Verified Expert in Engineering
Software and Algorithm Developer
Francesco is a software engineer and scientist specializing in algorithms. He has a Ph.D. in medical biochemistry and a Master's degree in bioinformatics. He has written algorithms to analyze biological, medical, and real forensic data and developed a part of the CLC Genomics Workbench, one of the most popular software for bioinformatics analysis used by tens of thousands of users. He is a fan of BDD and excels in bioinformatics, statistics, high-performance computing, and financial technology.
Apache Maven, Jenkins, Git, Debian Linux, IntelliJ
The most amazing...
...algorithms I wrote for QIAGEN are used to analyze biological, medical, and real forensic data.
Founder and CEO
- Consulted for a bioinformatics company developing a complete pipeline for single-cell analysis.
- Developed a system for retrieving data and estimating property values for buy-to-let applications.
- Set up project infrastructures for version control, continuous integration, and deployment.
- Development of an assembler for viral data using ML techniques.
Department of Health and Social Care, Joint Biosecurity Centre
- Monitored and analyzed SARS‑CoV‑2 lineages outside of the UK using data from GISAID.
- Reported findings at weekly meetings and contributed to technical reports.
- Built software to automate a part of the reporting pipeline.
Software Development Engineer in Test (High Tech)
- Developed and improved tests to ensure high quality of deliverables.
- Worked with payments systems, especially SEPA and MasterCard.
- Improved the test automation framework using Java, Cucumber, Spring, Hibernate, and Selenium.
Research and Development Scientist
- Led the team in charge of creating machine learning and statistical models.
- Built predictive models using preprocessed in-house biomedical data and public epidemiological data.
- Trained and mentored junior scientists across several teams and organized book clubs.
Lead Bioinformatics Scientist
- Developed algorithms and tools for classifying peaks in sequencing data using shape information. The tool is part of the CLC Genomics Workbench, one of the most popular software for bioinformatics analysis used by tens of thousands of users.
- Developed algorithms and tools for the analysis of metagenomics data, including statistical and visualization tools.
- Covered the test manager role for the CLC Microbial Genomics Module, checking the code and scientific quality of the product. Created and signed off test plans, strategies, and runs.
- Disseminated results through conferences and publications and collaborated with academia.
- Defined software architecture for new features and aligned with other software architects.
Webmaster and Manager of the Swedish Translation Group
Italia dall'estero (pro bono)
- Served as the main webmaster of the site italiadallestero.info. The website translated news about Italy from the foreign press into Italian and had about 1,000 unique viewers per day and approximately 100 volunteers.
- Developed WordPress plugins for database management.
- Managed the Scandinavian translation group and translated articles from Swedish and occasionally Danish into Italian.
Yale School of Medicine
- Built a novel algorithm for cancer subclonal deconvolution using Java.
- Developed tools to perform analysis of next-generation sequencing data (particularly ChIP-seq, Exome-seq, FAIRE-seq, and 4C-seq) and visualize results, primarily using Java.
- Created statistical methods for combining predictions from different algorithms.
- Developed machine learning-based methods (genetic algorithms) for predicting oligosaccharides 3D structures in Java.
- Optimized code and distributed computations over a small cluster using Java RMI.
- Developed and maintained a ligand-based database for screening purposes by extending PostgreSQL types.
QIAGEN CLC Microbial Genomics Module
I developed tools for performing OTU clustering, including demultiplexing, clustering, statistical analyses (i.e., alpha/beta diversity, PERMANOVA, differential abundance), and visualization. I also developed most of the current pipeline in the Microbial Genomics Module or functional annotation of metagenomic sequences, i.e., a gene finder to annotate nucleotide sequences using a variable-order Markov model and differential functional abundance.
CLC Shape-based Peak Callerhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1042-5
The tool implements all the signal detection steps, quality control, normalization, discovering obvious peaks, learning the peak shape, peak shape score, and peak detection in a single, easy-to-use algorithm. The algorithm delivers a QC report containing metrics about the ChIP-seq experiment's quality, a peak shape score value for every genomic position, and a list of all called peaks.
A performance evaluation showed that the CLC shape-based peak caller ranks well among popular state-of-the-art peak callers while requiring a minimum intervention and parameterization from the user.
TrAp - Tree Approach to Clonalityhttps://sourceforge.net/projects/klugerlab/files/TrAp/
More information is available in the paper at doi.org/10.1093/nar/gkt641.
Java, SQL, R, PHP, Python, Groovy
Cucumber, IntelliJ, Apache Maven, GitHub, Git, Jenkins, MATLAB, Biopython
Machine Learning, Optimization, Statistics, Software QA, Test Management, Scraping, Version Control, Chemistry, Genetic Algorithms, Cheminformatics, Data Engineering, SDET, Code Architecture, Genomics, Computational Biology
Distributed Computing, Microservices, Data Science
WordPress, Debian Linux, Oracle, Docker
Hibernate, Spring, Spring Boot, Selenium
Ph.D. Degree in Medical Biochemistry
Gothenburg University - Göteborg, Sweden
Master's Degree in Bioinformatics
Chalmers University of Technology - Göteborg, Sweden