Genes & Protein Networks
A web application to explore interologs network for multiple planarian transcriptomes, facilitating navigation through putative interactions and integrating RNA-seq expression data over the different transcriptome assemblies. The approach was presented in Castillo-Lara and Abril (Bioinformatics, aop 2017).
A visual network of retinitis pigmentosa gene-protein interactions to uncover new disease candidates, as described in Boloc et al (PLoS ONE, 2015).
RNA-seq, ATAC-seq and ChIP-seq analyses were combined to decypher tissue identity specification during regeneration, and described on the manuscript “Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration” (Pascual-Carreras et al, Nature Communications, 2023). Raw data is available through the NCBI-BioProject PRJNA800775; Computational Supplementary Material (CSM) can be retrieved from GitHub repository.
Integration of multiple planarian RNA-seq and single-cell RNA-seq datasets with PlanNET’s omic data. Further details available from the manuscript Castillo-Lara et al, (Bioinformatics, 2019).
Using the quantitative nature of Digital Gene Expression, we described the transcriptional profile of neoblasts and present 42 new neoblast genes. See Rodríguez-Esteban et al. (BMC Genomics, 2015), and DGE tags projected over Smed454.
Sequence analyses on the assembled reads obtained by 454-sequencing of transcripts from a mixture of non-irradiated and irradiated intact and regenerating planarians of species Schmidtea mediterranea. Further details available from the manuscript Abril, Cebrià et al. (BMC Genomics, 2010).
This supplementary material page contains both raw and processed data from the proteomics experiments and the downstream computational analyses described in “A proteomics approach to decipher the molecular nature of planarian stem cells” (Fernández-Taboada et al, BMC Genomics, 2011).
A project assessing different metagenomics techniques on irrigation water to provide a better understanding of the role of bacterial/viral load in the transmission of microbial infections to human populations. An initial assessment has been presented in Hjelmsø et al (PLoS ONE, 2017).
Coscinasterias muricata coelomic epithelium transcriptome analysis for Gabre et al (Marine Genomics, 2015) and the associated transcriptome contigs browser.
A brief description of the sources integrated on this web application to assist in SNP-centered screenings, to easily visualize selected SNPs in their genomic context. More details available at Boloc et al (Bioinformatics, 2018).
Links to the RGASP assessment results as well as many graphical analyses of those results. An updated version of those analyses has been published on Nature Methods journal (Steijger, Abril, et al., 2013), along with an assessment of RNA-seq mapping tools.