A5066374651- Marine Ecology and Invasive Species
- Planarian Biology and Electrostimulation
- Bioinformatics and Genomic Networks
- Plant and Biological Electrophysiology Studies
- Retinal Development and Disorders
- Retinal Diseases and Treatments
- Developmental Biology and Gene Regulation
- Single-cell and spatial transcriptomics
- Neuroinflammation and Neurodegeneration Mechanisms
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
Universitat de Barcelona
2015-2023
Institut de Biomedicina de la Universitat de Barcelona
2019
Abstract For successful regeneration, the identity of missing tissue must be specified according to pre-existing tissue. Planarians are ideal for study mechanisms underlying this process; same field cells can regrow a head or tail body part. After amputation, differential activation Wnt/β-catenin signal specifies anterior versus posterior identity. Initially, both wnt1 and notum (Wnt inhibitor) expressed in all wounds, but 48 hours later they restricted facing respectively, by an unknown...
Abstract Motivation Planarians are emerging as a model organism to study regeneration in animals. However, the little available data of protein–protein interactions hinders advances understanding mechanisms underlying its regenerating capabilities. Results We have developed protocol predict using sequence homology and reference Human interactome. This methodology was applied on 11 Schmidtea mediterranea transcriptomic datasets. Then, Neo4j our database manager, we PlanNET, web application...
There is an increasing amount of transcriptomic and genomic data available for planarians with the advent both traditional single-cell RNA sequencing technologies. Therefore, exploring, visualizing making sense all these in order to understand planarian regeneration development can be challenging.In this work, we present PlanExp, a web-application explore visualize gene expression from different RNA-seq experiments (both RNA-seq) planaria Schmidtea mediterranea. PlanExp provides tools...
Background Retinitis pigmentosa (RP) is a highly heterogeneous genetic visual disorder with more than 70 known causative genes, some of them shared other non-syndromic retinal dystrophies (e.g. Leber congenital amaurosis, LCA). The identification RP genes has increased steadily during the last decade, and 30% cases that still remain unassigned will soon decrease after advent exome/genome sequencing. A considerable amount functional data on single RD mutations been gathered, but comprehensive...
Abstract RPGeNet offers researchers a user-friendly queriable tool to visualize the interactome network of visual disorder genes, thus enabling identification new potential causative genes and assignment novel candidates specific retinal or cellular pathways. This can be highly relevant for clinical applications as dystrophies affect 1:3000 people worldwide, are still unknown 30% patients. is refined interaction interface that limits its skeleton shortest paths between each every known gene...
Abstract Embryonic specification of the first body axis requires formation an Organizer, a group cells with ability to instruct fates in surrounding tissue. The existence organizing regions adults, i.e. during regeneration, which also patterning new tissues, remains unstudied. To that aim, we study regeneration planarians, flatworms can regenerate any missing structure, even head, few days. In as described embryonic models, cWNT pathway specifies anterior-posterior axis. During 12-24h after...
Protein-protein interactions (PPIs) are very important to build models for understanding many biological processes. Although several databases hold of these interactions, exploring them, selecting those relevant a given subject and contextualizing them can be difficult task researchers. Extracting PPIs directly from the scientific literature helpful providing such context, as sentences describing may give insights researchers in ways.We have developed PPaxe, python module web application...