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Investigadores
- Michael Tress
Becarios Pre-Doctorales
- Santiago García
- María José Jiménez
- Laura Martínez
- Fernando Pozo
- Kevin Troulé
Técnicos de Laboratorio
- Daniel Cerdán
- Tomas Di Domenico
- Coral Fustero
- Gonzalo Gómez
- Osvaldo Graña
- Elena Piñeiro
- Thomas Anthony Walsh
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 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 scientific computing facilities at the CNIO and provide training in bioinformatics tools and methods.
Publicaciones
- (2020). TGF-ß-induced IGFBP-3 is a key paracrine factor from activated pericytes that promotes colorectal cancer cell migration and invasion. Mol Oncol (in press). Publicación CNIO.
Open Access
- (2020). DREIMT: a drug repositioning database and prioritization tool for immunomodulation. Bioinformatics (in press). Publicación CNIO.
- (2020). Pan-cancer analysis of whole genomes.. Nature 578, 82-93. Publicación CNIO.
- (2020). Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. NAR Genom Bioinform 2, qz023. Publicación CNIO.
- (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. Publicación CNIO.
- (2020). An analysis of tissue-specific alternative splicing at the protein level. PLoS Comput Biol 16, e1008287. Publicación CNIO.
Open Access
- (2020). Metatax: Metataxonomics with a Compi-Based Pipeline for Precision Medicine.. INTERDISCIPLINARY SCIENCES (in press). Publicación CNIO.
- (2020). Autocrine CCL5 Effect Mediates Trastuzumab Resistance by ERK Pathway Activation in HER2-positive Breast Cancer. Mol Cancer Ther 19, 1696-1707. Publicación CNIO.
- (2020). The Hippo Pathway Transducers YAP1/TEAD Induce Acquired Resistance to Trastuzumab in HER2-Positive Breast Cancer.. Cancers 12, pii: E1108. Publicación CNIO.
Open Access
- (2020). A User Guide for the Online Exploration and Visualization of PCAWG Data. Nat Commun 11, 3400. Publicación CNIO.
Open Access
- (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. Publicación CNIO.
- (2019). Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer. Mol Autism 10, 17. Publicación CNIO.
Open Access
- (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. Publicación CNIO.
Open Access
- (2019). In Silico Drug Prescription for Targeting Cancer Patient Heterogeneity and Prediction of Clinical Outcome. Cancers 11, E1361. Publicación CNIO.
Open Access
- (2019). vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. Bioinformatics 35, 4846-4848. Publicación CNIO.
- (2019). Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm.. J Cheminform 11, 42. Publicación CNIO.
Open Access
- (2019). p62/SQSTM1 Fuels Melanoma Progression by Opposing mRNA Decay of a Selective Set of Pro-metastatic Factors.. Cancer Cell 35, 46-63. Publicación CNIO.
- (2019). Clonal dynamics monitoring during clinical evolution in chronic lymphocytic leukaemia. Sci Rep 9, 975. Publicación CNIO.
Open Access
- (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. Publicación CNIO.
- (2019). vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. Bioinformatics (in press). Publicación CNIO.
- (2019). GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res 47, D776-D776. Publicación CNIO.
Open Access
- (2019). CXCL5 as regulator of neutrophil function in cutaneous melanoma. J Invest Dermatol 139, 186-194. Publicación CNIO.
- (2019). PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts.. Genomics Inform 17, e1. Publicación CNIO.
- (2019). The CAFA Challenge Reports Improved Protein Function Prediction and New Functional Annotations for Hundreds of Genes Through Experimental Screens. Genome Biol 20, 244. Publicación CNIO.
Open Access
- (2018). In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer. Nat Commun 9, 3501. Publicación CNIO.
Open Access
- (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. Publicación CNIO.
Open Access
- (2018). Somatic genome editing with the RCAS-TVA-CRISPR-Cas9 system for precision tumor modeling. Nat Commun 9, 1466. Publicación CNIO.
Open Access
- (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. Publicación CNIO.
- (2018). Loose ends: almost one in five human genes still have unresolved coding status. Nucleic Acids Res 46, 7070-7084. Publicación CNIO.
Open Access
- (2018). Terminal uridylyltransferases target RNA viruses as part of the innate immune system. Nat Struct Mol Biol 25, 778-786. Publicación CNIO.
- (2018). APPRIS 2017: principal isoforms for multiple gene sets. Nucleic Acids Res 46, D213-D217. Publicación CNIO.
Open Access
- (2018). PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data. Genome Med 10, 41. Publicación CNIO.
Open Access
- (2018). Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils. Cell Reports 24, 2784-2794. Publicación CNIO.
Open Access
- (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. Publicación CNIO.
Open Access
- (2018). bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data. Bioinformatics 34, 1414-1415. Publicación CNIO.
- (2018). CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation. Epigenetics & Chromatin 11, 30. Publicación CNIO.
Open Access
- (2018). Whole Exome Sequencing identifies PLEC, EXO5 and DNAH7 as novel susceptibility genes in testicular cancer. Int J Cancer 143, 1954-1962. Publicación CNIO.
- (2017). Information Retrieval and Text Mining Technologies for Chemistry.. Chem Rev 117, 7673-7761. Publicación CNIO.
- (2017). Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells.. Nat Genet 49, 866-875. Publicación CNIO.
- (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. Publicación CNIO.
- (2017). Targeted sequencing reveals low-frequency variants in EPHA genes as markers of paclitaxel-induced peripheral neuropathy.. Clin Cancer Res 23, 1227-1235. Publicación CNIO.
- (2017). Most Alternative Isoforms Are Not Functionally Important.. Trends Biochem Sci 42, 408-410. Publicación CNIO.
- (2017). Precision medicine needs pioneering clinical bioinformaticians.. Brief Bioinform (in press). Publicación CNIO.
- (2017). Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Res 45, 9244-9259. Publicación CNIO.
Open Access
- (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. Publicación CNIO.
- (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. Publicación CNIO.
- (2017). Genomic and molecular screenings identify different mechanisms for acquired resistance to MET inhibitors in lung cancer cells.. Mol Cancer Ther 16, 1366-1376. Publicación CNIO.
- (2017). PheoSeq: A Targeted Next-Generation Sequencing Assay for Pheochromocytoma and Paraganglioma Diagnostics.. J Mol Diagn 9, 575-588. Publicación CNIO.
- (2017). CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.. Bioinformatics 33, 2410-2412. Publicación CNIO.
- (2017). Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis.. Int J Cancer 141, 1365-1380. Publicación CNIO.
- (2017). Pancreas cancer precision treatment using avatar mice from a Bioinformatics Perspective.. Public Health Genomics 20, 81-91. Publicación CNIO.
- (2017). RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data.. Comput Meth Prog Bio 138, 73-81. Publicación CNIO.
- (2017). Prediction of miRNA-mRNA Interactions Using miRGate.. Methods Mol Biol 1580, 225-237. Publicación CNIO.
- (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. Publicación CNIO.
Open Access
- (2017). Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies. Syst Rev 6, 137. Publicación CNIO.
Open Access
- (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. Publicación CNIO.
Open Access
- (2017). A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer. Sci Rep 7, 4474. Publicación CNIO.
- (2016). Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers. Nat Commun 7, 13418. Publicación CNIO.
Open Access
- (2016). Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance.. PLoS ONE 11, e0155840. Publicación CNIO.
- (2016). Targeting Tumor Mitochondrial Metabolism Overcomes Resistance to Antiangiogenics. Cell Reports 15, 2705-2718. Publicación CNIO.
Open Access
- (2016). Chronic skin inflammation leads to bone loss by IL-17-mediated inhibition of Wnt signaling in osteoblasts.. Sci Transl Med 8, 330ra37. Publicación CNIO.
- (2016). Combined inhibition of DDR1 and Notch signaling is a therapeutic strategy for KRAS-driven lung adenocarcinoma.. Nat Med 22, 270-277. Publicación CNIO.
- (2016). Tissue damage and senescence provide critical signals for cellular reprogramming in vivo.. Science 354, pii: aaf4445.. Publicación CNIO.
- (2016). Telomeric RNAs are essential to maintain telomeres. Nat Commun 7, 12534. Publicación CNIO.
Open Access
- (2016). p21Cip1 plays a critical role in the physiological adaptation to fasting through activation of PPARa. Sci Rep 6, 34542. Publicación CNIO.
Open Access
- (2016). Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML.. Cell 165, 303-316. Publicación CNIO.
- (2016). Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation.. Cancer Discovery 6, 368-381. Publicación CNIO.
- (2016). Vitamin D receptor expression and associated gene signature in tumour stromal fibroblasts predict clinical outcome in colorectal cancer.. Gut (in press). Publicación CNIO.
- (2016). Metastatic risk and resistance to BRAF inhibitors in melanoma defined by selective allelic loss of ATG5.. Autophagy 12, 1776-1790. Publicación CNIO.
- (2016). Genomic profiling of patient-derived xenografts for lung cancer identifies B2M inactivation impairing immunorecognition.. Clin Cancer Res (in press). Publicación CNIO.
- (2016). NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation. Sci Rep 8, 32952. Publicación CNIO.
Open Access
- (2016). nextpresso: next generation sequencing expression analysis pipeline. Current Bioinformatics. Accepted for Publication. Current Bioinformatics (in press). Publicación CNIO.
- (2016). Somatic embryonic FGFR2 mutations in keratinocytic epidermal nevi.. J Invest Dermatol 136, 1718-1721. Publicación CNIO.
- (2016). Deep sequencing reveals microRNAs predictive of antiangiogenic drug response.. JCI Insight 7, e86051. Publicación CNIO.
- (2016). Proteomic Profiling of Ewing Sarcoma Reveals a Role for TRAF6 in Proliferation and Ribonucleoproteins/RNA Processing.. J Proteomics Bioinform 9, 166-175. Publicación CNIO.