Search | VHL CLAP/WR-PAHO/WHO

1.

MED27, SLC6A7, and MPPE1 Variants in a Complex Neurodevelopmental Disorder with Severe Dystonia.

Reid, Kimberley M; Spaull, Robert; Salian, Smrithi; Barwick, Katy; Meyer, Esther; Zhen, Juan; Hirata, Hiromi; Sheipouri, Diba; Benkerroum, Hind; Gorman, Kathleen M; Papandreou, Apostolos; Simpson, Michael A; Hirano, Yoshinobu; Farabella, Irene; Topf, Maya; Grozeva, Detelina; Carss, Keren; Smith, Martin; Pall, Hardev; Lunt, Peter; De Gressi, Susanna; Kamsteeg, Erik-Jan; Haack, Tobias B; Carr, Lucinda; Guerreiro, Rita; Bras, Jose; Maher, Eamonn R; Scott, Richard H; Vandenberg, Robert J; Raymond, F Lucy; Chong, Wui K; Sudhakar, Sniya; Mankad, Kshitij; Reith, Maarten E; Campeau, Philippe M; Harvey, Robert J; Kurian, Manju A.

Mov Disord ; 37(10): 2139-2146, 2022 10.

Article in English | MEDLINE | ID: mdl-35876425

2.

Hierarchical chromatin organization detected by TADpole.

Soler-Vila, Paula; Cuscó, Pol; Farabella, Irene; Di Stefano, Marco; Marti-Renom, Marc A.

Nucleic Acids Res ; 48(7): e39, 2020 04 17.

Article in English | MEDLINE | ID: mdl-32083658

3.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.

Nir, Guy; Farabella, Irene; Pérez Estrada, Cynthia; Ebeling, Carl G; Beliveau, Brian J; Sasaki, Hiroshi M; Lee, S Dean; Nguyen, Son C; McCole, Ruth B; Chattoraj, Shyamtanu; Erceg, Jelena; AlHaj Abed, Jumana; Martins, Nuno M C; Nguyen, Huy Q; Hannan, Mohammed A; Russell, Sheikh; Durand, Neva C; Rao, Suhas S P; Kishi, Jocelyn Y; Soler-Vila, Paula; Di Pierro, Michele; Onuchic, José N; Callahan, Steven P; Schreiner, John M; Stuckey, Jeff A; Yin, Peng; Aiden, Erez Lieberman; Marti-Renom, Marc A; Wu, C-Ting.

PLoS Genet ; 14(12): e1007872, 2018 12.

Article in English | MEDLINE | ID: mdl-30586358

4.

Conformational changes during pore formation by the perforin-related protein pleurotolysin.

Lukoyanova, Natalya; Kondos, Stephanie C; Farabella, Irene; Law, Ruby H P; Reboul, Cyril F; Caradoc-Davies, Tom T; Spicer, Bradley A; Kleifeld, Oded; Traore, Daouda A K; Ekkel, Susan M; Voskoboinik, Ilia; Trapani, Joseph A; Hatfaludi, Tamas; Oliver, Katherine; Hotze, Eileen M; Tweten, Rodney K; Whisstock, James C; Topf, Maya; Saibil, Helen R; Dunstone, Michelle A.

PLoS Biol ; 13(2): e1002049, 2015 Feb.

Article in English | MEDLINE | ID: mdl-25654333

5.

Genome-wide tracing to decipher nuclear organization.

Flores, Victoria; Farabella, Irene; Nir, Guy.

Curr Opin Cell Biol ; 82: 102175, 2023 Jun.

Article in English | MEDLINE | ID: mdl-37263058

6.

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.

Harris, Hannah L; Gu, Huiya; Olshansky, Moshe; Wang, Ailun; Farabella, Irene; Eliaz, Yossi; Kalluchi, Achyuth; Krishna, Akshay; Jacobs, Mozes; Cauer, Gesine; Pham, Melanie; Rao, Suhas S P; Dudchenko, Olga; Omer, Arina; Mohajeri, Kiana; Kim, Sungjae; Nichols, Michael H; Davis, Eric S; Gkountaroulis, Dimos; Udupa, Devika; Aiden, Aviva Presser; Corces, Victor G; Phanstiel, Douglas H; Noble, William Stafford; Nir, Guy; Di Pierro, Michele; Seo, Jeong-Sun; Talkowski, Michael E; Aiden, Erez Lieberman; Rowley, M Jordan.

Nat Commun ; 14(1): 3303, 2023 06 06.

Article in English | MEDLINE | ID: mdl-37280210

7.

Three-dimensional genome organization via triplex-forming RNAs.

Farabella, Irene; Di Stefano, Marco; Soler-Vila, Paula; Marti-Marimon, Maria; Marti-Renom, Marc A.

Nat Struct Mol Biol ; 28(11): 945-954, 2021 11.

Article in English | MEDLINE | ID: mdl-34759378

8.

3D reconstruction of genomic regions from sparse interaction data.

Mendieta-Esteban, Julen; Di Stefano, Marco; Castillo, David; Farabella, Irene; Marti-Renom, Marc A.

NAR Genom Bioinform ; 3(1): lqab017, 2021 Mar.

Article in English | MEDLINE | ID: mdl-33778492

9.

Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments.

Di Stefano, Marco; Castillo, David; Serra, François; Farabella, Irene; Goodstadt, Mike N; Marti-Renom, Marc A.

Methods Mol Biol ; 2157: 35-63, 2021.

Article in English | MEDLINE | ID: mdl-32820398

10.

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation.

Vilarrasa-Blasi, Roser; Soler-Vila, Paula; Verdaguer-Dot, Núria; Russiñol, Núria; Di Stefano, Marco; Chapaprieta, Vicente; Clot, Guillem; Farabella, Irene; Cuscó, Pol; Kulis, Marta; Agirre, Xabier; Prosper, Felipe; Beekman, Renée; Beà, Silvia; Colomer, Dolors; Stunnenberg, Hendrik G; Gut, Ivo; Campo, Elias; Marti-Renom, Marc A; Martin-Subero, José Ignacio.

Nat Commun ; 12(1): 651, 2021 01 28.

Article in English | MEDLINE | ID: mdl-33510161

11.

Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs.

Di Stefano, Marco; Stadhouders, Ralph; Farabella, Irene; Castillo, David; Serra, François; Graf, Thomas; Marti-Renom, Marc A.

Nat Commun ; 11(1): 2564, 2020 05 22.

Article in English | MEDLINE | ID: mdl-32444798

12.

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.

Morf, Jörg; Wingett, Steven W; Farabella, Irene; Cairns, Jonathan; Furlan-Magaril, Mayra; Jiménez-García, Luis F; Liu, Xin; Craig, Frank F; Walker, Simon; Segonds-Pichon, Anne; Andrews, Simon; Marti-Renom, Marc A; Fraser, Peter.

Nat Biotechnol ; 37(7): 793-802, 2019 07.

Article in English | MEDLINE | ID: mdl-31267103

13.

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.

Miguel-Escalada, Irene; Bonàs-Guarch, Silvia; Cebola, Inês; Ponsa-Cobas, Joan; Mendieta-Esteban, Julen; Atla, Goutham; Javierre, Biola M; Rolando, Delphine M Y; Farabella, Irene; Morgan, Claire C; García-Hurtado, Javier; Beucher, Anthony; Morán, Ignasi; Pasquali, Lorenzo; Ramos-Rodríguez, Mireia; Appel, Emil V R; Linneberg, Allan; Gjesing, Anette P; Witte, Daniel R; Pedersen, Oluf; Grarup, Niels; Ravassard, Philippe; Torrents, David; Mercader, Josep M; Piemonti, Lorenzo; Berney, Thierry; de Koning, Eelco J P; Kerr-Conte, Julie; Pattou, François; Fedko, Iryna O; Groop, Leif; Prokopenko, Inga; Hansen, Torben; Marti-Renom, Marc A; Fraser, Peter; Ferrer, Jorge.

Nat Genet ; 51(7): 1137-1148, 2019 07.

Article in English | MEDLINE | ID: mdl-31253982

14.

TADs without borders.

Farabella, Irene; Marti-Renom, Marc A.

Nat Genet ; 52(8): 752-753, 2020 08.

Article in English | MEDLINE | ID: mdl-32747821

15.

TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits.

Farabella, Irene; Vasishtan, Daven; Joseph, Agnel Praveen; Pandurangan, Arun Prasad; Sahota, Harpal; Topf, Maya.

J Appl Crystallogr ; 48(Pt 4): 1314-1323, 2015 Aug 01.

Article in English | MEDLINE | ID: mdl-26306092

16.

Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.

Stödberg, Tommy; McTague, Amy; Ruiz, Arnaud J; Hirata, Hiromi; Zhen, Juan; Long, Philip; Farabella, Irene; Meyer, Esther; Kawahara, Atsuo; Vassallo, Grace; Stivaros, Stavros M; Bjursell, Magnus K; Stranneheim, Henrik; Tigerschiöld, Stephanie; Persson, Bengt; Bangash, Iftikhar; Das, Krishna; Hughes, Deborah; Lesko, Nicole; Lundeberg, Joakim; Scott, Rod C; Poduri, Annapurna; Scheffer, Ingrid E; Smith, Holly; Gissen, Paul; Schorge, Stephanie; Reith, Maarten E A; Topf, Maya; Kullmann, Dimitri M; Harvey, Robert J; Wedell, Anna; Kurian, Manju A.

Nat Commun ; 6: 8038, 2015 Sep 03.

Article in English | MEDLINE | ID: mdl-26333769

17.

Allosteric signalling in the outer membrane translocation domain of PapC usher.

Farabella, Irene; Pham, Thieng; Henderson, Nadine S; Geibel, Sebastian; Phan, Gilles; Thanassi, David G; Delcour, Anne H; Waksman, Gabriel; Topf, Maya.

Elife ; 32014 Oct 28.

Article in English | MEDLINE | ID: mdl-25271373

18.

Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins.

Atherton, Joseph; Farabella, Irene; Yu, I-Mei; Rosenfeld, Steven S; Houdusse, Anne; Topf, Maya; Moores, Carolyn A.

Elife ; 3: e03680, 2014 Sep 10.

Article in English | MEDLINE | ID: mdl-25209998

19.

Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin.

Leung, Carl; Dudkina, Natalya V; Lukoyanova, Natalya; Hodel, Adrian W; Farabella, Irene; Pandurangan, Arun P; Jahan, Nasrin; Pires Damaso, Mafalda; Osmanovic, Dino; Reboul, Cyril F; Dunstone, Michelle A; Andrew, Peter W; Lonnen, Rana; Topf, Maya; Saibil, Helen R; Hoogenboom, Bart W.

Elife ; 3: e04247, 2014 Dec 02.

Article in English | MEDLINE | ID: mdl-25457051

20.

Correction: Allosteric signalling in the outer membrane translocation domain of PapC usher.