A5069693450- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Lung Cancer Research Studies
- Cancer Genomics and Diagnostics
- Immune cells in cancer
- Cell Image Analysis Techniques
- Cancer-related gene regulation
- CRISPR and Genetic Engineering
- Cancer Immunotherapy and Biomarkers
- Lung Cancer Treatments and Mutations
- Cancer-related molecular mechanisms research
- Immune Cell Function and Interaction
- Peptidase Inhibition and Analysis
- Genomics and Chromatin Dynamics
- Genetics and Neurodevelopmental Disorders
- Immunotherapy and Immune Responses
- Bioinformatics and Genomic Networks
- Genetic Syndromes and Imprinting
- T-cell and B-cell Immunology
- MicroRNA in disease regulation
- RNA Research and Splicing
- Cancer Cells and Metastasis
- CAR-T cell therapy research
- Glioma Diagnosis and Treatment
Universitat de Barcelona
2014-2025
Centro Nacional de Análisis Genómico
2016-2025
Centre for Genomic Regulation
2016-2024
Universitat Pompeu Fabra
2016-2024
Institute of Science and Technology
2017-2024
Center for Genomic Science
2024
Barcelona Institute for Science and Technology
2018
Shanghai Institute for Science of Science
2018
Institut d'Investigació Biomédica de Bellvitge
2011-2017
Institut Català d'Oncologia
2013-2016
Systematic studies of cancer genomes have provided unprecedented insights into the molecular nature cancer. Using this information to guide development and application therapies in clinic is challenging. Here, we report how cancer-driven alterations identified 11,289 tumors from 29 tissues (integrating somatic mutations, copy number alterations, DNA methylation, gene expression) can be mapped onto 1,001 molecularly annotated human cell lines correlated with sensitivity 265 drugs. We find...
Epigenetic Brainscape modifications and their potential changes during development are of high interest, but few studies have characterized such differences. Lister et al. ( 1237905 , published online 4 July; see the Perspective by Gabel Greenberg ) report whole-genome base-resolution analysis DNA cytosine transcriptome in frontal cortex human mouse brains at multiple developmental stages. The high-resolution mapping methylation (5mC) one its oxidation derivatives (5hmC) key stages provides...
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition progenitor stem-cell-like features. Here, we provide novel stemness indices for assessing degree oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic epigenetic feature sets derived from non-transformed pluripotent stem cells their progeny. Using OCLR, were able identify previously undiscovered biological mechanisms...
DNA methylation is the most studied epigenetic mark and CpG central to many biological processes human diseases. Since cancer has highlighted contribution disease of aberrant patterns, such as presence promoter island hypermethylation-associated silencing tumor suppressor genes global hypomethylation defects, their importance will surely become apparent in other pathologies. However, advances obtaining comprehensive methylomes are hampered by high cost time-consuming aspects single...
Human aging cannot be fully understood in terms of the constrained genetic setting. Epigenetic drift is an alternative means explaining age-associated alterations. To address this issue, we performed whole-genome bisulfite sequencing (WGBS) newborn and centenarian genomes. The DNA had a lower methylation content reduced correlation status neighboring cytosine--phosphate--guanine (CpGs) throughout genome comparison with more homogeneously methylated DNA. hypomethylated CpGs observed compared...
Spatially resolved gene expression profiles are key to understand tissue organization and function. However, spatial transcriptomics (ST) profiling techniques lack single-cell resolution require a combination with RNA sequencing (scRNA-seq) information deconvolute the spatially indexed datasets. Leveraging strengths of both data types, we developed SPOTlight, computational tool that enables integration ST scRNA-seq infer location cell types states within complex tissue. SPOTlight is centered...
DNA methylation patterns are important for establishing cell, tissue, and organism phenotypes, but little is known about their contribution to natural human variation. To determine variability, we have generated genome-scale profiles of three populations (Caucasian-American, African-American, Han Chinese-American) examined the differentially methylated CpG sites. The distinctly genes identified suggest an influence on phenotype differences, such as susceptibility certain diseases pathogens,...
Abstract Background Many functional analysis tools have been developed to extract and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible do such an for single cells. However, scRNA-seq data has characteristics as drop-out events low library sizes. It thus not clear if TF pathway established can be applied a meaningful way. Results To address this question, we perform benchmark studies on simulated real We...
Non-small-cell lung cancer (NSCLC) is a tumor in which only small improvements clinical outcome have been achieved. The issue critical for stage I patients whom there are no available biomarkers that indicate high-risk should receive adjuvant chemotherapy. We aimed to find DNA methylation markers could be helpful this regard.A microarray analyzes 450,000 CpG sites was used study tumoral obtained from 444 with NSCLC included 237 tumors. prognostic were validated by single-methylation...
Epigenetic alterations may contribute to the development of atherosclerosis. In particular, DNA methylation, a reversible and highly regulated modification, could influence disease onset progression because it functions as an effector for environmental influences, including diet lifestyle, both which are risk factors cardiovascular diseases.To address role methylation changes in atherosclerosis, we compared donor-matched healthy atherosclerotic human aorta sample using whole-genome shotgun...
Single-cell RNA sequencing (scRNA-seq) plays a pivotal role in our understanding of cellular heterogeneity. Current analytical workflows are driven by categorizing principles that consider cells as individual entities and classify them into complex taxonomies.We devise conceptually different computational framework based on holistic view, where single-cell datasets used to infer global, large-scale regulatory networks. We develop correlation metrics specifically tailored data, then generate,...
DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of changes between humans their closest relatives are still poorly understood. We performed a comparative analysis CpG patterns 9 23 primate samples including all species great apes (chimpanzee, bonobo, gorilla orangutan) using Illumina Methylation450 bead...
One of the hallmarks cancer is disruption gene expression patterns. Many molecular lesions contribute to this phenotype, and importance aberrant DNA methylation profiles increasingly recognized. Much research effort in area has examined proximal promoter regions epigenetic alterations at other loci are not well characterized. Using whole genome bisulfite sequencing examine uncharted epigenome, we identify a type far-reaching alteration cells distal regulatory sequences described as...
The tumor immune microenvironment is a main contributor to cancer progression and promising therapeutic target for oncology. However, microenvironments vary profoundly between patients, biomarkers prognosis treatment response lack precision. A comprehensive compendium of cells required pinpoint predictive cellular states their spatial localization. We generated single-cell atlas, jointly analyzing published data sets >500,000 from 217 patients 13 types, providing the basis patient...
Abstract Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in manifestation response to treatment. While the molecular basis for this remains uncharacterized, single-cell technologies allow us explore transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply RNA-sequencing human inflamed intestine show that largest differences among patients...