- Michael Tress
- Hector Tejero
- Laura Martínez
- Fernando Pozo
- Kevin Troulé
- Diana De la Iglesia
- Tomas Di Domenico
- Coral Fustero
- Gonzalo Gómez
- Osvaldo Graña
- 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 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.
- GENCODE reference annotation for the human and mouse genomes.(2019)
Nucleic Acids Res 47, D776-D776.
- CXCL5 as regulator of neutrophil function in cutaneous melanoma.(2019)
J Invest Dermatol 139, 186-194.
- Whole Exome Sequencing identifies PLEC, EXO5 and DNAH7 as novel susceptibility genes in testicular cancer.(2018)
Int J Cancer 143, 1954-1962.
- Somatic genome editing with the RCAS-TVA-CRISPR-Cas9 system for precision tumor modeling.(2018)
Nat Commun 9, 1466-.
- Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors.(2018)
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)
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)
Bmc Cancer 18, 430-.
- Terminal uridylyltransferases target RNA viruses as part of the innate immune system.(2018)
Nat Struct Mol Biol 25, 778-786.
- APPRIS 2017: principal isoforms for multiple gene sets.(2018)
Nucleic Acids Res 46, D213-D217.
- PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data.(2018)
Genome Med 10, 41-.
- Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.(2018)
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)
Front Inmmunol 9, 1963-.
- bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.(2018)
Bioinformatics 34, 1414-1415.
- CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation.(2018)
Epigenetics & Chromatin 11, 30-.
- Loose ends: almost one in five human genes still have unresolved coding status.(2018)
Nucleic Acids Res 46, 7070-7084.
- Targeted sequencing reveals low-frequency variants in EPHA genes as markers of paclitaxel-induced peripheral neuropathy.(2017)
Clin Cancer Res 23, 1227-1235.
- PheoSeq: A Targeted Next-Generation Sequencing Assay for Pheochromocytoma and Paraganglioma Diagnostics.(2017)
J Mol Diagn 9, 575-588.
- Information Retrieval and Text Mining Technologies for Chemistry.(2017)
Chem Rev 117, 7673-7761.
- Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells.(2017)
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)
Ann Oncol 28, 1158-1159.
- Most Alternative Isoforms Are Not Functionally Important.(2017)
Trends Biochem Sci 42, 408-410.
- Precision medicine needs pioneering clinical bioinformaticians.(2017)
Brief Bioinform (in press).
- Automatic identification of informative regions with epigenomic changes associated to hematopoiesis.(2017)
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)
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)
Hum Mol Genet 26, 33-43.
- Genomic and molecular screenings identify different mechanisms for acquired resistance to MET inhibitors in lung cancer cells.(2017)
Mol Cancer Ther 16, 1366-1376.
- CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.(2017)
Bioinformatics 33, 2410-2412.
- Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis.(2017)
Int J Cancer 141, 1365-1380.
- Pancreas cancer precision treatment using avatar mice from a Bioinformatics Perspective.(2017)
Public Health Genomics 20, 81-91.
- RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data.(2017)
Comput Meth Prog Bio 138, 73-81.
- Prediction of miRNA-mRNA Interactions Using miRGate.(2017)
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)
Syst Rev 6, 69-.
- Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies.(2017)
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)
Syst Rev 6, 189-.
- A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer.(2017)
Sci Rep 7, 4474-.
- Targeting Tumor Mitochondrial Metabolism Overcomes Resistance to Antiangiogenics.(2016)
Cell Reports 15, 2705-2718.
- Chronic skin inflammation leads to bone loss by IL-17-mediated inhibition of Wnt signaling in osteoblasts.(2016)
Sci Transl Med 8, 330ra37-.
- Tissue damage and senescence provide critical signals for cellular reprogramming in vivo.(2016)
Science 354, pii: aaf4445.-0.
- Telomeric RNAs are essential to maintain telomeres.(2016)
Nat Communications 7, 12534-.
- Combined inhibition of DDR1 and Notch signaling is a therapeutic strategy for KRAS-driven lung adenocarcinoma.(2016)
Nat Med 22, 270-277.
- Somatic embryonic FGFR2 mutations in keratinocytic epidermal nevi.(2016)
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)
PLoS ONE 11, e0155840-.
- Deep sequencing reveals microRNAs predictive of antiangiogenic drug response.(2016)
JCI Insight 7, e86051-.
- Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers.(2016)
Nat Communications 7, 13418-.
- p21Cip1 plays a critical role in the physiological adaptation to fasting through activation of PPARa.(2016)
Sci Rep 6, 34542-.
- Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML.(2016)
Cell 165, 303-316.
- Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation.(2016)
Cancer Discovery 6, 368-381.
- Vitamin D receptor expression and associated gene signature in tumour stromal fibroblasts predict clinical outcome in colorectal cancer.(2016)
Gut (in press).
- Metastatic risk and resistance to BRAF inhibitors in melanoma defined by selective allelic loss of ATG5.(2016)
Autophagy 12, 1776-1790.
- Genomic profiling of patient-derived xenografts for lung cancer identifies B2M inactivation impairing immunorecognition.(2016)
Clin Cancer Res (in press).
- NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation.(2016)
Sci Rep 8, 32952-.
- nextpresso: next generation sequencing expression analysis pipeline. Current Bioinformatics. Accepted for Publication(2016)
Current Bioinformatics (in press).
- Proteomic Profiling of Ewing Sarcoma Reveals a Role for TRAF6 in Proliferation and Ribonucleoproteins/RNA Processing.(2016)
J Proteomics Bioinform 9, 166-175.
- Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation(2015)
GENOMICS DATA 6, 21-24.
- Tumor MicroRNA Expression Profiling Identifies Circulating MicroRNAs for Early Breast Cancer Detection.(2015)
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)
Int J Cancer 136, 593-602.
- DNA repair capacity is impaired in healthy BRCA1 heterozygous mutation carriers.(2015)
Breast Cancer Res Treat 152, 271-282.
- miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors.(2015)
GENOMICS DATA 3, 75-79.
- The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies.(2015)
Bmc Genomics 16, 403-.
- The pluripotency factor NANOG promotes the formation of squamous cell carcinomas.(2015)
Sci Rep 5, 10205-.
- MicroRNA deep-sequencing reveals master regulators of follicular and papillary thyroid tumors.(2015)
Mod Pathol 28, 748-757.
- iMSRC: converting a standard automated microscope into an intelligent screening platform.(2015)
Sci Rep 5, 10502-.
- The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues.(2015)
Nucleic Acids Res 43, 3056-3067.
- MYC/PGC-1a Balance Determines the Metabolic Phenotype and Plasticity of Pancreatic Cancer Stem Cells.(2015)
Cell Metab 22, 590-605.
- Non-coding recurrent mutations in chronic lymphocytic leukaemia.(2015)
Nature 526, 519-524.
- Microenvironmental hCAP-18/LL-37 promotes pancreatic ductal adenocarcinoma by activating its cancer stem cell compartment.(2015)
Gut 64, 1921-1935.
- Intratumoral heterogeneity in EGFR mutant NSCLC results in divergent resistance mechanisms in response to EGFR tyrosine kinase inhibition.(2015)
Cancer Res 75, 4372-4383.
- Partial Loss of Rpl11 in Adult Mice Recapitulates Diamond-Blackfan Anemia and Promotes Lymphomagenesis.(2015)
Cell Reports 13, 712-722.
- High burden of copy number alterations and c-MYC amplification in prostate cancer from BRCA2 germline mutation carriers.(2015)
Ann Oncol 26, 2293-2300.
- Nuclear DICKKOPF-1 as a biomarker of chemoresistance and poor clinical outcome in colorectal cancer.(2015)
Oncotarget 6, 5903-5917.
- miRGate: a curated database of human, mouse and rat miRNA-mRNA targets.(2015)
DATABASE : THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015, bav035-.
- Inhibition of De Novo NAD+ Synthesis by Oncogenic URI Causes Liver Tumorigenesis through DNA Damage.(2014)
Cancer Cell 26, 826-839.
- Fos-dependent induction of Chk1 protects osteoblasts from replication stress.(2014)
Cell Cycle 13, 1980-1986.
- Identification of TERRA locus unveils a telomere protection role through association to nearly all chromosomes.(2014)
Nat Communications 5, 4723-.
- Sox4 links tumor suppression to accelerated aging in mice by modulating stem cell activation.(2014)
Cell Reports 8, 487-500.
- Genome-wide analysis of in vivo TRF1 binding to chromatin restricts its location exclusively to telomeric repeats.(2014)
Cell Cycle 13, 3742-3749.
- Exome sequencing reveals novel and recurrent mutations with clinical impact in blastic plasmacytoid dendritic cell neoplasm.(2014)
Leukemia 28, 823-829.
- Lineage-restricted function of the pluripotency factor NANOG in stratified epithelia.(2014)
Nat Communications 5, 4226-.
- PLCG1 mutations in cutaneous T-cell lymphomas.(2014)
Blood 123, 2034-2043.
- RAB7 controls melanoma progression by exploiting a lineage-specific wiring of the endolysosomal pathway.(2014)
Cancer Cell 26, 61-76.
- Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor.(2014)
Cancer Cell 26, 909-922.
- Lipoprotein(a) levels in familial hypercholesterolemia: an important predictor of cardiovascular disease independent of the type of LDL receptor mutation.(2014)
J Am Coll Cardiol 63, 1982-1989.
- Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia.(2014)
J Exp Med 211, 605-612.
- Musashi-2 controls cell fate, lineage bias, and TGF-ß signaling in HSCs.(2014)
J Exp Med 211, 71-87.
- Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis.(2014)
Blood 123, e123-e133.
- FireDB: a compendium of biological and pharmacologically relevant ligands.(2014)
Nucleic Acids Res 42, D267-D272.
- The Epstein Barr-encoded BART-6-3p microRNA affects regulation of cell growth and immuno response in Burkitt lymphoma.(2014)
Infect Agent Cancer 9, 12-.
- RAP1 protects from obesity through its extratelomeric role regulating gene expression.(2013)
Cell Reports 3, 2059-2074.
- ARF triggers senescence in Brca2-deficient cells by altering the spectrum of p53 transcriptional targets.(2013)
Nat Communications 4, 2697-.
- MicroRNA-based molecular classification of non-BRCA1/2 hereditary breast tumours.(2013)
Br J Cancer 109, 2724-2734.
- Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy.(2013)
Nat Genet 45, 1464-1469.
- Downregulation of specific miRNAs in hyperdiploid multiple myeloma mimics the oncogenic effect of IgH translocations occurring in the non-hyperdiploid subtype.(2013)
Leukemia 27, 925-931.
- CSF3R T618I co-occurs with mutations of splicing and epigenetic genes and with a new PIM3 truncated fusion gene in chronic neutrophilic leukemia.(2013)
Blood Cancer J 3, e158-.
- ASXL1, TP53 and IKZF3 mutations are present in the chronic phase and blast crisis of chronic myeloid leukemia.(2013)
Blood Cancer J 3, e157-.
- ARID1A alterations are associated with FGFR3-wild type, poor-prognosis, urothelial bladder tumors.(2013)
PLoS ONE 8, e62483-.
- Reprogramming in vivo produces teratomas and iPS cells with totipotency features.(2013)
Nature 502, 340-345.
- SIRT1 promotes thyroid carcinogenesis driven by PTEN deficiency.(2013)
Oncogene 32, 4052-4056.
- Differential gene expression of medullary thyroid carcinoma reveals specific markers associated with genetic conditions.(2013)
Am J Pathol 182, 356-362.
- INK4a/ARF limits the expansion of cells suffering from replication stress.(2013)
Cell Cycle 12, 1948-1954.
- Programmed Cell Senescence during Mammalian Embryonic Development.(2013)
Cell 155, 1104-1118.
- ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.(2013)
Nucleic Acids Res 41, D142-D151.
- RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.(2013)
Bioinformatics 29, 1687-1689.
- De novo assembly and functional annotation of the olive (Olea europaea) transcriptome.(2013)
Dna Res 20, 93-108.
- New insights into FoxE1 functions: identification of direct FoxE1 targets in thyroid cells.(2013)
PLoS ONE 8, e62849-.