.(2016)
  Puram RV, Kowalczyk MS, de Boer CG, Schneider RK, Miller PG, McConkey M, Tothova Z, Tejero H, Heckl D, Järås M, Chen MC, Li H, Tamayo A, Cowley GS, Rozenblatt-Rosen O, Al-Shahrour F, Regev A, Ebert BL
  Cell 165, 303-316.
• Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation.(2016)
  Elf S, Abdelfattah NS, Chen E, Perales-Patón J, Rosen EA, Ko A, Peisker F, Florescu N, Giannini S, Wolach O, Morgan EA, Tothova Z, Losman JA, Schneider RK, Al-Shahrour F, Mullally A
  Cancer Discovery 6, 368-381.
• Vitamin D receptor expression and associated gene signature in tumour stromal fibroblasts predict clinical outcome in colorectal cancer.(2016)
  Ferrer-Mayorga G, Gómez-López G, Barbáchano A, Fernández-Barral A, Peña C, Pisano DG, Cantero R, Rojo F, Muñoz A, Larriba MJ.
  Gut (in press).
• Metastatic risk and resistance to BRAF inhibitors in melanoma defined by selective allelic loss of ATG5.(2016)
  García-Fernández M, Karras P, Checinska A, Cañón E, Calvo GT, Gómez-López G, Cifdaloz M, Colmenar A, Espinosa-Hevia L, Olmeda D, Soengas MS
  Autophagy 12, 1776-1790.
• Genomic profiling of patient-derived xenografts for lung cancer identifies B2M inactivation impairing immunorecognition.(2016)
  Pereira C, Gimenez-Xavier P, Pros E, Pajares MJ, Moro M, Gomez A, Navarro A, Condom E, Moran S, Gómez-López G, Graña O, Rubio-Camarillo M, Martinez-Martí A, Yokota J, Carretero J, Galbis JM, Nadal E, Pisano DG, Sozzi G, Felip E, Montuenga LM, Roz L, Villanueva A, Sanchez-Cespedes M
  Clin Cancer Res (in press).
• NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation.(2016)
  García-Carpizo V, Sarmentero J, Han B, Graña O, Ruiz-Llorente S, Pisano DG, Serrano M, Brooks HB, Campbell RM, Barrero MJ
  Sci Rep 8, 32952-.
• nextpresso: next generation sequencing expression analysis pipeline. Current Bioinformatics. Accepted for Publication(2016)
  Graña O, Rubio-Camarillo M, Fdez-Riverola F, Pisano DG, Glez-Peña D
  Current Bioinformatics (in press).
• Proteomic Profiling of Ewing Sarcoma Reveals a Role for TRAF6 in Proliferation and Ribonucleoproteins/RNA Processing.(2016)
  Madoz-Gúrpide J, Herrero-Martín D, Gómez-López G, Hontecillas-Prieto L, Biscuola M, Chamizo C, García-Domínguez D, Marcilla D, Amaral AT, Ordóñez JL and De Álava E.
  J Proteomics Bioinform 9, 166-175.
• Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation(2015)
  Foronda M, Morgado-Palacin L, Gómez-López G, Domínguez O, Pisano DG, Blasco MA
  GENOMICS DATA 6, 21-24.
• Tumor MicroRNA Expression Profiling Identifies Circulating MicroRNAs for Early Breast Cancer Detection.(2015)
  Matamala N, Vargas MT, González-Cámpora R, Miñambres R, Arias JI, Menéndez P, Andrés-León E, Gómez-López G, Yanowsky K, Calvete-Candenas J, Inglada-Pérez L, Martínez-Delgado B, Benítez J.
  Clin Chem 61, 1098-1106.
• MicroRNA expression signatures for the prediction of BRCA1/2 mutation-associated hereditary breast cancer in paraffin-embedded formalin-fixed breast tumors.(2015)
  Tanic M, Yanowski K, Gómez-López G, Socorro Rodriguez-Pinilla M, Marquez-Rodas I, Osorio A, Pisano DG, Martinez-Delgado B, Benítez J
  Int J Cancer 136, 593-602.
• DNA repair capacity is impaired in healthy BRCA1 heterozygous mutation carriers.(2015)
  Vaclová T, Gómez-López G, Setién F, Bueno JM, Macías JA, Barroso A, Urioste M, Esteller M, Benítez J, Osorio A
  Breast Cancer Res Treat 152, 271-282.
• miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors.(2015)
  Tanic M, Yanowski K, Andrés E, Gómez-López G, Socorro MR, Pisano DG, Martinez-Delgado B, Benítez J
  GENOMICS DATA 3, 75-79.
• The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies.(2015)
  Earl J, Rico D, Carrillo-de-Santa-Pau E, Rodríguez-Santiago B, Méndez-Pertuz M, Auer H, Gómez G, Grossman HB, Pisano DG, Schulz WA, Pérez-Jurado LA, Carrato A, Theodorescu D, Chanock S, Valencia A, Real FX.
  Bmc Genomics 16, 403-.
• The pluripotency factor NANOG promotes the formation of squamous cell carcinomas.(2015)
  Palla AR, Piazzolla D, Alcazar N, Cañamero M, Graña O, Gómez-López G, Dominguez O, Dueñas M, Paramio JM, Serrano M.
  Sci Rep 5, 10205-.
• MicroRNA deep-sequencing reveals master regulators of follicular and papillary thyroid tumors.(2015)
  Mancikova V, Castelblanco E, Pineiro-Yanez E, Perales-Paton J, de Cubas AA, Inglada-Perez L, Matias-Guiu X, Capel I, Bella M, Lerma E, Riesco-Eizaguirre G, Santisteban P, Maravall F, Mauricio D, Al-Shahrour F, Robledo M
  Mod Pathol 28, 748-757.
• iMSRC: converting a standard automated microscope into an intelligent screening platform.(2015)
  Carro A, Perez-Martinez M, Soriano J, Pisano DG, Megias D
  Sci Rep 5, 10502-.
• The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues.(2015)
  Cuadrado A, Remeseiro S, Graña O, Pisano, DG, Losada A
  Nucleic Acids Res 43, 3056-3067.
• MYC/PGC-1a Balance Determines the Metabolic Phenotype and Plasticity of Pancreatic Cancer Stem Cells.(2015)
  Sancho P, Burgos-Ramos E, Tavera A, Kheir TB, Jagust P, Schoenhals M, Barneda D, Sellers K, Campos-Olivas R, Graña O, Viera CR, Yuneva M, Sainz, Jr. B, Heeschen C
  Cell Metab 22, 590-605.
• Non-coding recurrent mutations in chronic lymphocytic leukaemia.(2015)
  Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, Munar M, Rubio-Pérez C, Jares P, Aymerich M, Baumann T, Beekman R, Belver L, Carrio A, Castellano G, Clot G, Colado E, Colomer D, Costa D, Delgado J, Enjuanes A, Estivill X, Ferrando AA, Gelpí JL, González B, González S, González M, Gut M, Hernández-Rivas JM, López-Guerra M, Martín-García D, Navarro A, Nicolás P, Orozco M, Payer ÁR, Pinyol M, Pisano DG, Puente DA, Queirós AC, Quesada V, Romeo-Casabona CM, Royo C, Royo R, Rozman M, Russiñol N, Salaverría I, Stamatopoulos K, Stunnenberg HG, Tamborero D, Terol MJ, Valencia A, López-Bigas N, Torrents D, Gut I, López-Guillermo A, López-Otín C, Campo E
  Nature 526, 519-524.
• Microenvironmental hCAP-18/LL-37 promotes pancreatic ductal adenocarcinoma by activating its cancer stem cell compartment.(2015)
  Sainz B Jr, Alcala S, Garcia E, Sanchez-Ripoll Y, Azevedo MM, Cioffi M, Tatari M, Miranda-Lorenzo I, Hidalgo M, Gomez-Lopez G, Cañamero M, Erkan M, Kleeff J, García-Silva S, Sancho P, Hermann PC, Heeschen C.
  Gut 64, 1921-1935.
• Intratumoral heterogeneity in EGFR mutant NSCLC results in divergent resistance mechanisms in response to EGFR tyrosine kinase inhibition.(2015)
  Soucheray M, Capelletti M, Pulido I, Kuang Y, Paweletz CP, Becker JH, Kikuchi E, Xu C, Patel TB, Al-Shahrour F, Carretero J, Wong KK, Janne PA, Shapiro GI, Shimamura T
  Cancer Res 75, 4372-4383.
• Partial Loss of Rpl11 in Adult Mice Recapitulates Diamond-Blackfan Anemia and Promotes Lymphomagenesis.(2015)
  Morgado-Palacin L, Vareti G, Llanos S, Gomez-Lopez G, Martinez D, Serrano M
  Cell Reports 13, 712-722.
• High burden of copy number alterations and c-MYC amplification in prostate cancer from BRCA2 germline mutation carriers.(2015)
  Castro E, Jugurnauth-Little S, Karlsson Q, Al-Shahrour F, Piñeiro-Yañez E, Van de Poll F, Leongamornlert D, Dadaev T, Govindasami K, Guy M, Eeles R, Kote-Jarai, UKGPCS, EMBRACE and IMPACT studies.
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• Nuclear DICKKOPF-1 as a biomarker of chemoresistance and poor clinical outcome in colorectal cancer.(2015)
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  Oncotarget 6, 5903-5917.
• miRGate: a curated database of human, mouse and rat miRNA-mRNA targets.(2015)
  Andres Leon E, Gonzalez Pena D, Gomez-Lopez G, Pisano DG
  DATABASE : THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015, bav035-.
• Inhibition of De Novo NAD+ Synthesis by Oncogenic URI Causes Liver Tumorigenesis through DNA Damage.(2014)
  Tummala KS, Gomes AL, Yilmaz , Graña O, Bakiri L, Ruppen I, Ximénez-Embún P, Sheshappanavar V, Rodriguez-Justo M, Pisano DG, Wagner EF, Djouder N
  Cancer Cell 26, 826-839.
• Fos-dependent induction of Chk1 protects osteoblasts from replication stress.(2014)
  Schulze J, Lopez-Contreras AJ, Uluçkan O, Graña-Castro O, Fernandez-Capetillo O, Wagner EF
  Cell Cycle 13, 1980-1986.
• Identification of TERRA locus unveils a telomere protection role through association to nearly all chromosomes.(2014)
  de Silanes IL, Graña O, De Bonis ML, Dominguez O, Pisano DG, Blasco MA
  Nat Communications 5, 4723-.
• Sox4 links tumor suppression to accelerated aging in mice by modulating stem cell activation.(2014)
  Foronda M, Martínez P, Schoeftner S, Gómez-López G, Schneider R, Flores JM, Pisano DG, Blasco MA
  Cell Reports 8, 487-500.
• Genome-wide analysis of in vivo TRF1 binding to chromatin restricts its location exclusively to telomeric repeats.(2014)
  Garrobo I, Marión RM, Domínguez O, Pisano DG, Blasco MA
  Cell Cycle 13, 3742-3749.
• Exome sequencing reveals novel and recurrent mutations with clinical impact in blastic plasmacytoid dendritic cell neoplasm.(2014)
  Menezes J, Acquadro F, Wiseman M, Gómez-López G, Salgado RN, Talavera-Casañas JG, Buño I, Cervera JV, Montes-Moreno S, Hernández-Rivas JM, Ayala R, Calasanz MJ, Larrayoz MJ, Brichs LF, Gonzalez-Vicent M, Pisano DG, Piris MA, Alvarez S, Cigudosa JC.
  Leukemia 28, 823-829.
• Lineage-restricted function of the pluripotency factor NANOG in stratified epithelia.(2014)
  Piazzolla D, Palla AR, Pantoja C, Cañamero M, de Castro IP, Ortega S, Gómez-López G, Dominguez O, Megías D, Roncador G, Luque-Garcia JL, Fernandez-Tresguerres B, Fernandez AF, Fraga MF, Rodriguez-Justo M, Manzanares M, Sánchez-Carbayo M, García-Pedrero JM, Rodrigo JP, Malumbres M, Serrano M
  Nat Communications 5, 4226-.
• PLCG1 mutations in cutaneous T-cell lymphomas.(2014)
  Vaqué JP, Gómez-López G, Monsálvez V, Varela I, Martínez N, Pérez C, Domínguez O, Graña O, Rodríguez-Peralto JL, Rodríguez-Pinilla SM, González-Vela C, Rubio-Camarillo M, Martín-Sánchez E, Pisano DG, Papadavid E, Papadaki T, Requena L, García-Marco JA, Méndez M, Provencio M, Hospital M, Suárez-Massa D, Postigo C, San Segundo D, López-Hoyos M, Ortiz-Romero PL, Piris MA, Sánchez-Beato M.
  Blood 123, 2034-2043.
• RAB7 controls melanoma progression by exploiting a lineage-specific wiring of the endolysosomal pathway.(2014)
  Alonso-Curbelo D, Riveiro-Falkenbach E, Perez-Guijarro E, Cifdaloz M, karras P, Osterloh L, Megías D, Cañón E, Calvo TG, Olmeda D, Gómez-Lopez G, Graña O, Sánchez-Arévalo VJ, Pisano DG, Wang H-W, Ortiz-Romero P, Tormo D, Hoeck K, Rodríguez-Peralto JL, Joyce JA, Soengas MS
  Cancer Cell 26, 61-76.
• Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor.(2014)
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  Cancer Cell 26, 909-922.
• Lipoprotein(a) levels in familial hypercholesterolemia: an important predictor of cardiovascular disease independent of the type of LDL receptor mutation.(2014)
  Alonso R, Andres E, Mata N, Fuentes-Jiménez F, Badimón L, López-Miranda J, Padró T, Muñiz O, Díaz-Díaz JL, Mauri M, Ordovás JM, Mata P1; SAFEHEART Investigators
  J Am Coll Cardiol 63, 1982-1989.
• Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia.(2014)
  Järås M, Miller PG, Chu LP, Puram RV, Fink EC, Schneider RK, Al-Shahrour F, Peña P, Breyfogle LJ, Hartwell KA, McConkey ME, Cowley GS, Root DE, Kharas MG, Mullally A, Ebert BL
  J Exp Med 211, 605-612.
• Musashi-2 controls cell fate, lineage bias, and TGF-ß signaling in HSCs.(2014)
  Park SM, Deering RP, Lu Y, Tivnan P, Lianoglou S, Al-Shahrour F, Ebert BL, Hacohen N, Leslie C, Daley GQ, Lengner CJ, Kharas MG
  J Exp Med 211, 71-87.
• Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis.(2014)
  Rampal R, Al-Shahrour F, Abdel-Wahab O, Patel JP, Brunel JP, Mermel CH, Bass AJ, Pretz J, Ahn J, Hricik T, Kilpivaara O, Wadleigh M, Busque L, Gilliland DG, Golub TR, Ebert BL, Levine RL
  Blood 123, e123-e133.
• FireDB: a compendium of biological and pharmacologically relevant ligands.(2014)
  Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML
  Nucleic Acids Res 42, D267-D272.
• The Epstein Barr-encoded BART-6-3p microRNA affects regulation of cell growth and immuno response in Burkitt lymphoma.(2014)
  Ambrosio MR, Navari M, Di Lisio L, Leon EA, Onnis A, Gazaneo S, Mundo L, Ulivieri C, Gomez G, Lazzi S, Piris MA, Leoncini L, De Falco G
  Infect Agent Cancer 9, 12-.
• RAP1 protects from obesity through its extratelomeric role regulating gene expression.(2013)
  Martínez P, Gómez-López G, García F, Mercken E, Mitchell S, Flores JM, De Cabo R, Blasco MA
  Cell Reports 3, 2059-2074.
• ARF triggers senescence in Brca2-deficient cells by altering the spectrum of p53 transcriptional targets.(2013)
  Carlos AR, Escandell JM, Kotsantis P, Suwaki N, Bouwman P, Badie S, Folio C, Benitez J, Gomez-Lopez G, Pisano DG, Jonkers J, Tarsounas M
  Nat Communications 4, 2697-.
• MicroRNA-based molecular classification of non-BRCA1/2 hereditary breast tumours.(2013)
  Tanic M, Andrés E, M Rodriguez-Pinilla S, Marquez-Rodas I, Cebollero-Presmanes M, Fernandez V, Osorio A, Benítez J, Martinez-Delgado B.
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• Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy.(2013)
  Balbás-Martínez C, Sagrera A, Carrillo-de-Santa-Pau E, Earl J, Márquez M, Vazquez M, Lapi E, Castro-Giner F, Beltran S, Bayés M, Carrato A, Cigudosa JC, Domínguez O, Gut M, Herranz J, Juanpere N, Kogevinas M, Langa X, López-Knowles E, Lorente JA, Lloreta J, Pisano DG, Richart L, Rico D, Salgado RN, Tardón A, Chanock S, Heath S, Valencia A, Losada A, Gut I, Malats N, Real FX
  Nat Genet 45, 1464-1469.
• Downregulation of specific miRNAs in hyperdiploid multiple myeloma mimics the oncogenic effect of IgH translocations occurring in the non-hyperdiploid subtype.(2013)
  Rio-Machin A, Ferreira BI, Henry T, Gómez-López G, Agirre X, Alvarez S, Rodriguez-Perales S, Prosper F, Calasanz MJ, Martínez J, Fonseca R, Cigudosa JC
  Leukemia 27, 925-931.
• CSF3R T618I co-occurs with mutations of splicing and epigenetic genes and with a new PIM3 truncated fusion gene in chronic neutrophilic leukemia.(2013)
  Menezes J, Makishima H, Gomez I, Acquadro F, Gómez-López G, Graña O, Dopazo A, Alvarez S, Trujillo M, Pisano DG, Maciejewski JP, Cigudosa JC
  Blood Cancer J 3, e158-.
• ASXL1, TP53 and IKZF3 mutations are present in the chronic phase and blast crisis of chronic myeloid leukemia.(2013)
  Menezes J, Salgado RN, Acquadro F, Gómez-López G, Carralero MC, Barroso A, Mercadillo F, Espinosa-Hevia L, Talavera-Casañas JG, Pisano DG, Alvarez S, Cigudosa JC
  Blood Cancer J 3, e157-.
• ARID1A alterations are associated with FGFR3-wild type, poor-prognosis, urothelial bladder tumors.(2013)
  Balbás-Martínez C, Rodríguez-Pinilla M, Casanova A, Domínguez O, Pisano DG, Gómez G, Lloreta J, Lorente JA, Malats N, Real FX
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• Reprogramming in vivo produces teratomas and iPS cells with totipotency features.(2013)
  Abad M, Mosteiro Ll, Pantoja C, Cañamero M, Rayon T, Ors I, Graña O, Megías D, Domínguez O, Martinez D, Manzanares M, Ortega S, Serrano M
  Nature 502, 340-345.
• SIRT1 promotes thyroid carcinogenesis driven by PTEN deficiency.(2013)
  Herranz D, Maraver A, Cañamero M, Gómez-López G, Inglada-Pérez L, Robledo M, Castelblanco E, Matias-Guiu X, Serrano M
  Oncogene 32, 4052-4056.
• Differential gene expression of medullary thyroid carcinoma reveals specific markers associated with genetic conditions.(2013)
  Maliszewska A, Leandro-Garcia LJ, Castelblanco E, Macià A, de Cubas A, Goméz-López G, Inglada-Pérez L, Álvarez-Escolá C, De la Vega L, Letón R, Gómez-Graña Á, Landa I, Cascón A, Rodríguez-Antona C, Borrego S, Zane M, Schiavi F, Merante-Boschin I, Pelizzo MR, Pisano DG, Opocher G, Matias-Guiu X, Encinas M, Robledo M
  Am J Pathol 182, 356-362.
• INK4a/ARF limits the expansion of cells suffering from replication stress.(2013)
  Monasor A, Murga M, Lopez-Contreras AJ, Navas C, Gomez G, Pisano DG, Fernandez-Capetillo O
  Cell Cycle 12, 1948-1954.
• Programmed Cell Senescence during Mammalian Embryonic Development.(2013)
  Muñoz-Espín D, Cañamero M, Maraver A, Gómez-López G, Contreras J, Murillo-Cuesta S, Rodríguez-Baeza A, Varela-Nieto I, Ruberte J, Collado M, Serrano M
  Cell 155, 1104-1118.
• ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.(2013)
  Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A
  Nucleic Acids Res 41, D142-D151.
• RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.(2013)
  Rubio-Camarillo M, Gómez-López G, Fernández JM, Valencia A, Pisano DG
  Bioinformatics 29, 1687-1689.
• De novo assembly and functional annotation of the olive (Olea europaea) transcriptome.(2013)
  Muñoz-Mérida A, González-Plaza JJ, Cañada A, Blanco AM, García-López Mdel C, Rodríguez JM, Pedrola L, Sicardo MD, Hernández ML, De la Rosa R, Belaj A, Gil-Borja M, Luque F, Martínez-Rivas JM, Pisano DG, Trelles O, Valpuesta V, Beuzón CR
  Dna Res 20, 93-108.
• New insights into FoxE1 functions: identification of direct FoxE1 targets in thyroid cells.(2013)
  Fernández LP, López-Márquez A, Martínez AM, Gómez-López G, Santisteban P
  PLoS ONE 8, e62849-.