Irene Farabella


Ph. D. in Structural Biology, Institute of Structural and Molecular Biology (ISMB) University College London and Birkbeck College


Over the years, as a computational structural biologist, I have leveraged the integration of experimental data (mainly obtained using imaging techniques) and computational methods to learn more about the mechanisms by which the chromatin is organized within nuclei. My goal is to develop and apply transformative tools for the analysis and modelling of super-resolution genome images. This will significantly facilitate the investigation of spatial genome organization at an unprecedented scale and resolution.


1. Mendieta-Esteban J., Di Stefano M., Castillo D., Farabella I.$, Marti-Renom M.A.$. 3D reconstruction of genomic regions from sparse interaction data. bioRxiv (2020) DOI: ($corresponding authors).

2. Vilarrasa-Blasi R.*,Soler-Vila P.*, Verdaguer-Dot N.,Russinyol N., Di Stefano M., Chapaprieta V., Clot G., Farabella I., Cuscó P., Agirre X., Prosper F., Torrents D., Royo R., Beekman R., Beà S., Colomer D., Stunnenberg H., Gut I., Campo E., Marti-Renom M.A., Martin-Subero J.I. Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation. Nat Commun (2020) in press

3. Di Stefano M., Castillo D., Serra F., Farabella I., Goodstadt M.N., Marti-Renom M.A., Analysis, modelling and visualization of Chromosome Conformation Capture experiments. Methods Mol Biol. 2021;2157:35-63

4. Farabella I., Marti-Renom M.A. TADs without borders. Invited News and View Nature Genetics 52 (8), 752-753

5. Di Stefano M., Stadhouders R., Farabella I., Castillo D., Serra F., Graf T., Marti-Renom M.A., Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs. Nat Commun 2020 11, 2564

6. Soler-Vila P., Cuscó Pons P., Farabella I., Di Stefano M., Marti-Renom M.A., Hierarchical chromatin organization detected by TADpole Nucleic Acids Res. 2020 Feb 21.

7. Morf, J., Wingett, S. W., Farabella, I., Cairns, J., Furlan-Magaril, M., Jiménez-García, L. F., Liu, X., Craig, F. F., Walker, S., Segonds-Pichon, A., Andrews, S., Marti-Renom, M. A. & Fraser, P. RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus, Nat Biotechnol. 2019 Jul;37(7):793-802.

8. Miguel-Escalada, I., Bonàs-Guarch, S., Cebola, I., Ponsa-Cobas, J., Mendieta-Esteban, J., Rolando, D., Javierre, B.M., Atla, G., Farabella, I., Morgan, C.C., García-Hurtado, J., Beucher, A., Morán, I., Pasquali, L., Ramos, M., Appel, E.V.R., Linneberg, L., Gjesing, A.P., Witte, D.R., Pedersen, O., Grarup, N., Ravassard, P., Mercader, J.M., Torrents, D., Piemonti, L., Berney, T., de Koning E., Kerr-Conte, J., Pattou, F., Hansen, T., Marti-Renom, M.A., Fraser, P. and Ferrer, J.; Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes. Nat Genet. 2019 Jul;51(7):1137-1148.

9. Nir G.*, Farabella I.*, Pérez Estrada C.*, Ebeling C.G.*, Beliveau B.J., Sasaki H.M., Lee S.H., Nguyen S.C., McCole R.B., Chattoraj S., Erceg J., Abed J.A., Martins N.M.C., Nguyen H.Q., Hannan M.A., Russell S., Durand N.C., Rao S.S.P., Kishi J.Y., Soler-Vila P., Di Pierro M., Onuchic J.N., Callahan S., Schreiner J., Stuckey J.$, Yin P.$, Lieberman-Aiden E.$, Marti-Renom M.A.$, Wu T.$; Walking along chromosomes with super-resolution imaging, contact maps, and integrative modelling. PLoS Genet. 2018 Dec 26;14(12):e1007872. (*These authors contributed equally to this work)

10. Farabella I., Vasishtan D., Joseph A. P., Pandurangan A. P., Sahota H., Topf M.; TEMPy: a Python Library for Assessment of 3D Electron Microscopy Density Fits, J Appl Crystallogr. 2015 Jun. 27;48 (Pt 4):1314-1323. 11. Stödberg T., McTague A., Ruiz A. J., Hirata H., Zhen J., Long P., Farabella I., Meyer E., Kawahara A., Vassallo G., Stivaros S. M., Bjursell M. K., Stranneheim H., Tigerschiöld S., Persson B., Bangash I., Das K., Hughes D., Lesko N., Lundeberg J., Scott R.C., Poduri A., Scheffer I. E., Schorge S., Reith M., Topf M., Kullmann D. M., Harvey R. J., Wedell A., Kurian M. A.; Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures. Nat Commun. 2015 Sep 3;6:8038.

12. Lukoyanova N., Kondos S., Farabella I., Law R., Reboul C. F., Caradoc-Davies T.,Spicer B., Kleifeld O.,Traore D.,Ekkel S.,Voskoboinik I.,Trapani J.,Hatfaludi T.,Oliver K.,Hotze E., Tweten R., Whisstock J. C.,Topf M.,Saibil H.,Dunstone M. A.; Conformational changes during pore formation by the perforin-related protein

pleurotolysin. PLoS Biol., 2015 Feb. 5;13(2) (Paper highlighted in NewScientist).

13. Leung C., Dudkina N. V., Lukoyanova N., Hodel A. W., Farabella I., Pandurangan A. P., Dino Osmanović D., Reboul C., Dunstone M. A., Topf M., Lonnen R., Andrew P.W., Saibil H., and Hoogenboom B. W.; Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin, Elife. 2014 Dec 2;3.

14. Farabella I., Pham T., Henderson N.S., Geibel S., Phan G., Thanassi D. G., Delcour A. H., Waksman G. and Topf M.; Allosteric Signalling in the Outer Membrane Translocation Domain of PapC Usher, Elife. 2014 Oct 28;3 (Cover highlighted in 10.7554/eLife.04997).

15. Atherton J., Farabella I., Yu I.M., Rosenfeld S. S., Houdusse A., Topf M., Moores C.; Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins, Elife. 2014 Sep 10;3.

16. Nan R., Farabella I., Schumacher F. F., Miller A., Gor J., Martin A. C. R., Jones D. T., Lengyel I. and Perkins S. J.; Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degeneration, J. Mol. Biol. 2011 May 13;408 (4):714-35.