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Irene Farabella

Researcher Tenure Track - Principal Investigator
Integrative Nuclear Architecture
Irene Farabella
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Research center
About

Irene Farabella leads the Armenise-Harvard Integrative Nuclear Architecture Lab at the Istituto Italiano di Tecnologia (IIT), within the Center for Human Technologies in Genoa. Her research investigates the structural variability and plasticity of 3D genome organization at the nanoscale, seeking to understand how nuclear architecture shapes gene regulation in physiological and pathological contexts.

Her laboratory integrates imaging techniques, genomics, structural bioinformatics, and theoretical physics to investigate genome organization in single cells at an unprecedented level of detail. The group pioneers chromatin tracing techniques and implements computational tools to visualize and analyse multiple genomic loci within their native nuclear context, supporting multi-omics single-cell investigations. These approaches are complemented by integrative modelling for 3D genome reconstruction to characterize the relationship between genome structure and function, with particular attention to the potential influence of noncoding RNAs on nuclear organization. A central focus is understanding how nuclear components interact across scales during development and differentiation.

Farabella received her MSc in Medical Biotechnology from the University of Milano-Bicocca in 2008. During her studies, she undertook a visiting research period at the Centre for Molecular and Biomolecular Informatics (CMBI) in Nijmegen, supported by an EXTRA PLUS fellowship funded by Fondazione Cariplo, under the supervision of Prof. Gert Vriend and Prof. Marialuisa Lavitrano.

She earned her PhD in Structural Biology in 2013 at the Institute of Structural and Molecular Biology (ISMB), UCL and Birkbeck College, London, supported by a Wellcome Trust-funded studentship and supervised by Prof. Maya Topf and Prof. Gabriel Waksman. She pursued her postdoctoral training in Marc Marti-Renom’s laboratory at the Centre Nacional d’Anàlisi Genòmica–Centre de Regulació Genòmica (CNAG-CRG) in Barcelona as a Juan de la Cierva Incorporación Postdoctoral Fellow. During this period, she also worked as a researcher in C.-ting Wu’s laboratory at Harvard Medical School.

In September 2022, she established her independent Armenise-Harvard Integrative Nuclear Architecture Lab at IIT, bringing together her expertise in structural biology, computational modelling, and genome architecture to investigate the functional relationships between the components of the nucleus.

Education

Title: Wellcome Trust Funded PhD in Structural Biology
Institute: Institute of Structural and Molecular Biology (ISMB) University College London and Birkbeck College
Location: London
Country: UK
From: 2008 To: 2013

Top Publications
2026
Reinkensmeier L., Aufmkolk S., Farabella I., Egner A., Bates M.
Cost-Function Optimized Maximal Overlap Drift Estimation for Single Molecule Localization Microscopy
Biorxiv
Article E-print Archive
2025
Navelkar R., Cosolo A., Bintu B., Cheng Y., Gardeux V., Gutnik S., Fujimori T., Hafner A., Jay A., Jia BB., Jussila AP., Llimos G., Lioutas A., Martins NMC., Moore WJ., Takei Y., Wong F., Yang K., Zhang H., Zhu Q., Bienko M., Bintu L., Cai L., Deplancke B., Nollmann M., Mango SE., Ren B., Park PJ., Sawh AN., Schroeder A., Swedlow JR., Vahedi G., Wu CT., Aufmkolk S., Boettiger AN., Farabella I., Strambio-De-Castillia C., Wang S.
FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format
arXiv
Article E-print Archive
2023
Harris H.L., Gu H., Olshansky M., Wang A., Farabella I., Eliaz Y., Kalluchi A., Krishna A., Jacobs M., Cauer G., Pham M., Rao S.S.P., Dudchenko O., Omer A., Mohajeri K., Kim S., Nichols M.H., Davis E.S., Gkountaroulis D., Udupa D., Aiden A.P., Corces V.G., Phanstiel D.H., Noble W.S., Nir G., Di Pierro M., Seo J.-S., Talkowski M.E., Aiden E.L., Rowley M.J.
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization
Nature Communications, vol. 14, (no. 1)
2023
Flores V., Farabella I., Nir G.
Genome-wide tracing to decipher nuclear organization
Current Opinion in Cell Biology, vol. 82
2021
Mendieta-Esteban J., Di Stefano M., Castillo D., Farabella I., Marti-Renom M.A.
3D reconstruction of genomic regions from sparse interaction data
NAR Genomics and Bioinformatics, vol. 3, (no. 1)
Dissemination
2025
Farabella I.
Algoritmi per navigare la topografia del genoma umano
Festa della scienza e filosofia 2025
Public Event
2024
Farabella I.
Quel cromosoma di mammut
https://www.raiplaysound.it/audio/2024/07/Radio3-Scienza-del-24072024-43a90809-19bc-4a07-a238-7edc739795e9.html
Media
2023
Farabella I.
Cervelli di ritorno, la storia di Irene
https://www.rainews.it/tgr/piemonte/video/2023/02/tgr-piemonte-web-gregori-da-ge---iit-genoma-3dmxf-ricercatrice-istituto-italiano-tecnologia-e2bc0ccf-e470-4db2-9037-67c0b77a8b04.html
Media
Scientific Talks
2026
Farabella I.
Decoding Genome Folding with Chromatin Tracing
Premio Zucchelli in SISSA
Workshop/Symposium
2026
Farabella I.
Decoding Genome Folding with Chromatin Tracing.
IFOM
Institute
2026
Farabella I.
Nanoscale investigation of 3D genome structures
Synergic Entanglements Between Structural Biology & Machine Learning: Looking into the Future
Conference
2026
Frabella I.
Nanoscale investigation of 3D genome structures
Synergic Entanglements Between Structural Biology & Machine Learning: Looking into the Future Conference
Conference
2026
Farabella I.
Seeing the genome in 3D: towards a structural biology of genomes
NHGRI Centers of Excellence in Genomic Science (CEGS) Annual Meeting 2026
Conference