MazzaLab Bioinformatics

Ready to Dive into the #VRare Experience? We're thrilled to announce that the VRare adventure is officially underway, and YOU are invited! Come visit us and #experience the #journey of a rare genetic disorder through the eyes of a #researcher, all brought to life through #VirtualReality. Immerse yourself in a groundbreaking VR experience that takes you from the intricate details of #DNA mutations to a broader understanding of #raregeneticdiseases. This is a unique opportunity to explore the frontiers of #biology and #genetics like never before. Don't miss out—our doors are open! Find us at: •⁠ Frascati Scienza on September 25 and 26, 2024 (https://lnkd.in/dx3upXdQ) •⁠ ⁠Notte Europea dei Ricercatori e delle Ricercatrici Roma on September 27 and 28, 2024 (https://lnkd.in/dxjmRUK) •⁠ ⁠Maker Faire Rome - The European Edition on October 25-27, 2024 (https://lnkd.in/dCrpAxN) Ospedale Casa Sollievo della Sofferenza Sapienza Università di Roma Tommaso Mazza niccolò liorni Agnese Giovannetti Francesco Petrizzelli Salvatore Daniele Bianco Alessandro Napoli Tommaso Biagini Manuel Mangoni Marta Adinolfi Andrea Villani Viviana Caputo

MitImpact, our collection of genomic, clinical and functional annotations for all nucleotide changes that cause non-synonymous substitutions in human mitochondrial protein coding genes, was updated to its version 3.1.3. This latest release includes: - minor fixes in the search engine and vcf annotator; - updated content of MITOMAP, ClinVar, and dbSNP; - added OMIM and HGNC ids; - added HGVS-based descriptions of variants to help diagnosis reporting; - added AlphaMissense predictions; - added MLC, the mitochondrial local constraint assessments; - added ToMMo 54KJPN allelic frequencies. Check it out at: https://lnkd.in/dWDsQdhH Developed at Ospedale Casa Sollievo della Sofferenza by MazzaLab Bioinformatics #bioinformatics #mitochondrial #genome #database #missense #mitimpact #annotation

We are excited to announce the publication of our latest research paper in Genetics in Medicine, titled "Heterozygosity for loss-of-function variants in LZTR1 is associated with isolated multiple café-au-lait macules." Available at: https://lnkd.in/dnKiGKyD This study sheds new light on the phenotypic variability associated with LZTR1 variants, expanding our understanding of their role beyond schwannomatosis and Noonan syndrome. Our research shows that heterozygous loss-of-function variants in LZTR1 are linked to isolated multiple café-au-lait macules (CaLMs) in a significant number of individuals. Through rigorous in vitro and in silico functional assessments, we demonstrated how these variants lead to accelerated protein degradation or mislocalization and impair the regulation of MAPK signaling. This discovery offers new insights into the molecular spectrum of LZTR1-related conditions and opens up potential avenues for further research and clinical investigation. Gioia Mastromoro Claudia Santoro motta marialetizia Ugo Sorrentino Paola Daniele Cristina Peduto Francesco Petrizzelli Martina Tripodi Valentina Pinna Mariateresa Zanobio Giovannina Rotundo Emanuele Bellacchio Francesca R. Lepri Antonella Farina Maria Cecilia D'Asdia francesca piceci sparascio Tommaso Biagini Daniela Melis Maria Accadia Giovanna Traficante LUIGI TARANI Paolo Fontana Fabio Sirchia Roberto Paparella Aurora Currò Francesco Benedicenti Iris Scala Maria Lisa Dentici Chiara Leoni Valentina Trevisan antonella cecconi Sandra Giustini Antonio Pizzuti Leonardo Salviati Antonio Novelli Giuseppe Zampino Martin Zenker Maurizio Genuardi Maria Cristina Digilio Laura Papi Silverio Perrotta Vincenzo Nigro Elisabeth Castellanos Tommaso Mazza Eva Trevisson Marco Tartaglia Giulio Piluso Alessandro De Luca Ospedale Casa Sollievo della Sofferenza Ospedale Pediatrico Bambino Gesù Fondazione Policlinico Universitario Agostino Gemelli IRCCS Sapienza Università di Roma University of Campania "Luigi Vanvitelli" Università degli Studi di Padova Università degli Studi di Salerno Azienda Ospedaliera Cardinale G. Panico Ospedale Pediatrico Meyer Università di Pavia Regional Hospital of Bolzano Azienda Usl Toscana centro #GeneticsInMedicine #LZTR1 #CaféAuLaitMacules #Schwannomatosis #NoonanSyndrome #GeneticResearch #Bioinformatics #MolecularBiology #GenomicMedicine #bioinformatics #structuralbiology

Read our computational #protocol entitled: "Integrative Analysis of CUT&Tag and RNA-Seq Data Through Bioinformatics: A Unified Workflow for Enhanced Insights" at: https://lnkd.in/d-mW5iQ7 Cleavage Under Targets and Tagmentation (CUT&Tag) is a recent methodology used for robust epigenomic profiling that, unlike conventional chromatin immunoprecipitation (ChIP-Seq), requires only a limited amount of cells as starting material. RNA sequencing (RNA-Seq) reveals the presence and quantity of RNA in a biological sample, describing the continuously changing cellular transcriptome. The integrated analysis of transcriptional activity, histone modifications, and chromatin accessibility via CUT&Tag is still in its infancy compared to the well-established ChIP-Seq. This chapter describes a robust bioinformatics methodology and workflow to perform an integrative CUT&Tag/RNA-Seq analysis. #bioinformatics #rnaseq #chipseq #cutandtag #histonmodification #chromatin #integrativebiology by niccolò liorni, Alessandro Napoli, Marta Adinolfi, Manlio Vinciguerra, and Tommaso Mazza

FastqWiper, our tool to recover corrupted fastq files as well as drop or fix pesky lines, remove unpaired reads, and settle reads interleaving, is now in beta. Link: https://lnkd.in/db4P_dPu We need a community support to masively test it. - Do you want to give it a try? - Do you have corrupted fastq.gz files to recover (or to share, we could do it for you)? - Have you any feature request? Drop us a line of comment! #bioinformatics #fastq #corrupted #NGS #read #FastqWiper #Python #Snakemake #parallelcomputing

🔬 Exploring the Gut Microbiome's Role in IBD Treatment Response 🔬 This new research highlights the crucial role of the #gutmicrobiome in influencing the effectiveness of biologic therapies for #InflammatoryBowelDiseases (IBD), including Crohn’s Disease (CD) and Ulcerative Colitis (UC). In a study analyzing microbiomes from 39 IBD patients and 29 healthy controls using Next-Generation Sequencing (#NGS) and advanced #metagenomic tools, significant findings emerged: • Dysbiosis Levels: CD patients showed more pronounced dysbiosis compared to UC and healthy controls, correlating with a limited response to biologic drugs. • Microbial Signatures: Specific microbial genera, such as Odoribacter and Ruminococcus, were abundant in patients who responded well to biologics, while others like Collinsella were more prevalent in non-responders. • SCFA-Producing Bacteria: Responders to biologic therapies, particularly Vedolizumab, had a higher presence of bacteria that produce short-chain fatty acids (SCFAs), essential for gut health. This research underscores the need for #biomarkers to predict #treatment responses and guide #personalizedtherapy for IBD patients. The findings also highlight the potential for targeting the gut microbiome to enhance therapeutic outcomes. 📑 Link to the article: https://lnkd.in/dAkSgjGy 📑 Orazio Palmieri Fabrizio Bossa Sonia Carparelli Giuseppina Martino Manuel Mangoni marianna nardella Maria Guerra Giuseppe Biscaglia Francesco Perri Tommaso Mazza Ospedale Casa Sollievo della Sofferenza MDPI Microorganisms (MDPI) #IBD #CrohnsDisease #UlcerativeColitis #GutHealth #Microbiome #Biologics #MedicalResearch #HealthcareInnovation #PrecisionMedicine #bioinformatics

🗞 🆕 Article! ALK fusions, found in 5-7% of NSCLC cases, have evolving therapeutic approaches. Our case study revealed a novel SPECC1L::ALK fusion variant in a 60-year-old former smoker with NSCLC. This new fusion, identified using AMP-NGS technology, showed positive clinical responses to first-, second-, and third-generation ALK inhibitors over four years. This discovery underscores the importance of advanced molecular profiling in uncovering rare genetic events and tailoring precise therapies. #NSCLC #CancerResearch #ALKFusion #NGS #PersonalizedMedicine #bioinformatics 📑 Link to the article: https://lnkd.in/dbFqUBij 📑 Tommaso Mazza Francesco Petrizzelli Ospedale Casa Sollievo della Sofferenza Domenico Trombetta Lucia Anna Muscarella Stefano Castellana Federico Pio Fabrizio Fabrizio T. Luisella Righi Alessandra Merlini Paolo Graziano

🚀 Exciting Research Alert! 🚀 We are thrilled to share our latest study on the #epigenetic and transcriptional control of adipocyte function by centenarian-associated #SIRT6 N308K/A313S mutant, recently published in #ClinicalEpigenetics 🔍 Obesity remains a significant #health challenge, and understanding the adipogenic process is key to developing new #therapeuticapproaches. Our research investigates the role of the stress-responsive enzyme SIRT6, specifically focusing on the centenarian-associated N308K/A313S mutants found in Ashkenazi Jews. 🧬 Findings • Overexpression of the centenarian-associated SIRT6 mutant boosts adipogenic differentiation comparable to the wild-type (WT) form. • Distinct histone post-translational modifications (PTMs) with significantly higher acetylation levels were observed in mature adipocytes. • Divergent transcriptional programs were activated, particularly those related to sympathetic innervation and PI3K pathway signaling. • Mature adipocytes overexpressing SIRT6 N308K/A313S exhibited enhanced insulin sensitivity through a neuropeptide Y (NPY)-dependent mechanism. • The SIRT6 N308K/A313S mutant improves glucose sensitivity and influences sympathetic innervation signaling, highlighting the potential of targeting SIRT6 activities to manage obesity-related co-morbidities. 📑 Link for the article: https://lnkd.in/dCS9bNsU 📑 Tommaso Mazza Manlio Vinciguerra niccolò liorni Gabriela Lochmanova Pille Pata Illar Pata Vera Gorbunova Manuel Mangoni

Interested in "Ten simple rules for computational biologists collaborating with wet lab researchers"? Here a few insights from a recent article published in PLOS Computational Biology by Mark D. Robinson et al. In today's multidisciplinary scientific landscape, computational biologists often engage in "collaborative data analysis" projects rather than mere support roles. These collaborations are crucial for developing and refining computational tools to interpret complex molecular data. However, they come with their own set of challenges and opportunities. The article provides ten practical tips to navigate these collaborations effectively, highlighting the importance of clear communication, mutual respect, and understanding the intricacies of cross-disciplinary work. It acknowledges the occasional tensions and egos involved but emphasizes the rewarding nature of harmonizing computational and experimental research. Read the full article here: https://lnkd.in/dQxQ2hz9 #ComputationalBiology #Bioinformatics #Collaboration #ScientificResearch #DataAnalysis #WetLab #DryLab #ResearchTips #MultidisciplinaryScience PLOS Computational Biology

A new tool for Mitochondrial Genome Visualization is out in Bioinformatics: "Drawing mitochondrial genomes with circularMT" by Simon J. Goodman and Ian M. Carr. Mitochondrial DNA sequences are essential for phylogeographic and phylogenetic studies. With affordable, high-throughput DNA sequencing and user-friendly bioinformatics pipelines, whole mitochondrial genome analysis has become crucial, especially for taxa with high species diversity but limited other genomic resources. Evaluating structural rearrangements relative to reference taxa is key. CircularMT is an innovative tool that allows researchers to create highly customizable, publication-quality images of linear and circular mitochondrial genome maps, either individually or integrated into an analysis pipeline. Both applications are implemented in C#, with binaries, source code, and user guides available on GitHub: https://lnkd.in/dSRqHtZe. Check out the full paper here: https://lnkd.in/deBdnxTX This tool is a significant advancement for the scientific community, simplifying the visualization process and enhancing the quality of mitochondrial genome studies. Kudos to the authors for this excellent contribution! #Bioinformatics #Genomics #MitochondrialDNA #NextGenerationSequencing #Phylogenetics #ResearchTools #ScienceInnovation #CircularMT