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Research Group

Detalle de: Genomics of Gene Expression

Title Genomics of Gene Expression
Description

We are interested in understanding functional aspects of gene expression by combining a wide variety of high-throughput molecular techniques, including transcriptomics, epigenomics, proteomics, metabolomics, metagenomics and single-cell data, both for model and non-model species. Our lab develops statistical methods and user-friendly software tools to analyze these multi-omics data. Our most current interest is the application of long reads sequencing technologies for transcriptome analysis and the integration of multi-omics data to model chromatin-metabolome regulation.
Home Page https://conesalab.org/
Contact Email conesalab@csic.es
Collaborating Companies BioBam Bioinformatics S.L. Oxford Nanopore Ltd. Wobble Genomics, Ltd.
Spin Off BioBam Bioinformatics S.L.
Patents
Hpc Resources Garnatxa
Institution I2SYSBIO
Ontology Omics, Computational Methods, Resources, Transcriptomics, RNA Sequencing (RNA-seq), Data Analysis, Artificial Intelligence, Machine Learning in Biology, Bioinformatics Software and Tools, Annotation tools, Analysis packages (R, Python, etc.), Data Visualization, Applications of Computational Biology, Model organisms, Bioinformatics enabling techniques, Standards in Computational Biology, Benchmarking, Genomics, Genome Assembly, Large language models, Functional genomics, Functional annotation, Function prediction, Bioinformatics Infrastructure, Expression Profiling, Computational models and simulations, Gene regulatory networks, Metabolic modelling, Computational Techniques, High-performance Computing, Parallel Computing, Desktop application, Personal medicine, Systems Biology, Genomic Annotation, Epigenomics, Integrative Analysis, Regulatory biology, Containers Computing, Statistical Methods for Biology, Web-service, Data Repositories, FAIRfication, Bioinformatics education, Workflow managers, Sequence analysis, Pathway analysis, Metabolomics, Metabolome profiling, Multivariate statistics, Network Biology, Single-cell omics, Single-cell (scRNA-seq), Microbial communities, Text mining, Natural Language Processing (NLP), Deep Learning in Biology, Animal genomics, Cloud Computing, Clinical data, Spatial transcriptomics, Green Computing, Sequence error correction, Behavioral Ecology
Tools SQANTI3, DeCovid, MirCure, SQANTI-SIM, PaintOmics 4, tappAS, maSigPro, NOISeq, MOSim, SQANTI-reads, SQANTI-browser
Service Units
Research Lines Development of methods for long-reads transcriptomics, Statistial methods for multi-omics integration, Single cell and spatial transcriptomics of tissue regeneration, Long-reads multiomics data analysis, Transcript divergence in aging and disease, Outreach for bioinformatics research
Funded Projects FAIRification of IsoSeq Evidence-driven annotation of the biodiversity, NovelMO: Novel methodologies for multi-omics integrative analysis with cutting-edge sequencing technologies, Genomic Insights into Three Locally Adapted Diatoms from the Albufera Coastal Lagoon, Cells2Spine: Spatial Transcriptomics and Cell Communication Models applied to tissue regeneration and treatment in Spinal Cord Injury with Precision Nanomedicine, LongTREC: The Long Reads European Transcriptomics Consortium. The next generation transcriptome biology revealed by single molecule sequencing technologies, Conexión CSIC en Biología Computacional y Bioinformática (BCBHub), Promoting CSIC presence within ELIXIR-Spain, Broad transformation of CSIC’s digital capabilities through dedicated AI support from BCBHub, Integración de datos multi-ómicos para la inferencia de modelos multi-capa de enfermedad, Identifying the determinants of high protein content in seeds of Phaseolus, Microbial Dark Matter, A Novel Antimicrobial Approach To Combat Huanglongbing, Development of methods for transcript quantification and differential expression analysis using long-read sequencing technologies, Critical role for alternative splicing in conferring risk for T1D, Genotype by Environment interaction analysis to understand mechanisms of T1D pathogenesis, Galaxy platform for integrative metabolomics and transcriptomics analysis, Facilitating knowledge exchange between microbiology and computer science students: a computationally intensive approach to discover new adaptation genes in extreme environment, Developing the Functional Iso-Transcriptomics framework, Development of multiomics methods for the integrative study of the Yeast Metabolic Cycle, Novel methods for new challenges in the analysis of high-throughput sequencing data (NOVELSEQ), The Next Systems Biology: statistical methods for multiomics systems biology, Computational methods for the integration of ChIP-seq, metabolomics and RNA-seq data to model chromatin metabolism, STATegra: User-driven Development of Statistical Methods for Experimental Planning, Data Gathering, and Integrative Analysis of Next Generation Sequencing, Proteomics and Metabolomics data, Desarrollo de nuevos conceptos y herramientas bioinformáticas de nueva generación para la priorización de genes candidatos en enfermedades y la elaboración de las correspondientes estrategias terapéuticas, GENÓMICA Y TRANSCRIPTÓMICA DE LAS RUTAS DE DETOXIFICACIÓN EN DROSOPHILA, ANÁLISIS DE GEMELOS DISCORDANTES PARA INVESTIGAR LA CORRELACIÓN ENTRE ALTERACIONES EN EXPRESIÓN Y METILACIÓN DE DNA EN LUPUS ERITEMATOSO SISTÉMICO, Secuenciación, genotipado y desarrollo de herramientas genómicas para la mejora de los cítricos (CITRUSEQ), Exploring novel genome-transcriptome relationships by next generation sequencing approaches, Pathogenomics: Redes transcripcionales controladoras de la virulencia en hongos filamentosos patógenos, Pathomics: metabolomica e interactomica de la relacion huespedparasito, Estudio de perfiles moleculares de expresión génica de pólipos con morfología serrada para la identificación de nuevos marcadores pronósticos de cáncer colorrectal, Development of tools of new generation for gene expression data analysis and implementation in the improved GEPAS platform, SISTEMAS INTEGRADOS INTELIGENTES EN CITRICOS (CITRUS-SII), Identification and modelling of molecular and cellular events of the immune response associated to the appearance of minimal hepatic encephalopathy in cirrhotic patients, Plataformas de apoyo a la investigación en ciencias y tecnologías de la salud de la convocatoria 2017 de la Acción Estratégica en Salud, Understanding the functional role of alternative splicing in crop traits, Desarrollo de métodos estadísticos para la integración de múltiples datos ómicos y de secuenciación masiva, Developing a European American NGS Network (DEANN), Integrative Analysis of TEDDY data to improve T1D diagnosis, Development of Computational Approaches for the characterization and functional annotation of long-non-coding RNA (Annot-lncRNA), Ayuda complementaria para el proyecto STATegra, Ayuda complementaria para PATHOGENOMICS - Metabolomics and Interactiomics of the relationship host-pathogen, Técnico de Apoyo para Redes Transcripcionales Controladoras de Virulencia en Hongos Filamentosos Patógenos, RBNAGE. Deciphering the role of RNA biological noise in aging using long-reads transcriptomics., Estudio de nuevas relaciones genoma-transcriptoma mediante técnicas de ultra-secuenciación, Plataforma de Bioinformática, Desarrollo de recursos computacionales para la caracterización y anotación funcional de ARN no codificante
Selected Publications
View all (134 more)
Researchers Carlos Blanco Gómez, Carolina Monzó Cataluña, Enrique Vidal Beneyto, Fabian Jetzinger, Fabián Robledo Yagüe, Víctor Gaya-Martín, Ana Conesa, Roxana Andreea Moldovan, Julen Santiago Agredano, Silvia Talavera Marcos, Pablo Atienza López

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