FOM is an internationally recognized non-profit cancer research institute supported by the Italian Association for Cancer Research (AIRC) based in Milan within a highly dynamic urban environment.

IFOM’s continuous success is ensured by the recruitment of highly-competitive undergraduate, graduate and post-graduate researchers worldwide, with over 24 countries currently represented in IFOM.

IFOM labs are hosted within a research campus shared with the European Institute of Oncology and the Italian Institute of Technology.

IFOM is committed to creating a safe and inclusive work environment, based on mutual respect and on the enhancement of diversity, offering equal job opportunities to all qualified candidates.

Francesco Ferrari's Laboratory at IFOM ETS, the AIRC Institute of Molecular Oncology in Milan, invites applications for postdoctoral researchers with expertise in computational biology to join our computational genomics group.

This postdoctoral position offers the opportunity to join an exciting and cutting-edge research program aimed at uncovering how pro-metastatic signals reshape chromatin architecture in colorectal cancer. The project is built around the hypothesis that phenotypic plasticity, such as epithelial-to-mesenchymal transition, and biophysical cues from the tumor microenvironment, including extracellular matrix remodeling and mechanical stress, converge on heterochromatin perturbation as a shared downstream mechanism. By studying how heterochromatin compartmentalization and nuclear lamina association influence epigenetic homeostasis, we aim to reveal the molecular programs that enable cancer cells to acquire metastatic potential. The work combines innovative experimental systems, including engineered cell models, mechanobiology platforms, patient-derived organoids, and retrospective tissue cohorts, with multi-omics profiling (transcriptomics, epigenomics, chromatin 3D architecture, proteomics, and single-cell data) and advanced computational analysis. The successful candidate will have the opportunity to lead the integration of these complex datasets, applying state-of-the-art machine learning, statistical modeling, and multi-omics approaches to identify enhancer-gene regulatory network rewiring and molecular signatures predictive of early metastatic progression. This project provides a dynamic, interdisciplinary, and highly collaborative environment for candidates eager to apply computational genomics skills to biologically and clinically impactful questions.

Francesco Ferrari - computational genomics laboratory

https://www.ifom.eu/en/cancer-research/programs/computational-genomics.php

Our research group is especially expert on chromatin 3D architecture, its connection to epigenetic and transcriptional regulation, and how this regulatory axis ultimately affects cell identity homeostasis in physiological and pathological conditions, with a special focus on cancer. Chromatin architecture is studied at different levels of resolution:

• Valentina Rosti§,‡, Giovanni Lembo‡, Cristiano Petrini‡, Francesca Gorini, Roberto Quadri, Chiara Cordiglieri, Margherita Mutarelli, Elisa Salviato, Elisabetta Casari, Emanuele di Patrizio Soldateschi, Emanuele Montanari, Giancarlo Albo, Francesco Ripa, Alessandra Fasciani, Mariacristina Crosti, Elisa De Lorenzis, Marco Maggioni, Valentina Vaira, Maria Vivo, Francesco Ferrari*,§, Chiara Lanzuolo*,§. Chromatin remodeling restrains oncogenic functions in prostate cancer. Nature Communications 2025 - Accepted IN PRESS (‡ co-first authors, § co-corresponding authors, * co-last authors)

• Lucini F, Petrini C, Salviato E, Pal K, Rosti V, Gorini F, Santarelli P, Quadri R, Lembo G, Graziano G, Di Patrizio Soldateschi E, Tagliaferri I, Pinatel E, Sebestyén E, Rotta L, Gentile F, Vaira V, Lanzuolo C*, Ferrari F*. Biochemical properties of chromatin domains define genome compartmentalization. Nucleic Acids Research 2024 Jul 8;52(12):e54. (* co-corresponding/co-last authors)

• Hariprakash JM, Salviato E, La Mastra F, Sebestyén E, Tagliaferri I, Silva RS, Lucini F, Farina L, Cinquanta M, Rancati I, Riboni M, Minardi SP, Roz L, Gorini F, Lanzuolo C, Casola S, Ferrari F. Leveraging tissue-specific enhancer-target gene regulatory networks identifies enhancer somatic mutations that functionally impact lung cancer. Cancer Research 2024 Jan 2;84(1):133-153.

• Salviato E*, Djordjilović V, Hariprakash JM, Tagliaferri I, Pal K, Ferrari F*. Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions. Nucleic Acids Research 2021 Sep 27;49(17):e97. (* co-corresponding authors)

• Sebestyén E, Marullo F, Lucini F, Petrini C, Bianchi A, Valsoni S, Olivieri I, Antonelli L, Gregoretti F, Oliva G, Ferrari F*, Lanzuolo C*. SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome. Nature Communications 2020 Dec 8;11(1):6274. (* co-corresponding/co-last authors)

We are especially looking for outstanding, motivated, and ambitious candidates with a proven track record of experience and publications in the field of genomics and computational biology, interested in working in an international and competitive research environment.

The successful candidate will work primarily on the analysis of genomics data, especially genome-wide data obtained by high-throughput sequencing-based techniques, including gene expression (e.g. RNA-seq, single cell RNA-seq), chromatin marks (e.g. ChIP-seq, ATAC-seq), chromatin 3D architecture (e.g. Hi-C), proteomic and spatial omics data. The development of new methods and tools for data analysis is expected to be part of the postdoctoral research activity as well, but the focus of the research activity will be on applied data analysis to investigate in depth biological questions, integrating multiple types of large-scale datasets from heterogeneous sources.

Proficiency in English for speaking and writing;

English is the working language at the Institute.

PhD degree in Computational Biology, Statistics, Biophysics, Computer Science, Molecular Biology, Genetics, Bioinformatics or other related fields;

International work environment, flextime, agreements with discounts for Gym, Pharmacy, Psychology service and various shops around IFOM area, bar and canteen inside the campus & lunch benefit, Company Nursery, continuous support to candidates thanks to the activities of the Welcome Office, Medical Seervice, Laptop, Caf service-tax declaration.

Annual Renewable fellowship (post-doc);

Milan – Scalo di Porta Romana area

Candidates should send their CV together with a cover letter describing their interest in applying for the role and explain how they meet the set criteria, and contact details of their referees to francesco.ferrari@ifom.eu