About me
Computational biologist with 10+ years experience working with NGS data analysis focusing on functional genomics. Currently supporting EMBL Rome research fellows in their data analysis tasks and developing a Genomics Data Platform.
Led 5 scientific projects and contributed to 15 in total. Authored 5 peer-reviewed publications as first or co-first author, 10 more as collaborator. Certified Carpentries Instructor who reached >300 scientists through workshops and courses.
Results-oriented independent bioinformatician with strong community-building focus and extensive multi-disciplinary team experience.
Experience
2025 - Present
Genomics Data Platform Developer
EMBL Rome - Data Science Center • Monterotondo (Rome), Italy
- Responsible for the development of an in-house platform for data-intensive pipeline management
- Consulting activity on multiple research projects
- Delivery of training in foundational computational skills
- Onboarding of new Fellows on EMBL computational infrastructure
RPythonNextflowDockerDevOpsPipeline managementHPCScientific computing
Strategic planningTechnical consultingTraining & mentorshipKnowledge transferCross-functional collaboration
2020 - 2025
Postdoctoral Fellow
EMBL Rome - Epigenetics and Neurophysiology unit • Monterotondo (Rome), Italy
- Led data analysis for published work on Trim66's paternal deficiency and intrauterine overgrowth
- Developed and implemented 3t-seq pipeline for integrated gene expression analyses of mRNA, transposable elements and tRNA
- Performed transcriptomic analyses at single cell and bulk level for epigenetic regulation studies
- Designed novel computational method for transcription factor binding motif discovery from bacterial-1-hybrid assay data
- Conducted comparative analyses of ChIP-seq and Cut&Run data for chromatin profiling studies
- Provided Bio-IT support to research fellows from six different research laboratories
- Organized and taught workshops, reaching >300 participants
Bulk RNA-seqSingle-cell RNA-seqChIP-seqCut&RunSpatial transcriptomicsTransposable elements analysisRPythonSnakemakeNextflowHPCScientific computing
Experimental designProject leadershipMulti-disciplinary collaborationStakeholder managementTeaching & public speakingCommunity buildingCode reviewTechnical support
2018 - 2020
Technology Specialist
Genevia Technologies • Tampere, Finland
- Worked on antibiotic microbial resistance prediction
- Planned requirements, managed and led development of a Snakemake pipeline with a custom web frontend
- EU-funded project
SnakemakePythonWeb development
2014 - 2020
PhD Student
Faculty of Medicine and Health Technology - University of Tampere • Tampere, Finland
- Carried out doctorate project titled 'Analysis of Chromatin and Proteins in Cancer'
- Worked on prostate, lung, ovary and brain cancer transcriptomic and epigenetic data
- Presented posters at 5 international conferences
RPythonNGS analysisBioconductorHPCScientific computing
Independent researchScientific communicationPoster presentationsConference networkingTime managementSelf-directed learning
2015 - 2017
Visiting Student
University of Padova • Padova, Italy
- Contributed to the planning, management and co-led development of multiple web applications
- Assisted in Structural Bioinformatics and Bioinformatics courses
Web developmentDatabase designJavascriptMongoDBAngular
2013 - 2014
Graduate Student
BioMediTech - University of Tampere • Tampere, Finland
- Performed data analysis on ovarian cancer microarray data
- Image processing based prediction of chemotherapy sensitivity
MatlabPythonImage processingMachine learningHPCScientific computing
Professional Development and Community Building
- Mentored Master-level student for 1 year (currently PhD student in Paris)
- Delivered training at Carpentries and internal EMBL workshops, reaching 300+ Master, PhD and postdoctoral-level scientists
- Organized and chaired the Bioinformatics Club at EMBL Rome
- Chaired the Scientific Workflows Club across all EMBL sites
- Provided computational analysis support to the Boulard lab and multiple research groups at EMBL Rome
Education
2014 - 2020
PhD in Computational Biology
University of Tampere • Tampere, Finland
Analysis of Chromatin and Proteins in Cancer
2011 - 2013
Master Degree in Bioinformatics
Alma Mater Studiorum - Università di Bologna • Bologna, Italy
110/110 cum laude
2007 - 2011
Bachelor Degree in Biotechnologies
Alma Mater Studiorum - Università di Bologna • Bologna, Italy
Skills
Domain Knowledge
Genomics (short reads)Bulk and single-cell transcriptomicsEpigenetics and chromatin profilingDifferential gene expressionPeak callingPathway enrichment analysisSurvival analysis
Workflow Management
Snakemake (5 years)Nextflow (5 years)nf-core contribution
NGS Analysis Tools
FastQCMultiQCSTARBowtie2BWAcellrangerDESeq2SalmonKallistoMACS2DeepToolsBismarkBedtoolsHomerSeuratSamtools
Programming Languages
Python (14 years)R (12 years)Bash (12 years)JavaScript/TypeScript (2 years)
Python Ecosystem
pandasnumpyDjangoSQLAlchemy
R Ecosystem
tidyverseBioconductorggplot2
Computing & DevOps
HPC/Slurm (12 years)Linux (15 years)Docker/Singularity (6 years)GitLab CI (3 years)GitHub Actions (3 years)Google Cloud
Conferences
2025
- Elixir Europe Biohackathon3-7 November 2025 • Berlin, Germany
- EMBL Data Science Day15-16 October 2025 • Hinxton, UKSharing data across EMBL sites
2024
- EMBL Data Science Day15-16 October 2024 • Hinxton, UK
2023
- Epigenetics Society Meeting12-14 October 2023 • Rome, Italy
2019
- RSG/DREAM - Regulatory and Systems Genomics with DREAM Challenges4-6 November 2019 • New York, USAChromatin accessibility in human prostate cancer progression
2017
- ISMB/ECCB - Intelligent Systems for Molecular Biology and 16th European Conference on Computational Biology21-25 July 2017 • Prague, Czech RepublicVHLdb: a curated community resource for Von Hippel Lindau syndrome
2016
- ECCB - 15th European Conference on Computational Biology3-7 September 2016 • The Hague, Netherlands
2013
- WCSB - 10th International Workshop on Computational Systems Biology10-12 June 2013 • Tampere, FinlandImage Processing Based Classifier for Automated Prediction of Ovarian Cancer Recurrence
Fellowships
2018
- Doctorate School ScholarshipUniversity of Tampere • 2018-2020Project: Computational analysis of chromatin and proteins in cancer
2016
- Francesco Scanferla AIRC Fellowship for ItalyUniversity of Padova • January - December 2016Project: Prediction of Clear Cell Renal Carcinoma Most Effective Drug Combinations from Cellular Subpopulation Genotyping
- Short Term Scientific MissionConway Institute of Biomolecular and Biomedical Research, University College Dublin • October - December 2016Project: Generation of a framework for community-sourced curation of experimentally validated functional modules in intrinsically disordered regionsFunded by European Union COST Action BM1405