Publications
For the complete list of publications click here .
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.
Harris HL*, Gu H*, Olshansky M, Wang A, Farabella I, Eliaz Y, Kalluchi A, Krishna A, Jacobs M, Cauer G, Pham M, Rao SSP, Dudchenko O, Omer A, Mohajeri K, Kim S, Nichols MH, Davis ES, Gkountaroulis D, Udupa D, Aiden AP, Corces VG, Phanstiel DH, Noble WS, Nir G, Di Pierro M, Seo JS, Talkowski ME, Aiden EL$, Rowley MJ$.
Nat Commun. 14(1) 3303.; 2023 .
Genome-wide tracing to decipher nuclear organization.
Flores V., Farabella I.$, Nir G.$. ($corresponding author).
Curr. Opin. Cell Biol 2023
Three-dimensional genome organization via triplex forming RNAs.
Farabella I.$, Di Stefano M., Soler-Vila P., Marti-Marimon M., and Marti-Renom M.A.$. ($corresponding author).
Nat. Struct. Mol. Biol. 2021
3D reconstruction of genomic regions from sparse interaction data.
Mendieta-Esteban J., Di Stefano M., Castillo D., Farabella I.$, Marti-Renom M.A.$ ($corresponding author).
NAR Genomics and Bioinformatics, Volume 3, Issue 1, 2021.
Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation.
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. (*These authors contributed equally to this work)
Nat Commun 2021 12, 651
TADs without borders.
Farabella I., Marti-Renom M.A.
Nat. Genet. 52, 752–753; 2020. Invited News & Views
Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs.
Di Stefano M., Stadhouders R., Farabella I., Castillo D., Serra F., Graf T., Marti-Renom M.A.
Nat. Commun. 2020 11, 2564
Hierarchical chromatin organization detected by TADpole.
Soler-Vila P., Cuscó Pons P.,Farabella I., Di Stefano M., Marti-Renom M.A.
Nucleic Acids Res. 2020 Feb 21.
RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.
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.
Nat Biotechnol. 2019 Jul;37(7):793-802.
Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.
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.
Nat Genet. 2019 Jul;51(7):1137-1148.
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modelling.
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.$, Wu T.$ (*These authors contributed equally to this work)
PLoS Genet. 2018 Dec 26;14(12):e1007872.
Main PhD work
TEMPy: a Python Library for Assessment of 3D Electron Microscopy Density Fits
Farabella I., Vasishtan D., Joseph A. P., Pandurangan A. P., Sahota H., Topf M.
J Appl Crystallogr. 2015 Jun. 27;48 (Pt 4):1314-1323.
Allosteric Signalling in the Outer Membrane Translocation Domain of PapC Usher.
Farabella I., Pham T., Henderson N.S., Geibel S., Phan G., Thanassi D. G., Delcour A. H., Waksman G. and Topf M.
Elife. 2014 Oct 28;3