Fátima Al-Shahrour Head of Unit
T +34 (+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.

Publications

• GENCODE reference annotation for the human and mouse genomes(2019)
  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 47, D776-D776.
• CXCL5 as regulator of neutrophil function in cutaneous melanoma(2019)
  Forsthuber A, Lipp K, Andersen L, Ebersberger S, Graña-Castro O, Ellmeier W, Petzelbauer P, Lichtenberger BM, Loewe R
  J Invest Dermatol 139, 186-194.
• Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment(2019)
  Urdinguio RG, Lopez V, Bayón GF, Diaz de la Guardia R, Sierra MI, García-Toraño E, Perez RF, García MG, Carella A, Pruneda PC, Prieto C, Dmitrijeva M, Santamarina P, Belmonte T, Mangas C, Diaconu E, Ferrero C, Tejedor JR, Fernandez-Morera JL, Bravo C, Bueno C, Sanjuan-Pla A, Rodriguez RM, Suarez-Alvarez B, López-Larrea C, Bernal T, Colado E, Balbín M, García-Suarez O, Chiara MD, Sáenz-de-Santa-María I, Rodríguez F, Pando-Sandoval A, Rodrigo L, Santos L, Salas A, Vallejo-Díaz J, C Carrera A, Rico D, Hernández-López I, Vayá A, Ricart JM, Seto E, Sima-Teruel N, Vaquero A, Valledor L, Cañal MJ, Pisano D, Graña-Castro O, Thomas T, Voss AK, Menéndez P, Villar-Garea A, Deutzmann R, Fernandez AF, Fraga MF
  Nucleic Acids Res (in press).
• p62/SQSTM1 Fuels Melanoma Progression by Opposing mRNA Decay of a Selective Set of Pro-metastatic Factors.(2019)
  Karras P, Riveiro-Falkenbach E, Cañón E, Tejedo C, Calvo TG, Martínez-Herranz R, Alonso-Curbelo D, Cifdaloz M, Perez-Guijarro E, Gómez-López G, Ximenez-Embun P, Muñoz J, Megias D, Olmeda D, Moscat J, Ortiz-Romero PL, Rodríguez-Peralto JL, Soengas MS.
  Cancer Cell 35, 46-63.
• Clonal dynamics monitoring during clinical evolution in chronic lymphocytic leukaemia(2019)
  González-Rincón J, Gómez S, Martinez N, Troulé K, Perales-Patón J, Derdak S, Beltrán S, Fernández-Cuevas B, Pérez-Sanz N, Nova-Gurumeta S, Gut I, Al-Shahrour F, Piris MA, García-Marco JA, Sánchez-Beato M
  Sci Rep 9, 975-.
• Whole Exome Sequencing identifies PLEC, EXO5 and DNAH7 as novel susceptibility genes in testicular cancer(2018)
  Paumard-Hernández B, Calvete O, Inglada Pérez L, Tejero H, Al-Shahrour F, Pita G, Barroso A, Triviño JC, Urioste M, Valverde C, González Billalabeitia E, Quiroga V, Rodríguez Moreno JF, Fernández Aramburo A, López C, Maroto P, Sastre J, Juan Fita MJ, Duran I, Lorenzo-Lorenzo I, Iranzo P, García Del Muro X, Ros S, Zambrana F, Autran AM, Benítez J
  Int J Cancer 143, 1954-1962.
• 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-.
• RNA-Seq reveals the existence of a CDKN1C-E2F1-TP53 axis that is altered in human T-cell lymphoblastic lymphomas(2018)
  López-Nieva P, Fernández-Navarro P, Vaquero-Lorenzo C, Villa-Morales M, Graña-Castro O, Cobos-Fernández MÁ, López-Lorenzo JL, Llamas P, González-Sanchez L, Sastre I, Pollan M, Malumbres M, Santos J, Fernández-Piqueras J
  Bmc Cancer 18, 430-.
• 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 25, 778-786.
• 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.
• 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)
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• High burden of copy number alterations and c-MYC amplification in prostate cancer from BRCA2 germline mutation carriers.(2015)
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• miRGate: a curated database of human, mouse and rat miRNA-mRNA targets.(2015)
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• Fos-dependent induction of Chk1 protects osteoblasts from replication stress.(2014)
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• Sox4 links tumor suppression to accelerated aging in mice by modulating stem cell activation.(2014)
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• Genome-wide analysis of in vivo TRF1 binding to chromatin restricts its location exclusively to telomeric repeats.(2014)
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• Exome sequencing reveals novel and recurrent mutations with clinical impact in blastic plasmacytoid dendritic cell neoplasm.(2014)
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• Lineage-restricted function of the pluripotency factor NANOG in stratified epithelia.(2014)
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• PLCG1 mutations in cutaneous T-cell lymphomas.(2014)
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• RAB7 controls melanoma progression by exploiting a lineage-specific wiring of the endolysosomal pathway.(2014)
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• Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor.(2014)
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• Lipoprotein(a) levels in familial hypercholesterolemia: an important predictor of cardiovascular disease independent of the type of LDL receptor mutation.(2014)
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• Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia.(2014)
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• Musashi-2 controls cell fate, lineage bias, and TGF-ß signaling in HSCs.(2014)
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• Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis.(2014)
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• RAP1 protects from obesity through its extratelomeric role regulating gene expression.(2013)
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• ARF triggers senescence in Brca2-deficient cells by altering the spectrum of p53 transcriptional targets.(2013)
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• MicroRNA-based molecular classification of non-BRCA1/2 hereditary breast tumours.(2013)
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• Downregulation of specific miRNAs in hyperdiploid multiple myeloma mimics the oncogenic effect of IgH translocations occurring in the non-hyperdiploid subtype.(2013)
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• CSF3R T618I co-occurs with mutations of splicing and epigenetic genes and with a new PIM3 truncated fusion gene in chronic neutrophilic leukemia.(2013)
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• ASXL1, TP53 and IKZF3 mutations are present in the chronic phase and blast crisis of chronic myeloid leukemia.(2013)
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• ARID1A alterations are associated with FGFR3-wild type, poor-prognosis, urothelial bladder tumors.(2013)
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• Reprogramming in vivo produces teratomas and iPS cells with totipotency features.(2013)
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• SIRT1 promotes thyroid carcinogenesis driven by PTEN deficiency.(2013)
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• Differential gene expression of medullary thyroid carcinoma reveals specific markers associated with genetic conditions.(2013)
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• INK4a/ARF limits the expansion of cells suffering from replication stress.(2013)
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• Programmed Cell Senescence during Mammalian Embryonic Development.(2013)
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• ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.(2013)
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• RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.(2013)
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• De novo assembly and functional annotation of the olive (Olea europaea) transcriptome.(2013)
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• New insights into FoxE1 functions: identification of direct FoxE1 targets in thyroid cells.(2013)
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