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Articles by Samuel Valentini
A TranSNP in the DDIT4 mRNA can impact its translation efficiency and modulate p53-dependent responses in cancer cells
Abstract Relatively few studies have examined the link between SNPs and mRNA translation, despite the established importance of translational regulation in shaping cell phenotypes. We developed a pipeline analyzing the allelic imbalance in total and polysome-bound mRNAs from paired RNA-seq data of HCT116 cells and identified 40 candidate tranSNPs, i.e. SNPs associated with allele-specific translation.
NGSTroubleFinder: A tool for detection and quantification of contamination and kinship across human NGS data
Abstract Quality control is a fundamental but often neglected step in any NGS pipeline. Detecting issues like cross-sample contamination and sample swaps is essential to control the data integrity. Here, we present NGSTroubleFinder, a novel python tool to detect cross-sample contamination in human Whole-Genome and Whole-Transcriptome Sequencing data, sample swaps and mismatches between the reported and the inferred genetic and transcriptomic sexes.
Antibacterial action, proteolytic immunity, and in vivo activity of a Vibrio cholerae microcin
Microcins are small antibacterial proteins (<10 kDa) secreted by gram-negative bacteria.1,2 They recognize specific surface protein receptors of target bacteria and cross the outer membrane, eventually reaching the inner membrane or cytoplasm, where they exert antibacterial action.1,2 Microcins are divided into class I and class II.1,2 Class I microcins are highly post-translationally modified, while class II microcins are either unmodified, except for internal disulfide bonds (class IIa), or...
3Dmapper: A Command Line Tool For BioBank-scale Mapping Of Variants To Protein Structures
Abstract The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional context to genetic coding variants. However, mapping genes to proteins is a tedious and error-prone task due to inconsistencies in data formats.
The structural coverage of the human proteome before and after AlphaFold
Structural coverage of regions with biomedical interest Next, we focused on different subsets of genes of biomedical interest, as their protein structures can be useful in the design of new treatments [33] or to understand the consequences of genetic variants [34,35]. For this purpose, we focused on the protein structural coverage of disease related genes and mutations extracted from DisGeNet [36], OncoKB [37], TCGA [15] and ClinVar [38] databases (Methods).
The structural coverage of the human proteome before and after AlphaFold
New Results View ORCID ProfileEduard Porta-Pardo, Victoria Ruiz-Serra, Samuel Valentini, Alfonso Valencia doi: https://doi.org/10.1101/2021.08.03.454980 Abstract The protein structure field is experiencing a revolution.
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