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.
About the position
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.
Department overview
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:
- On a large scale, we are interested in mechanisms for the coordinated control of large chromatin domains in physiological and disease conditions. These involve the compartmentalization of the genome in structural domains, e.g. Topologically Associating Domains (TADs) or Lamina Associated Domains (LADs), as well as the spatial segregation of heterochromatin and euchromatin. We investigate their functional and structural reorganization dynamics in cancer.
- On a finer scale, we study how chromatin 3D folding controls the physical association of distal regulatory elements (enhancers) and their target genes. We use this complex network or physical (in the 3D space) and regulatory (epigenetics and transcriptional) connections to dissect the combinatorial effect of epigenetic or genetic alterations in cancer.
Selected recent publications
- 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)
Profile Description
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.
Language skills
Proficiency in English for speaking and writing;
English is the working language at the Institute.
Required Skills
- Previous research experience in the field of genomics and computational biology;
- Track record of publications in peer-reviewed journals;
- Experience in functional genomics data analysis, and especially in High Throughput Sequencing data, with priority to candidates with specific expertise in transcriptomics, epigenomics, single cell genomics, proteomics, or other "omics" data types;
- Proficiency in scripting environments for statistics and data analysis (preferentially R/Bioconductor), in addition to Bash/Shell scripting skills;
- Proficiency in other scripting or programming languages (Python, Matlab, Julia, C/C++, or others);
- Excellent communication skills;
Additionally desired skills
- Research experience in an interdisciplinary environment
- Previous work experience in an international/multi-cultural environment
- Strong publication track record
- Expertise in statistical methods and algorithms development in the context of biological data analysis
- experience in working with high-performance computing or cloud computing systems
Educational experience
PhD degree in Computational Biology, Statistics, Biophysics, Computer Science, Molecular Biology, Genetics, Bioinformatics or other related fields;
What we offer
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.
Type of Contract
Annual Renewable fellowship (post-doc);
Location
Milan – Scalo di Porta Romana area
Contacts
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
[email protected]Consideration of applications will begin as they are received and will continue until the position is filled.
This announcement is addressed to both sexes pursuant to Laws 903/77 and 125/91 and to people of all ages and nationalities pursuant to Legislative Decrees 215/03 and 216/03.
