Bioinformatics Unit

Fátima Al-Shahrour Head of Unit
T +34 (+34) 917 328 000 (Ext 2940)
falshahrour@cnio.es

Staff Scientists

Michael Tress

Graduate Students

María José Jiménez
Laura Martínez
Fernando Pozo
Kevin Troulé

Technicians

Tomas Di Domenico
Coral Fustero
Gonzalo Gómez
Osvaldo Graña
Elena Piñeiro

Bioinformatics is a key discipline for furthering our understanding of 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 in order 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 CNIO’s scientific computing facilities and provide training in bioinformatics tools and methods.

Publications

Forés-Martos J, Catalá-López F, Sánchez-Valle J, Ibáñez K, Tejero H, Palma-Gudiel H, Climent J, Pancaldi V, Fañanás L, Arango C, Parellada M, Baudot A, Vogt D, Rubenstein JL, Valencia A, Tabarés-Seisdedos R (2019). Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer. Mol Autism (in press). Open Access
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 (2019). Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment. Nucleic Acids Res (in press).
Perales-Patón J, Domenico TD, Fustero-Torre C, Piñeiro-Yáñez E, Carretero-Puche C, Tejero H, Valencia A, Gómez-López G, Al-Shahrour F (2019). vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. Bioinformatics (in press).
Pérez-Pérez M, Pérez-Rodríguez G, Blanco-Míguez A, Fdez-Riverola F, Valencia A, Krallinger M, Lourenço A (2019). Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm.. J Cheminform 11, 42.
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. (2019). p62/SQSTM1 Fuels Melanoma Progression by Opposing mRNA Decay of a Selective Set of Pro-metastatic Factors.. Cancer Cell 35, 46-63.
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 (2019). Clonal dynamics monitoring during clinical evolution in chronic lymphocytic leukaemia. Sci Rep 9, 975. Open Access
Perales-Patón J, Domenico TD, Fustero-Torre C, Piñeiro-Yáñez E, Carretero-Puche C, Tejero H, Valencia A, Gómez-López G, Al-Shahrour F (2019). vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. Bioinformatics (in press).
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 (2019). GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res 47, D776-D776.
Forsthuber A, Lipp K, Andersen L, Ebersberger S, Graña-Castro O, Ellmeier W, Petzelbauer P, Lichtenberger BM, Loewe R (2019). CXCL5 as regulator of neutrophil function in cutaneous melanoma. J Invest Dermatol 139, 186-194.
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 (2018). In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer. Nat Commun 9, 3501.
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 (2018). RNA-Seq reveals the existence of a CDKN1C-E2F1-TP53 axis that is altered in human T-cell lymphoblastic lymphomas. Bmc Cancer 18, 430.
Oldrini B, Curiel-García Á, Marques C, Matia V, Uluçkan Ö, Graña-Castro O, Torres-Ruiz R, Rodriguez-Perales S, Huse JT, Squatrito M (2018). Somatic genome editing with the RCAS-TVA-CRISPR-Cas9 system for precision tumor modeling. Nat Commun 9, 1466.
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 (2018). Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors. Proc Natl Acad Sci USA 115, E1147-E1156.
Abascal F, Juan D, Jungreis I, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML (2018). Loose ends: almost one in five human genes still have unresolved coding status. Nucleic Acids Res 46, 7070-7084.
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 (2018). Terminal uridylyltransferases target RNA viruses as part of the innate immune system. Nat Struct Mol Biol 25, 778-786.
Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML (2018). APPRIS 2017: principal isoforms for multiple gene sets. Nucleic Acids Res 46, D213-D217.
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 (2018). PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data. Genome Med 10, 41.
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 (2018). Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils. Cell Reports 24, 2784-2794.
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 (2018). 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. Front Inmmunol 9, 1963.
Graña O, López-Fernández H, Fdez-Riverola F, González Pisano D, Glez-Peña D (2018). bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data. Bioinformatics 34, 1414-1415.
Garcia-Carpizo V, Ruiz-Llorente S, Sarmentero J, Graña-Castro O, Pisano DG, Barrero MJ (2018). CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation. Epigenetics & Chromatin 11, 30.
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 (2018). Whole Exome Sequencing identifies PLEC, EXO5 and DNAH7 as novel susceptibility genes in testicular cancer. Int J Cancer 143, 1954-1962.
Krallinger M, Rabal O, Lourenço A, Oyarzabal J, Valencia A (2017). Information Retrieval and Text Mining Technologies for Chemistry.. Chem Rev 117, 7673-7761.
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. (2017). Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells.. Nat Genet 49, 866-875.
Romero-Laorden N, Piñeiro-Yañez E, Gutierrez-Pecharroman A, Pacheco MI, Calvo E, Al-Shahrour F, Castro E, Olmos D (2017). Somatic BRCA2 bi-allelic loss in the primary prostate cancer was associated to objective response to PARPi in a sporadic CRPC patient.. Ann Oncol 28, 1158-1159.
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 (2017). Targeted sequencing reveals low-frequency variants in EPHA genes as markers of paclitaxel-induced peripheral neuropathy.. Clin Cancer Res 23, 1227-1235.
Tress ML, Abascal F, Valencia A (2017). Most Alternative Isoforms Are Not Functionally Important.. Trends Biochem Sci 42, 408-410.
Gómez-López G, Dopazo J, Cigudosa JC, Valencia A, Al-Shahrour F (2017). Precision medicine needs pioneering clinical bioinformaticians.. Brief Bioinform (in press).
Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A (2017). Automatic identification of informative regions with epigenomic changes associated to hematopoiesis.. Nucleic Acids Res 45, 9244-9259.
Frenkel-Morgenstern M, Gorohovski A, Tagore S, Sekar V, Vazquez M, Valencia A. (2017). ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.. Nucleic Acids Res 45, 7094-7105.
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 (2017). MIB2 variants altering NOTCH signalling result in left ventricle hypertrabeculation/non-compaction and are associated with Ménétrier-like gastropathy.. Hum Mol Genet 26, 33-43.
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 (2017). Genomic and molecular screenings identify different mechanisms for acquired resistance to MET inhibitors in lung cancer cells.. Mol Cancer Ther 16, 1366-1376.
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 (2017). PheoSeq: A Targeted Next-Generation Sequencing Assay for Pheochromocytoma and Paraganglioma Diagnostics.. J Mol Diagn 9, 575-588.
Flobak Å, Vazquez M, Lægreid A, Valencia A (2017). CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.. Bioinformatics 33, 2410-2412.
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 (2017). Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis.. Int J Cancer 141, 1365-1380.
Perales-Patón J, Piñeiro-Yañez E, Tejero H, López-Casas PP, Hidalgo M, Gómez-López G, Al-Shahrour F (2017). Pancreas cancer precision treatment using avatar mice from a Bioinformatics Perspective.. Public Health Genomics 20, 81-91.
Rubio-Camarillo M, López-Fernández H, Gómez-López G, Carro Á, Fernández JM, Torre CF, Fdez-Riverola F, Glez-Peña D (2017). RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data.. Comput Meth Prog Bio 138, 73-81.
Andrés-León E, Gómez-López G, Pisano DG. (2017). Prediction of miRNA-mRNA Interactions Using miRGate.. Methods Mol Biol 1580, 225-237.
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 (2017). Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of observational studies.. Syst Rev 6, 69.
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. (2017). Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies.. Syst Rev 6, 137.
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 (2017). 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.. Syst Rev 6, 189.
Sánchez-Valle J, Tejero H, Ibáñez K, Portero JL, Krallinger M, Al-Shahrour F, Tabarés-Seisdedos R, Baudot A, Valencia A (2017). A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer. Sci Rep 7, 4474.
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 (2016). Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers.. Nat Communications 7, 13418.
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 (2016). Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance.. PLoS ONE 11, e0155840.
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 (2016). Targeting Tumor Mitochondrial Metabolism Overcomes Resistance to Antiangiogenics.. Cell Reports 15, 2705-2718.
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 (2016). Chronic skin inflammation leads to bone loss by IL-17-mediated inhibition of Wnt signaling in osteoblasts.. Sci Transl Med 8, 330ra37.
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 (2016). Combined inhibition of DDR1 and Notch signaling is a therapeutic strategy for KRAS-driven lung adenocarcinoma.. Nat Med 22, 270-277.
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 (2016). Tissue damage and senescence provide critical signals for cellular reprogramming in vivo.. Science 354, pii: aaf4445..
Montero JJ, López de Silanes I, Graña O, Blasco MA (2016). Telomeric RNAs are essential to maintain telomeres.. Nat Communications 7, 12534.
López-Guadamillas E, Fernández-Marcos PJ, Pantoja C, Muñoz-Martin M, Martínez D, Gómez-López G, Campos-Olivas R, Valverde AM, Serrano M (2016). p21Cip1 plays a critical role in the physiological adaptation to fasting through activation of PPARa.. Sci Rep 6, 34542.
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 (2016). Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML.. Cell 165, 303-316.
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 (2016). Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation.. Cancer Discovery 6, 368-381.
Ferrer-Mayorga G, Gómez-López G, Barbáchano A, Fernández-Barral A, Peña C, Pisano DG, Cantero R, Rojo F, Muñoz A, Larriba MJ. (2016). Vitamin D receptor expression and associated gene signature in tumour stromal fibroblasts predict clinical outcome in colorectal cancer.. Gut (in press).
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 (2016). Metastatic risk and resistance to BRAF inhibitors in melanoma defined by selective allelic loss of ATG5.. Autophagy 12, 1776-1790.
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 (2016). Genomic profiling of patient-derived xenografts for lung cancer identifies B2M inactivation impairing immunorecognition.. Clin Cancer Res (in press).
García-Carpizo V, Sarmentero J, Han B, Graña O, Ruiz-Llorente S, Pisano DG, Serrano M, Brooks HB, Campbell RM, Barrero MJ (2016). NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation.. Sci Rep 8, 32952.
Graña O, Rubio-Camarillo M, Fdez-Riverola F, Pisano DG, Glez-Peña D (2016). nextpresso: next generation sequencing expression analysis pipeline. Current Bioinformatics. Accepted for Publication. Current Bioinformatics (in press).
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 (2016). Somatic embryonic FGFR2 mutations in keratinocytic epidermal nevi.. J Invest Dermatol 136, 1718-1721.
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. (2016). Deep sequencing reveals microRNAs predictive of antiangiogenic drug response.. JCI Insight 7, e86051.
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. (2016). Proteomic Profiling of Ewing Sarcoma Reveals a Role for TRAF6 in Proliferation and Ribonucleoproteins/RNA Processing.. J Proteomics Bioinform 9, 166-175.
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. (2015). The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies.. Bmc Genomics 16, 403.
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. (2015). Tumor MicroRNA Expression Profiling Identifies Circulating MicroRNAs for Early Breast Cancer Detection.. Clin Chem 61, 1098-1106.
Tanic M, Yanowski K, Gómez-López G, Socorro Rodriguez-Pinilla M, Marquez-Rodas I, Osorio A, Pisano DG, Martinez-Delgado B, Benítez J (2015). MicroRNA expression signatures for the prediction of BRCA1/2 mutation-associated hereditary breast cancer in paraffin-embedded formalin-fixed breast tumors.. Int J Cancer 136, 593-602.
Vaclová T, Gómez-López G, Setién F, Bueno JM, Macías JA, Barroso A, Urioste M, Esteller M, Benítez J, Osorio A (2015). DNA repair capacity is impaired in healthy BRCA1 heterozygous mutation carriers.. Breast Cancer Res Treat 152, 271-282.
Palla AR, Piazzolla D, Alcazar N, Cañamero M, Graña O, Gómez-López G, Dominguez O, Dueñas M, Paramio JM, Serrano M. (2015). The pluripotency factor NANOG promotes the formation of squamous cell carcinomas.. Sci Rep 5, 10205.
Carro A, Perez-Martinez M, Soriano J, Pisano DG, Megias D (2015). iMSRC: converting a standard automated microscope into an intelligent screening platform.. Sci Rep 5, 10502.
Tanic M, Yanowski K, Andrés E, Gómez-López G, Socorro MR, Pisano DG, Martinez-Delgado B, Benítez J (2015). miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors.. GENOMICS DATA 3, 75-79.
Cuadrado A, Remeseiro S, Graña O, Pisano, DG, Losada A (2015). The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues.. Nucleic Acids Res 43, 3056-3067.
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 (2015). MYC/PGC-1a Balance Determines the Metabolic Phenotype and Plasticity of Pancreatic Cancer Stem Cells.. Cell Metab 22, 590-605.
Foronda M, Morgado-Palacin L, Gómez-López G, Domínguez O, Pisano DG, Blasco MA (2015). Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation. GENOMICS DATA 6, 21-24.
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 (2015). Non-coding recurrent mutations in chronic lymphocytic leukaemia.. Nature 526, 519-524.
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. (2015). Microenvironmental hCAP-18/LL-37 promotes pancreatic ductal adenocarcinoma by activating its cancer stem cell compartment.. Gut 64, 1921-1935.
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 (2015). Intratumoral heterogeneity in EGFR mutant NSCLC results in divergent resistance mechanisms in response to EGFR tyrosine kinase inhibition.. Cancer Res 75, 4372-4383.
Morgado-Palacin L, Vareti G, Llanos S, Gomez-Lopez G, Martinez D, Serrano M (2015). Partial Loss of Rpl11 in Adult Mice Recapitulates Diamond-Blackfan Anemia and Promotes Lymphomagenesis.. Cell Reports 13, 712-722.
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. (2015). High burden of copy number alterations and c-MYC amplification in prostate cancer from BRCA2 germline mutation carriers.. Ann Oncol 26, 2293-2300.
Aguilera Ó, González-Sancho JM, Zazo S, Rincón R, Fernández AF, Tapia O, Canals F, Morte B, Calvanese V , Orgaz JL, Niell N, Aguilar S, Freije JM, Graña O, Pisano DG, Borrero A, Martínez-Useros J, Jiménez B, Fraga MF, García-Foncillas J, López-Otín C, Lafarga M, Rojo F, Muñoz A (2015). Nuclear DICKKOPF-1 as a biomarker of chemoresistance and poor clinical outcome in colorectal cancer.. Oncotarget 6, 5903-5917.
Andres Leon E, Gonzalez Pena D, Gomez-Lopez G, Pisano DG (2015). miRGate: a curated database of human, mouse and rat miRNA-mRNA targets.. DATABASE : THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015, bav035.
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 (2015). MicroRNA deep-sequencing reveals master regulators of follicular and papillary thyroid tumors.. Mod Pathol 28, 748-757.
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 (2014). Lineage-restricted function of the pluripotency factor NANOG in stratified epithelia.. Nat Communications 5, 4226.
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. (2014). PLCG1 mutations in cutaneous T-cell lymphomas.. Blood 123, 2034-2043.
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 (2014). RAB7 controls melanoma progression by exploiting a lineage-specific wiring of the endolysosomal pathway.. Cancer Cell 26, 61-76.
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 (2014). Inhibition of De Novo NAD+ Synthesis by Oncogenic URI Causes Liver Tumorigenesis through DNA Damage.. Cancer Cell 26, 826-839.
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. (2014). Exome sequencing reveals novel and recurrent mutations with clinical impact in blastic plasmacytoid dendritic cell neoplasm.. Leukemia 28, 823-829.
Schulze J, Lopez-Contreras AJ, Uluçkan O, Graña-Castro O, Fernandez-Capetillo O, Wagner EF (2014). Fos-dependent induction of Chk1 protects osteoblasts from replication stress.. Cell Cycle 13, 1980-1986.
de Silanes IL, Graña O, De Bonis ML, Dominguez O, Pisano DG, Blasco MA (2014). Identification of TERRA locus unveils a telomere protection role through association to nearly all chromosomes.. Nat Communications 5, 4723.
Foronda M, Martínez P, Schoeftner S, Gómez-López G, Schneider R, Flores JM, Pisano DG, Blasco MA (2014). Sox4 links tumor suppression to accelerated aging in mice by modulating stem cell activation.. Cell Reports 8, 487-500.
Garrobo I, Marión RM, Domínguez O, Pisano DG, Blasco MA (2014). Genome-wide analysis of in vivo TRF1 binding to chromatin restricts its location exclusively to telomeric repeats.. Cell Cycle 13, 3742-3749.
Christensen CL, Kwiatkowski N, Abraham B, Carretero J, Al-Shahrour F, Zhang T, Chipumuro R, Herter-Sprie G, Akbay E, Altabef A, Zhang J, Shimamura T, Capelletti M, Reibel JB, Cavanaugh J, Gao P, Liu Y, Michaelsen SR, Poulsen HS, Bradner JE, George R, Gray NS, Young RA, Wong KK (2014). Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor.. Cancer Cell 26, 909-922.
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 (2014). Lipoprotein(a) levels in familial hypercholesterolemia: an important predictor of cardiovascular disease independent of the type of LDL receptor mutation.. J Am Coll Cardiol 63, 1982-1989.
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 (2014). Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia.. J Exp Med 211, 605-612.
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 (2014). Musashi-2 controls cell fate, lineage bias, and TGF-ß signaling in HSCs.. J Exp Med 211, 71-87.
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 (2014). Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis.. Blood 123, e123-e133.
Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML (2014). FireDB: a compendium of biological and pharmacologically relevant ligands.. Nucleic Acids Res 42, D267-D272.
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 (2014). The Epstein Barr-encoded BART-6-3p microRNA affects regulation of cell growth and immuno response in Burkitt lymphoma.. Infect Agent Cancer 9, 12.
Herranz D, Maraver A, Cañamero M, Gómez-López G, Inglada-Pérez L, Robledo M, Castelblanco E, Matias-Guiu X, Serrano M (2013). SIRT1 promotes thyroid carcinogenesis driven by PTEN deficiency.. Oncogene 32, 4052-4056.
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 (2013). Differential gene expression of medullary thyroid carcinoma reveals specific markers associated with genetic conditions.. Am J Pathol 182, 356-362.
Balbás-Martínez C, Rodríguez-Pinilla M, Casanova A, Domínguez O, Pisano DG, Gómez G, Lloreta J, Lorente JA, Malats N, Real FX (2013). ARID1A alterations are associated with FGFR3-wild type, poor-prognosis, urothelial bladder tumors.. PLoS ONE 8, e62483.
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 (2013). Reprogramming in vivo produces teratomas and iPS cells with totipotency features.. Nature 502, 340-345.
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 (2013). ARF triggers senescence in Brca2-deficient cells by altering the spectrum of p53 transcriptional targets.. Nat Communications 4, 2697.
Tanic M, Andrés E, M Rodriguez-Pinilla S, Marquez-Rodas I, Cebollero-Presmanes M, Fernandez V, Osorio A, Benítez J, Martinez-Delgado B. (2013). MicroRNA-based molecular classification of non-BRCA1/2 hereditary breast tumours.. Br J Cancer 109, 2724-2734.
Martínez P, Gómez-López G, García F, Mercken E, Mitchell S, Flores JM, De Cabo R, Blasco MA (2013). RAP1 protects from obesity through its extratelomeric role regulating gene expression.. Cell Reports 3, 2059-2074.
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 (2013). Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy.. Nat Genet 45, 1464-1469.
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 (2013). Downregulation of specific miRNAs in hyperdiploid multiple myeloma mimics the oncogenic effect of IgH translocations occurring in the non-hyperdiploid subtype.. Leukemia 27, 925-931.
Monasor A, Murga M, Lopez-Contreras AJ, Navas C, Gomez G, Pisano DG, Fernandez-Capetillo O (2013). INK4a/ARF limits the expansion of cells suffering from replication stress.. Cell Cycle 12, 1948-1954.
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 (2013). CSF3R T618I co-occurs with mutations of splicing and epigenetic genes and with a new PIM3 truncated fusion gene in chronic neutrophilic leukemia.. Blood Cancer J 3, e158.
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 (2013). ASXL1, TP53 and IKZF3 mutations are present in the chronic phase and blast crisis of chronic myeloid leukemia.. Blood Cancer J 3, e157.
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 (2013). Programmed Cell Senescence during Mammalian Embryonic Development.. Cell 155, 1104-1118.
Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A (2013). ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.. Nucleic Acids Res 41, D142-D151.
Rubio-Camarillo M, Gómez-López G, Fernández JM, Valencia A, Pisano DG (2013). RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.. Bioinformatics 29, 1687-1689.
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 (2013). De novo assembly and functional annotation of the olive (Olea europaea) transcriptome.. Dna Res 20, 93-108.
Fernández LP, López-Márquez A, Martínez AM, Gómez-López G, Santisteban P (2013). New insights into FoxE1 functions: identification of direct FoxE1 targets in thyroid cells.. PLoS ONE 8, e62849.