Vincenzo Belcastro Email & Phone Number

Lausanne, Vaud, Switzerland

Development and management of a graph database for a multicentric, population-based cohort, ensuring data FAIRification and alignment with SPHN standards.Deployment of AI solutions, specifically large language models (LLMs), to interact with and query the database, enabling advanced, natural language-based querying capabilities.

Designing and optimizing prompts that guide AI models, particularly language models, to generate desired and accurate outputs.

Geneva, Switzerland

- Support and maintenance of Biomarker Data Management platform- Automated data processing pipelines powered by a cloud based infrastructure- Research and development activities (Translational Informatics)- Participating in CloudOps infrastructure setup and maintenance

Neuchâtel, Switzerland

Coordinating the development of a software platform for High Content Screening data.- Refined and deployed core software packages increased data integrity and reproducibility- Developed graphical user interfaces increased experimental design harmonization whileaccelerating stake holders decision making via rich graphics reports- Deployed software infrastructure positively impacted manuscript publication rate

Neuchâtel, Switzerland

Integrating automated processing solutions for multiple biological data types.- Developed automated pipelines for multiple data types resulted in a two-fold speed up ofdata processing while reducing costs of the computational infrastructure- Coordinated biologists and developers Increased improved implementation and productivity

Naples Area, Italy

The aim of our lab is to design and develop Systems Biology approaches that help us gain insight into the dis-regulated signaling and regulatory pathways involved in genetic diseases. Given that reverse-engineering algorithms have been developed since the advent of high-throughput technologies for gene expression, our primary focus and the first aim of our project is to develop an integrative approach to leveraging microarray and RNA-Seq data in a unique framework for gene co-regulatory network… Show more The aim of our lab is to design and develop Systems Biology approaches that help us gain insight into the dis-regulated signaling and regulatory pathways involved in genetic diseases. Given that reverse-engineering algorithms have been developed since the advent of high-throughput technologies for gene expression, our primary focus and the first aim of our project is to develop an integrative approach to leveraging microarray and RNA-Seq data in a unique framework for gene co-regulatory network inference.Co-regulation analyses have so far helped identify, among others, master-regulators, such as Transcription Factors (TFs). TFs are proteins directly responsible for the transcriptional response observable from microarray and RNA-Seq experiments. Posttranslational modifications, such as phosphorylation, play a crucial role in this process by controlling the behavior of proteins; furthermore, kinases may activate/promote the nuclear translocation of TFs. The link TF-mRNA expression sits at the very bottom of cue-induced signaling cascades. The second aim of our project is to develop computational reverse-engineering approaches to elucidate the role of kinases by associating them to transcriptional responses.Stimuli-induced signaling transduction and, eventually, posttranslational modifications occur within seconds or minutes after stimulus detection, whereas transcriptional responses are commonly observed after many hours. Early responses involve receptors, adaptors, kinase cascades and protein posttranslational modifications. Mass Spectrometry and other high-throughput proteomic experiments help characterize upstream signaling events encompassing posttranslational modifications. The third aim of the project focuses on developing reverse-engineering algorithms to exploit phosphoproteomic data to build models of early signaling events. Show less

Bern Area, Switzerland

In November 2010, Vincenzo joined Philip Morris International (PMI), Research and Development, Systems Biology Application and Verification Department, few months before his final PhD examination (February 2011). The research in PMI focused on studying the impact of smoke on both in-vivo and in-vitro biological systems. As Computational Biologist Dr Belcastro first contributed to the development of a web platform hosting diagnostic tools for biological data, and then applied those tools on… Show more In November 2010, Vincenzo joined Philip Morris International (PMI), Research and Development, Systems Biology Application and Verification Department, few months before his final PhD examination (February 2011). The research in PMI focused on studying the impact of smoke on both in-vivo and in-vitro biological systems. As Computational Biologist Dr Belcastro first contributed to the development of a web platform hosting diagnostic tools for biological data, and then applied those tools on time-course gene expression experiments, which eventually resulted in co-authoring a scientific publication.While working at PMI, Dr Belcastro expanded his input to the field of gene network inference by contributing to apply a graph-based gene network model on expression data , and by evaluating and boost the performances of an algorithm to quantify the impact of in-vitro and in-vivo external perturbations on biological systems, for which he was honored of an excellence award. Dr Belcastro has been the major contributor for the evaluation of upstream transcriptional regulators in the context of a cellular proliferation network.Since the very first months, Dr Belcastro was involved in an innovative research project jointly run by PMI and IBM, the Systems Biology Verification (SBV), IMPROVER. Dr Belcastro actively contributed to the organization of the Species Translation challenge, and to the set-up of the Network Verification challenge (https://www.sbvimprover.com/). These activities eventually resulted in the publication of scientific manuscripts in leading journals.Moreover, during his period at PMI, Dr Belcastro led the TOX Portal project, consisting in developing a web platform for toxicological assessment of cellular perturbations. The platform prototype was successfully released before he moved to his next work experience. Show less

Naples Area, Italy

In September 2007 Vincenzo was awarded of a PhD fellowship to join the three years International PhD program with the Open University of Cambridge. As project he developed a reverse-engineering techniques to study the function of mammalian genes. He hypothesized that, despite the extreme heterogeneity of conditions across experiments, it was still possible to infer a consensus, time-independent and modular gene network, which summarizes the circuitry of a prototype cell.Vincenzo derived… Show more In September 2007 Vincenzo was awarded of a PhD fellowship to join the three years International PhD program with the Open University of Cambridge. As project he developed a reverse-engineering techniques to study the function of mammalian genes. He hypothesized that, despite the extreme heterogeneity of conditions across experiments, it was still possible to infer a consensus, time-independent and modular gene network, which summarizes the circuitry of a prototype cell.Vincenzo derived a gene network, for both human and mouse, from a massive and heterogeneous dataset of gene expression profiles (~30K). This work has been published in a high impact Systems Biology journal. Both mammalian gene networks can be explored at http://netview.tigem.it.Vincenzo showed how the network could be used to predict protein product localization in the cell, and experimentally validated the lysosomal localization of the Granulin gene product. Furthermore, by extracting a subset gene-gene predicted connections, not reported in literature, he successfully identified proteins physically interacting with the dystrophy-causing gene. His contribution to reverse-engineering is also resumed in two book chapters.Besides the PhD project just described, in the same period Vincenzo has contributed to different other research works. He co-authored a Cell manuscript by applying various reverse-engineering algorithms to assess an in-vivo yeast synthetic network. The same yeast network was then proposed the DREAM 2, the Dialogue for Reverse Engineering Assessments and Methods (http://wiki.c2b2.columbia.edu/dream/index.php/D2c3). Vincenzo participated and won the synthetic network inference challenge, DREAM 3, applying the Network Identification by Multiple Regression algorithm. Finally, he contributed to the validation of a drug-repositioning algorithm, and the characterization of mammalian microRNA target genes. Show less

Development of a reverse-engineering algorithm to infer gene-gene regulatory networks from expression profiles on mammalian cells.

Doctor Of Philosophy - Phd, Biomathematics, Bioinformatics, And Computational Biology

System Biology

Activities and Societies: Embo practical course on "Network in Biology: analysis, modeling and reverse engineering.

System Biology

Activities and Societies: ABS08 – 2008 Applied Bayesian Statistics School on Bayesian Decision Problems in Biostatistics and Clinical.

Bayesian Modeling

Activities and Societies: Bayesian modeling and computation.

M.Sc., Computer Science

Computer Science

Bioinformatic And Scientific Discovery

Courses attended in Aarhus: Data mining; Machine learning and scientific discovery; Algorithms in bioinformatics: trees and structure.