CV
FRANCESCO EDOARDO VALLONE
PhD candidate (Computational Biology) — CLL & Richter transformation • Multi-omics (bulk RNA-seq, CUT&Tag, ONT methylation) • R/Bioconductor • HPC (SLURM/OCCAM) • EGA/Crypt4GH
Email: francesco.edo.vallone@gmail.com · GitHub: Francesco-E-Vallone · ORCID: 0009-0006-0824-1038 · Location: Turin, Italy
Research focus (short)
PhD candidate at the University of Turin (Functional Genomics Unit, Italy) in computational cancer biology.
My main track is chronic lymphocytic leukemia (CLL): I study how B-cell receptor (BCR) stereotyped subsets and NOTCH1 mutation status shape transcriptional and regulatory programs using multi-omics. In parallel, I work on Richter transformation (RT) - the aggressive lymphoma that can arise from CLL - as a separate line focused on cross-cohort signatures and actionable vulnerabilities.
Education
- PhD, Medical Physiopathology (Computational Biology/Bioinformatics) — University of Turin — 2024–present (expected defense: Feb–Mar 2027)
- Master II livello, Omics Data Analysis — University of Padua — 2023–2024 (Ottimo) (completed during first PhD year)
- MSc, Molecular Biotechnology — University of Turin — 2021–2023 (110/110 cum laude + honors)
- BSc, Biomedical Biotechnology — University of Palermo — 2018–2021 (102/110)
Research experience
PhD Researcher (Bioinformatics) — University of Turin, Dept. of Medical Sciences (2024–present)
- Main PhD project — BCR stereotypy × NOTCH1 in CLL. Quantify genotype-linked transcriptional and regulatory programs across stereotyped subsets (IGHV4-34, IGHV1-69, IGHV3-21), comparing NOTCH1-mut vs wt, and translate signals into mechanistic hypotheses and testable predictions.
- Multi-batch RNA-seq design & QC ownership. Managed a 3-batch study under real constraints (dropouts/uneven libraries): rebuilt contrasts when designs became invalid, enforced QC gates, and prevented analysis choices that would have confounded batch with biology.
- Multi-omics integration. Integrate bulk RNA-seq with CUT&Tag (TFs, H3K27ac) and ONT methylation to connect regulatory state to genotype/context and prioritize perturbation-ready hypotheses.
- External collaborations. Ongoing analysis collaboration with CLL groups at IRCCS San Raffaele Hospital (HSR, Milan) (study design support and bulk RNA-seq analysis).
- Data stewardship (EGA). Controlled-access submissions (metadata, manifests, checksums, Crypt4GH; DAC coordination).
- Internal tooling. Built/maintain tools used in practice: TranscripTools (R) and RNAseq-DB-explorer (Shiny).
Research Fellow (Bioinformatics) — University of Turin, Dept. of Medical Sciences (Nov 2023–Jan 2024)
- Bulk genomics/transcriptomics analyses supporting CLL/RT projects; delivered reusable notebooks and Quarto reports for follow-up validation.
MSc Research Intern — University of Turin, Dept. of Medical Sciences (Mar 2022–Oct 2023)
- Genomic/transcriptomic characterization projects in hematology and genetics; produced analysis outputs and manuscript-ready figures/methods.
Bachelor’s Internship — University of Palermo, Dept. of Biological, Chemical and Pharmaceutical Sciences (Mar–Jul 2021)
Supervisor: Prof. Anna Maria Almerico
- Computational study of ligand–protein interactions using pharmacophore models.
Publications
Submitted / under review
Vallone FE, Omezzolli G, Micillo M, Iannello A, Ferrero G, Berrino E, et al.
Common genomic and transcriptomic signatures in Richter transformation highlight druggable vulnerabilities and guide drug repurposing strategies. Submitted (first author).Fascì A, Vallone FE, et al.
NOTCH1 orchestrates metabolic reprogramming to drive proliferation in chronic lymphocytic leukemia. Submitted.
Peer-reviewed
- Migliorero M, Marsalla D, Vallone FE, et al. Genome editing strategies to generate working models of Polycystic Kidney Disease. Scientific Reports (2025).
- Omezzolli G, Iannello A, Vallone FE, et al. Complementary approaches define the metabolic features that accompany Richter syndrome transformation. Cellular and Molecular Life Sciences (2025).
- Nardi F, Del Prete R, Drago R, Di Rita A, Vallone FE, et al. Apolipoprotein E-mediated ferroptosis controls cellular proliferation in chronic lymphocytic leukemia. Leukemia (2024).
- Faini AC, Arruga F, Pinon M, Bracciamà V, Vallone FE, et al. Genomic and Transcriptomic Profile of HNF1A-Mutated Liver Adenomas… Int. J. Mol. Sci. (2024).
- Sorbini M, Aidala E, Carradori T, Vallone FE, et al. Donor-derived cell-free DNA evaluation in pediatric heart transplant recipients… Transplant Direct (2024).
Teaching
- Teaching (selected modules) — University of Turin (2025–present)
BSc Biotechnology: Medical & Cancer Genetics; Epigenetics · MSc Medical Biotechnology: Biotech Therapies
Selected training
- ELIXIR-IIB scRNA-seq Workshop — Sapienza University of Rome — 25–28 Nov 2025
- EMBL-EBI / Wellcome — Intro to multi-omics data integration & visualisation (Hinxton) — Mar 2026 (scheduled)
- University of Melbourne — mixOmics (R) Essentials for Biological Data Integration — Feb–Apr 2026 (scheduled)
Technical skills
- R/Bioconductor: DESeq2/edgeR/limma, fgsea/GSEA, ggplot2/ComplexHeatmap; Quarto/R Markdown
- Pipelines/HPC: Bash, SLURM (sbatch/arrays/logging), conda/mamba, renv, Git/GitHub
- RNA-seq: fastp, STAR/Salmon, MultiQC, IGV
- Epigenomics: CUT&Tag (TFs, H3K27ac), ONT methylation
- Python: pandas/numpy/matplotlib; notebooks; small CLIs
Data & code
- TranscripTools (R): https://github.com/Francesco-E-Vallone/TranscripTools
- RNAseq-DB-explorer (Shiny): https://github.com/Francesco-E-Vallone/RNAseq-DB-explorer
- script-archive: https://github.com/Francesco-E-Vallone/script-archive
Languages
Italian (native); English (C1); German (A1); Spanish (A1)