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

Santiago García
María José Jiménez
Laura Martínez

Technicians

Daniel Cerdán
Tomas Di Domenico
Gonzalo Gómez
Elena Piñeiro

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 vast amount of biological data into comprehensive models that provide a deep understanding of cancer disease and the complex genotype-phenotype relationships needed to identify molecular cancer-driving alterations and novel therapeutic targets.

The CNIO Bioinformatics Unit (BU) has several objectives: (i) to develop new computational methodologies and bioinformatics tools to enable the integration of biological and clinical data, (ii) to achieve genome analysis in cancer patients’ data to identify new biomarkers and drug response mechanisms, (iii) to provide bioinformatics support with data analysis and interpretation using computational and statistical methods, (iv) to maintain the scientific computing facilities at the CNIO, and (iv) to provide training in bioinformatics tools and methods.

Publications

Jutzi JS, Marneth AE, Ciboddo M, Guerra-Moreno A, Jiménez-Santos MJ, Kosmidou A, Dressman JW, Liang H, Hamel R, Lozano P, Rumi E, Doench JG, Gotlib J, Krishnan A, Elf S, Al-Shahrour F, Mullally A (2022). Whole-genome CRISPR screening identifies N-glycosylation as a genetic and therapeutic vulnerability in CALR-mutant MPNs. Blood 140, 1291-1304. CNIO Publication.
Kovtonyuk LV, Caiado F, Garcia-Martin S, Manz EM, Helbling PM, Takizawa H, Boettcher S, Al-Shahrour F, Nombela-Arrieta C, Slack E, Manz MG (2022). IL-1 Mediates Microbiome-Induced Inflamm-Ageing of Hematopoietic Stem Cells in Mice. Blood 139, 44-58. CNIO Publication.
Rodriguez JM, Pozo F, Cerdán-Vélez D, Di Domenico T, Vázquez J, Tress ML (2022). APPRIS: selecting functionally important isoforms.. Nucleic Acids Res 50, D54-D59. CNIO Publication.
Sanchez-Burgos L, Navarro-González B, García-Martín S, Sirozh O, Mota-Pino J, Fueyo-Marcos E, Tejero H, Antón ME, Murga M, Al-Shahrour F, Fernandez-Capetillo O (2022). Activation of the integrated stress response is a vulnerability for multidrug-resistant FBXW7-deficient cells. EMBO Mol Med 0, e15855. CNIO Publication.
Jiménez-Santos MJ, García-Martín S, Fustero-Torre C, Di Domenico T, Gómez-López G, Al-Shahrour F (2022). Bioinformatics roadmap for therapy selection in cancer genomics.. Mol Oncol (in press). CNIO Publication.
Rogado J, Pozo F, Troule K, Sánchez-Torres JM, Romero-Laorden N, Mondejar R, Donnay O, Ballesteros A, Pacheco-Barcia V, Aspa J, Al-Shahrour F, Alfranca A, Colomer R. (2022). Peripheral Blood Mononuclear Cells Predict Therapeutic Efficacy of Immunotherapy in NSCLC. Cancers 14, 2898. CNIO Publication.
Sanchez-Burgos L, Gómez-López G, Al-Shahrour F, Fernandez-Capetillo O (2022). An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection.. Sci Rep 12, 1626. CNIO Publication. Open Access
Rogado J, Pozo F, Troulé K, Sánchez-Torres JM, Romero-Laorden N, Mondejar R, Donnay O, Ballesteros A, Pacheco-Barcia V, Aspa J, Al-Shahrour F, Alfranca A, Colomer R. (2022). Excess weight and anti-PD-1 immune checkpoint inhibitor’s outcomes in non-small cell lung cancer. Clin Transl Oncol 24, 2241-2249. CNIO Publication.
Pinel GD, Horder JL, King JR, McIntyre A, Mongan NP, López GG, Benest AV (2022). Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching. Methods Mol Biol 2441, 369-426. CNIO Publication.
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P (2021). GENCODE 2021. Nucleic Acids Res 49, D916-D923. CNIO Publication.
Martinez Gomez L, Pozo F, Walsh TA, Abascal F, Tress ML (2021). The clinical importance of tandem exon duplication-derived substitutions.. Nucleic Acids Res 49, 8232-8246. CNIO Publication.
Fustero-Torre C, Jiménez-Santos MJ, García-Martín S, Carretero-Puche C, García-Jimeno L, Ivanchuk V, Di Domenico T, Gómez-López G, Al-Shahrour F (2021). Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data. Genome Med 13, 187. CNIO Publication.
Xiong H, Mancini M, Gobert M, Shen S, Furtado GC, Lira SA, Parkhurst CN, Garambois V, Brengues M, Tadokoro CE, Trimarchi T, Gómez-López G, Singh A, Khiabanian H, Minuzzo S, Indraccolo S, Lobry C, Aifantis I, Herranz D, Lafaille JJ, Maraver A (2021). Spleen plays a major role in DLL4-driven acute T-cell lymphoblastic leukemia. Theranostics 11, 1594-1608. CNIO Publication. Open Access
Pawluczyk IZA, Didangelos A, Barbour SJ, Er L, Becker JU, Martin R, Taylor S, Bhachu JS, Lyons EG, Jenkins RH, Fraser D, Molyneux K, Perales-Patón J, Saez-Rodriguez J, Barratt J. (2021). Differential expression of microRNA miR-150-5p in IgA nephropathy as a potential mediator and marker of disease progression. Kidney Int 99, 1127-1139. CNIO Publication.
García-Jimeno L, Fustero-Torre C, Jiménez-Santos MJ, Gómez-López G, Di Domenico T, Al-Shahrour F (2021). bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses.. Bioinformatics (in press). CNIO Publication.
Jiménez-Alcázar M, Curiel-García Á, Nogales P, Perales-Patón J, Schuhmacher AJ, Galán-Ganga M, Zhu L, Lowe SW, Al-Shahrour F, Squatrito M. (2021). Dianhydrogalactitol Overcomes Multiple Temozolomide Resistance Mechanisms in Glioblastoma. Mol Cancer Ther 20, 1029-1038. CNIO Publication.
Kinget L, Roussel E, Lambrechts D, Boeckx B, Vanginderhuysen L, Albersen M, Rodríguez-Antona C, Graña-Castro O, Inglada-Pérez L, Verbiest A, Zucman-Rossi J, Couchy G, Caruso S, Laenen A, Baldewijns M, Beuselinck (2021). MicroRNAs possibly involved in the development of bone metastasis in clear-cell renal cell carcinoma.. Cancers 13, 1554. CNIO Publication.
Troulé K, López-Fernández H, García-Martín S, Reboiro-Jato M, Carretero-Puche C, Martorell-Marugán J, Martín-Serrano G, Carmona-Sáez P, Glez-Peña D, Al-Shahrour F, Gómez-López G. (2021). DREIMT: a drug repositioning database and prioritization tool for immunomodulation. Bioinformatics 37, 578-579. CNIO Publication.
Martorell-Marugán J, López-Domínguez R, García-Moreno A, Toro-Domínguez D, Villatoro-García JA, Barturen G, Martín-Gómez A, Troule K, Gómez-López G, Al-Shahrour F, González-Rumayor V, Peña-Chilet M, Dopazo J, Sáez-Rodríguez J, Alarcón-Riquelme ME, Carmona-Sáez P (2021). A comprehensive database for integrated analysis of omics data in autoimmune diseases. BMC Bioinformatics 22, 343. CNIO Publication.
Pozo F, Martinez-Gomez L, Walsh TA, Rodriguez JM, Di Domenico T, Abascal F, Vazquez J, Tress ML (2021). Assessing the functional relevance of splice isoforms. NAR Genom Bioinform 3, lqab044. CNIO Publication.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020). Pan-cancer analysis of whole genomes.. Nature 578, 82-93. CNIO Publication.
Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M (2020). A User Guide for the Online Exploration and Visualization of PCAWG Data. Nat Commun 11, 3400. CNIO Publication. Open Access
Dimitrov-Markov S, Perales-Patón J, Bockorny B, Dopazo A, Muñoz M, Baños N, Bonilla V, Menendez C, Duran Y, Huang L, Perea S, Muthuswamy SK, Al-Shahrour F, Lopez-Casas PP, Hidalgo M. (2020). Discovery of new targets to control metastasis in pancreatic cancer by single cell transcriptomics analysis of circulating tumor cells.. Mol Cancer Ther 19, 1751-1760. CNIO Publication.
González-Alonso P, Zazo S, Martín-Aparicio E, Luque M, Chamizo C, Sanz-Álvarez M, Minguez P, Gómez-López G, Cristóbal I, Caramés C, García-Foncillas J, Eroles P, Lluch A, Arpí O, Rovira A, Albanell J, Piersma SR, Jimenez CR, Madoz-Gúrpide J, Rojo F (2020). The Hippo Pathway Transducers YAP1/TEAD Induce Acquired Resistance to Trastuzumab in HER2-Positive Breast Cancer.. Cancers 12, pii: E1108. CNIO Publication. Open Access
Navarro R, Tapia-Galisteo A, Martín-García L, Tarín C, Corbacho C, Gómez-López G, Sánchez-Tirado E, Campuzano S, González-Cortés A, Yáñez-Sedeño P, Compte M, Álvarez-Vallina L, Sanz L (2020). TGF-ß-induced IGFBP-3 is a key paracrine factor from activated pericytes that promotes colorectal cancer cell migration and invasion. Mol Oncol 14, 2609-2628. CNIO Publication. Open Access
Troulé K, López-Fernández H, García-Martín S, Reboiro-Jato M, Carretero-Puche C, Martorell-Marugán J, Martín-Serrano G, Carmona-Sáez P, González-Peña D, Al-Shahrour F, Gómez-López G (2020). DREIMT: a drug repositioning database and prioritization tool for immunomodulation. Bioinformatics (in press). CNIO Publication.
Zazo S, González-Alonso P, Martin-Aparicio E, Chamizo C, Luque M, Sanz-Alvarez M, Mínguez P, Gómez-López G, Cristobal I, Caramés C, García-Foncillas J, Eroles P, Lluch A, Arpí O, Rovira A, Albanell J, Madoz-Gúrpide J, Rojo F (2020). Autocrine CCL5 Effect Mediates Trastuzumab Resistance by ERK Pathway Activation in HER2-positive Breast Cancer. Mol Cancer Ther 19, 1696-1707. CNIO Publication.
Rodriguez JM, Pozo F, di Domenico T, Vazquez J, Tress ML (2020). An analysis of tissue-specific alternative splicing at the protein level. PLoS Comput Biol 16, e1008287. CNIO Publication. Open Access
Graña-Castro O, López-Fernández H, Nogueira-Rodríguez A, Fdez-Riverola F, Al-Shahrour F, Glez-Peña D (2020). Metatax: Metataxonomics with a Compi-Based Pipeline for Precision Medicine.. INTERDISCIPLINARY SCIENCES 12, 252-257. CNIO Publication.
Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M, Mudge JM, Tress ML. (2020). Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. NAR Genom Bioinform 2, qz023. CNIO Publication.
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). CNIO Publication.
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. CNIO Publication.
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. CNIO Publication. 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 47, 5016-5037. CNIO Publication. Open Access
Zhou N, et al. (2019). The CAFA Challenge Reports Improved Protein Function Prediction and New Functional Annotations for Hundreds of Genes Through Experimental Screens. Genome Biol 20, 244. CNIO Publication. Open Access
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. CNIO Publication.
Soldevilla B, Carretero-Puche C, Gomez-Lopez G, Al-Shahrour F, Riesco MC, Gil-Calderon B, Alvarez-Vallina L, Espinosa-Olarte P, Gomez-Esteves G, Rubio-Cuesta B, Sarmentero J, La Salvia A, Garcia-Carbonero R (2019). The correlation between immune subtypes and consensus molecular subtypes in colorectal cancer identifies novel tumour microenvironment profiles, with prognostic and therapeutic implications.. Eur J Cancer 123, 118-129. CNIO Publication.
Piñeiro-Yáñez E, Jiménez-Santos MJ, Gómez-López G, Al-Shahrour F (2019). In Silico Drug Prescription for Targeting Cancer Patient Heterogeneity and Prediction of Clinical Outcome. Cancers 11, E1361. CNIO Publication. Open Access
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 10, 17. CNIO Publication. 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 35, 4846-4848. CNIO Publication.
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. CNIO Publication. Open Access
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. CNIO Publication. Open Access
Fernández-Navarro P, López-Nieva P, Piñeiro-Yañez E, Carreño-Tarragona G, Martinez-López J, Sánchez Pérez R, Aroca Á, Al-Shahrour F, Cobos-Fernández MÁ, Fernández-Piqueras J (2019). The use of PanDrugs to prioritize anticancer drug treatments in a case of T-ALL based on individual genomic data.. Bmc Cancer 19, 1005. CNIO Publication.
Armengol-Estapé J, Soares F, Marimon M, Krallinger M. (2019). PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts.. Genomics Inform 17, e1. CNIO Publication.
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. CNIO Publication.
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. CNIO Publication. Open Access
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. CNIO Publication. Open Access
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. CNIO Publication. Open Access
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. CNIO Publication. Open Access
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. CNIO Publication. Open Access
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. CNIO Publication.
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. CNIO Publication. Open Access
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. CNIO Publication. Open Access
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. CNIO Publication.
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. CNIO Publication. Open Access
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. CNIO Publication.
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. CNIO Publication. Open Access
Krallinger M, Rabal O, Lourenço A, Oyarzabal J, Valencia A (2017). Information Retrieval and Text Mining Technologies for Chemistry. Chem Rev 117, 7673-7761. CNIO Publication.
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. CNIO Publication.
Tress ML, Abascal F, Valencia A (2017). Most Alternative Isoforms Are Not Functionally Important. Trends Biochem Sci 42, 408-410. CNIO Publication.
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. CNIO Publication.
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. CNIO Publication. Open Access
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. CNIO Publication.
Gómez-López G, Dopazo J, Cigudosa JC, Valencia A, Al-Shahrour F (2017). Precision medicine needs pioneering clinical bioinformaticians. Brief Bioinform (in press). CNIO Publication.
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. CNIO Publication.
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 (2017). Genomic profiling of patient-derived xenografts for lung cancer identifies B2M inactivation impairing immunorecognition. Clin Cancer Res 23, 3203-3213. CNIO Publication.
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. CNIO Publication.
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. CNIO Publication.
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. CNIO Publication.
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. CNIO Publication.
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. CNIO Publication.
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. CNIO Publication.
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. CNIO Publication.
Andrés-León E, Gómez-López G, Pisano DG (2017). Prediction of miRNA-mRNA Interactions Using miRGate. Methods Mol Biol 1580, 225-237. CNIO Publication.
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. CNIO Publication. Open Access
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. CNIO Publication. Open Access
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. CNIO Publication. Open Access
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. CNIO Publication.