Bioinformatics Unit

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

Research Scientists

Michael Tress

Post-Doctoral Fellows

Dido Carrero

Graduate Students

María González

Technicians

Ruth Álvarez
Daniel Cerdán
Tomas Di Domenico
Gonzalo Gómez
Beatriz Ocaña
Elena Piñeiro
Ignacio Sanz
Laura Serrano
Francisco José Villena

Bioinformatics is essential for understanding cancer genomics and shaping future cancer therapies. Bioinformatics approaches can transform vast quantities of biological data into comprehensive models, providing insights into cancer and the genotype-phenotype relationships crucial for identifying cancer-driving alterations and therapeutic targets.

The CNIO Bioinformatics Unit is a multidisciplinary team that uses computational methods to solve scientific questions. BU’s objectives include developing computational tools for integrating biological and clinical data, analysing cancer genomes to identify biomarkers and drug response mechanisms, providing bioinformatics support for data analysis, maintaining CNIO’s scientific computing facilities, and offering training in bioinformatics methodologies.

BU is an active node of ELIXIR, leading the Cancer Data Focus Group to enhance cancer genome analysis across Europe.

Recent publications

Rogado J, Pozo F, Troule K, Pacheco M, Adrados M, Sánchez-Torres JM, Al-Shahrour F, Aspa J, Alfranca A, Romero-Laorden N, Colomer R (2026). The role of the CXCL12/CXCR4 axis in the immunotherapy of non-small cell lung cancer. Clin Transl Oncol 27, 2970-2981. CNIO Publication.
Rigual MDM, Angulo-Aguado M, Zagorac S, Álvarez-Díaz R, Benítez-Mondéjar M, Yi F, Martínez-Garay C, Santos-de-Frutos K, Kim E, Campos-Olivas R, Djouder N. (2025). Macrophages harness hepatocyte glutamate to boost liver regeneration. Nature 641, 1005-1016. CNIO Publication.
Priego N, de Pablos-Aragoneses A, Perea-García M, Pieri V, Hernandez-Oliver C, Alvaro-Espinosa L, Rojas A, Sanchez O, Steindl A, Caleiras E, Garcia F, Garcia-Martin S, Grana-Castro O, Garcia-Mulero S, Serrano D, Velasco-Beltran P, Jimenez-Lasheras B, Egia-Mendikute L, Rupp L, Stammberger A, Meinhardt M, Chaachou-Charradi A, Martínez-Saez E, Bertero L, Cassoni P, Mangherini L, Pellerino A, Ruda R, Soffietti R, Al-Shahrour F, Saftig P, Sanz-Pamplona R, Schmitz M, Crocker SJ, Calvo A, Palazon A, Group R, Valiente M. (2025). TIMP1 mediates astrocyte-dependent local immunosuppression in brain metastasis acting on infiltrating CD8+ T cells. Cancer Discovery 15, 179-201. CNIO Publication.
Rodriguez JM, Maquedano M, Cerdán-Vélez D, Laguillo-Gómez A, Calvo E, Abascal F, Vázquez J, Tress ML. (2025). An audit of the PeptideAtlas database uncovers evidence for repurposed pseudogenes and co-opted retroviral ORFs. Bmc Genomics 26, 1087. CNIO Publication.
Tress ML. (2025). The degradation of extended protein isoforms points to a misfiring translation initiation process. Mol Genet Genomics (in press). CNIO Publication.
Delgado-López PD, Cárdenas Montes M, Troya García J, Ocaña-Tienda B, Cepeda S, Martínez Martínez R, Corrales-García EM. (2025). Artificial intelligence in neuro-oncology: methodological bases, practical applications and ethical and regulatory issues. Clin Transl Oncol 27, 4117-4130. CNIO Publication.
Mellid S, Caleiras E, Martínez-Montes ÁM, Arenas A, Jiménez S, Monteagudo M, Letón R, Radu R, Álvarez-Díaz R, Arroba E, Diaz-Talavera A, Martínez-Puente N, Álvarez-Escolá C, Pineda M, Balbín M, Al-Shahrour F, Rodriguez-Antona C, Montero-Conde C, Leandro-García LJ, Honrado E, Soria-Tristán M, Robledo M, Cascón A, (2025). Molecular profiling unveils genetic complexity and identifies potential new driver mechanisms in head and neck paragangliomas. Genes Dis 13, 101705. CNIO Publication.
Riba M, Sala C, Culhane AC, Flobak Å, Patocs A, Boye K, Plevova K, Pospíšilová Š, Gandolfi G, Morelli MJ, Bucci G, Edsjö A, Lassen U, Al-Shahrour F, Lopez-Bigas N, Hovland R, Cuppen E, Valencia A, Poirel HA, Rosenquist R, Scollen S, Arenas Marquez J, Belien J, De Nicolo A, De Maria R, Torrents D, Tonon G. (2024). The 1+Million Genomes Minimal Dataset for Cancer. Nat Genet 56, 733-736. CNIO Publication.
Herms A, Fernandez-Antoran D, Alcolea MP, Kalogeropoulou A, Banerjee U, Piedrafita G, Abby E, Valverde-Lopez JA, Ferreira IS, Caseda I, Bejar MT, Dentro SC, Vidal-Notari S, Ong SH, Colom B, Murai K, King C, Mahbubani K, Saeb-Parsy K, Lowe AR, Gerstung M, Jones PH. (2024). Self-sustaining long-term 3D epithelioid cultures reveal drivers of clonal expansion in esophageal epithelium. Nat Genet 56, 2158-2173. CNIO Publication.
Rodriguez JM, Abascal F, Cerdán-Vélez D, Gómez LM, Vázquez J, Tress ML. (2024). Evidence for widespread translation of 5′ untranslated regions. Nucleic Acids Res 52, 8112-8126. CNIO Publication.
Plata-Gómez AB, de Prado-Rivas L, Sanz A, Deleyto-Seldas N, García F, de la Calle Arregui C, Silva C, Caleiras E, Graña-Castro O, Piñeiro-Yáñez E, Krebs J, Leiva-Vega L, Muñoz J, Jain A, Sabio G, Efeyan A. (2024). Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver. Nat Commun 15, 1878. CNIO Publication.
Fernández-García F, Fernández-Rodríguez A, Fustero-Torre C, Piñeiro-Yáñez E, Wang H, Lechuga CG, Callejas S, Álvarez R, Lopez-García A, Esteban-Burgos L, Salmón M, San Román M, Guerra C, Ambrogio Ch, Drosten M, Santamaria D, Al-Shahrour F, Dopazo A, Barbacid M, Musteanu M (2024). Type I interferon signaling pathway enhances immune-checkpoint inhibition in KRAS mutant lung tumors. Proc Natl Acad Sci USA 121, e2402913121. CNIO Publication. Open Access
Saraswati S, Martínez P, Serrano R, Mejías D, Graña-Castro O, Álvarez Díaz R, Blasco MA. (2024). Renal fibroblasts are involved in fibrogenic changes in kidney fibrosis associated with dysfunctional telomeres. Exp Mol Med 6, 2216-2230. CNIO Publication.
Cerdán-Vélez D, Tress ML. (2024). The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues. Bioinform Adv 28, vbae029. CNIO Publication.
Chaib S, López-Domínguez JA, Lalinde-Gutiérrez M, Prats N, Marin I, Boix O, García-Garijo A, Meyer K, Muñoz MI, Aguilera M, Mateo L, Stephan-Otto Attolini C, Llanos S, Pérez-Ramos S, Escorihuela M, Al-Shahrour F, Cash TP, Tchkonia T, Kirkland JL, Abad M, Gros A, Arribas J, Serrano M (2024). The efficacy of chemotherapy is limited by intratumoral senescent cells expressing PD-L2. Nat Cancer 5, 448-462. CNIO Publication.
Lapuente-Santana Ó, Kant J, Eduati F. (2024). Integrating histopathology and transcriptomics for spatial tumor microenvironment profiling in a melanoma case study. NPJ PRECIS ONCOL 8, 254. CNIO Publication.
Nikolski M, Hovig E, Al-Shahrour F, Blomberg N, Scollen S, Valencia A, Saunders G. (2024). Roadmap for a European cancer data management and precision medicine infrastructure. Nat Cancer 5, 367-372. CNIO Publication.
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, Calvet F, Cerdán-Vélez D, Cunningham F, Davidson C, Donaldson S, Dursun C, Fatima R, Giorgetti S, Giron CG, Gonzalez JM, Hardy M, Harrison PW, Hourlier T, Hollis Z, Hunt T, James B, Jiang Y, Johnson R, Kay M, Lagarde J, Martin FJ, Gómez LM, Nair S, Ni P, Pozo F, Ramalingam V, Ruffier M, Schmitt BM, Schreiber JM, Steed E, Suner MM, Sumathipala D, Sycheva I, Uszczynska-Ratajczak B, Wass E, Yang YT, Yates A, Zafrulla Z, Choudhary JS, Gerstein M, Guigo R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Flicek (2023). GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res 51, D942. CNIO Publication.
Jiménez-Santos MJ, Nogueira-Rodríguez A, Piñeiro-Yáñez E, López-Fernández H, García-Martín S, Gómez-Plana P, Reboiro-Jato M, Gómez-López G, Glez-Peña D, Al-Shahrour F. (2023). PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data. Nucleic Acids Res 51, W411-W418. CNIO Publication.
Calsina B, Piñeiro-Yáñez E, Martínez-Montes ÁM, Caleiras E, Fernández-Sanromán Á, Monteagudo M, Torres-Pérez R, Fustero-Torre C, Pulgarín-Alfaro M, Gil E, Letón R, Jiménez S, García-Martín S, Martin MC, Roldán-Romero JM, Lanillos J, Mellid S, Santos M, Díaz-Talavera A, Rubio Á, González P, Hernando B, Bechmann N, Dona M, Calatayud M, Guadalix S, Álvarez-Escolá C, Regojo RM, Aller J, Del Olmo-Garcia MI, López-Fernández A, Fliedner SMJ, Rapizzi E, Fassnacht M, Beuschlein F, Quinkler M, Toledo RA, Mannelli M, Timmers HJ, Eisenhofer G, Rodríguez-Perales S, Domínguez O, Macintyre G, Currás-Freixes M, Rodríguez-Antona C, Cascón A, Leandro-García LJ, Montero-Conde C, Roncador G, García-García JF, Pacak K, Al-Shahrour F, Robledo M. (2023). Genomic and immune landscape Of metastatic pheochromocytoma and paraganglioma. Nat Commun 14, 1122. CNIO Publication. Open Access
García-Vílchez R, Añazco-Guenkova AM, Dietmann S, López J, Morón-Calvente V, D'Ambrosi S, Nombela P, Zamacola K, Mendizabal I, García-Longarte S, Zabala-Letona A, Astobiza I, Fernández S, Paniagua A, Miguel-López B, Marchand V, Alonso-López D, Merkel A, García-Tuñón I, Ugalde-Olano A, Loizaga-Iriarte A, Lacasa-Viscasillas I, Unda M, Azkargorta M, Elortza F, Bárcena L, Gonzalez-Lopez M, Aransay AM, Di Domenico T, Sánchez-Martín MA, De Las Rivas J, Guil S, Motorin Y, Helm M, Pandolfi PP, Carracedo A, Blanco S. (2023). METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer. Mol Can 22, 119. CNIO Publication.
Sánchez-Sanz A, García-Martín S, Sabín-Muñoz J, Moreno-Torres I, Elvira V, Al-Shahrour F, García-Grande A, Ramil E, Rodríguez-De la Fuente O, Brea-Álvarez B, García-Hernández R, García-Merino A, Sánchez-López AJ. (2023). Dimethyl fumarate-related immune and transcriptional signature is associated with clinical response in multiple sclerosis-treated patients. Front Inmmunol 14, 1209923. CNIO Publication.
Fueyo-Marcos E, Lopez-Pernas G, Fustero-Torre C, Antón ME, Al-Shahrour F, Fernández-Capetillo O, Murga M. (2023). PD-L1ATTAC mice reveal the potential of depleting PD-L1 expressing cells in cancer therapy. Aging (Albany NY) 15, 1791-1807. CNIO Publication.
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.
Jodkowska K, Pancaldi V, Rigau M, Almeida R, Fernández-Justel JM, Graña-Castro O, Rodríguez-Acebes S, Rubio-Camarillo M, Carrillo-de Santa Pau E, Pisano D, Al-Shahrour F, Valencia A, Gómez M, Méndez J. (2022). 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells. Nucleic Acids Res 50, 12149-12165. CNIO Publication. Open Access
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.
Barradas M, Plaza A, Colmenarejo G, Lázaro I, Costa-Machado LF, Martín-Hernández R, Micó V, López-Aceituno JL, Herranz J, Pantoja C, Tejero H, Diaz-Ruiz A, Al-Shahrour F, Daimiel L, Loria-Kohen V, Ramirez de Molina A, Efeyan A, Serrano M, Pozo OJ, Sala-Vila A, Fernandez-Marcos PJ. (2022). Fatty acids homeostasis during fasting predicts protection from chemotherapy toxicity. Nat Commun 13, 5677. CNIO Publication. Open Access
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. Open Access
Jutzi JS, Marneth AE, Jiménez-Santos MJ, Hem J, Guerra-Moreno A, Rolles B, Bhatt S, Myers SA, Carr SA, Hong Y, Pozdnyakova O, van Galen P, Al-Shahrour F, Nam AS, Mullally A. (2022). CALR-mutated cells are vulnerable to combined inhibition of the proteasome and the endoplasmic reticulum stress response. Leukemia 37, 359-369. 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 16, 3881-3908. 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.