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1.

Cell-type specialization is encoded by specific chromatin topologies.

Winick-Ng, Warren; Kukalev, Alexander; Harabula, Izabela; Zea-Redondo, Luna; Szabó, Dominik; Meijer, Mandy; Serebreni, Leonid; Zhang, Yingnan; Bianco, Simona; Chiariello, Andrea M; Irastorza-Azcarate, Ibai; Thieme, Christoph J; Sparks, Thomas M; Carvalho, Sílvia; Fiorillo, Luca; Musella, Francesco; Irani, Ehsan; Torlai Triglia, Elena; Kolodziejczyk, Aleksandra A; Abentung, Andreas; Apostolova, Galina; Paul, Eleanor J; Franke, Vedran; Kempfer, Rieke; Akalin, Altuna; Teichmann, Sarah A; Dechant, Georg; Ungless, Mark A; Nicodemi, Mario; Welch, Lonnie; Castelo-Branco, Gonçalo; Pombo, Ana.

Nature ; 599(7886): 684-691, 2021 11.

Article in English | MEDLINE | ID: mdl-34789882

2.

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.

Beagrie, Robert A; Thieme, Christoph J; Annunziatella, Carlo; Baugher, Catherine; Zhang, Yingnan; Schueler, Markus; Kukalev, Alexander; Kempfer, Rieke; Chiariello, Andrea M; Bianco, Simona; Li, Yichao; Davis, Trenton; Scialdone, Antonio; Welch, Lonnie R; Nicodemi, Mario; Pombo, Ana.

Nat Methods ; 20(7): 1037-1047, 2023 07.

Article in English | MEDLINE | ID: mdl-37336949

3.

Methods for mapping 3D chromosome architecture.

Kempfer, Rieke; Pombo, Ana.

Nat Rev Genet ; 21(4): 207-226, 2020 04.

Article in English | MEDLINE | ID: mdl-31848476

4.

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.

Fiorillo, Luca; Musella, Francesco; Conte, Mattia; Kempfer, Rieke; Chiariello, Andrea M; Bianco, Simona; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Esposito, Andrea; Abraham, Alex; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario.

Nat Methods ; 18(5): 482-490, 2021 05.

Article in English | MEDLINE | ID: mdl-33963348

5.

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.

Markowski, Julia; Kempfer, Rieke; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Loof, Gesa; Kehr, Birte; Pombo, Ana; Rahmann, Sven; Schwarz, Roland F.

Bioinformatics ; 37(19): 3128-3135, 2021 Oct 11.

Article in English | MEDLINE | ID: mdl-33830196

6.

Formation of new chromatin domains determines pathogenicity of genomic duplications.

Franke, Martin; Ibrahim, Daniel M; Andrey, Guillaume; Schwarzer, Wibke; Heinrich, Verena; Schöpflin, Robert; Kraft, Katerina; Kempfer, Rieke; Jerkovic, Ivana; Chan, Wing-Lee; Spielmann, Malte; Timmermann, Bernd; Wittler, Lars; Kurth, Ingo; Cambiaso, Paola; Zuffardi, Orsetta; Houge, Gunnar; Lambie, Lindsay; Brancati, Francesco; Pombo, Ana; Vingron, Martin; Spitz, Francois; Mundlos, Stefan.

Nature ; 538(7624): 265-269, 2016 Oct 13.

Article in English | MEDLINE | ID: mdl-27706140

7.

Publisher Correction: Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.

Fiorillo, Luca; Musella, Francesco; Conte, Mattia; Kempfer, Rieke; Chiariello, Andrea M; Bianco, Simona; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Esposito, Andrea; Abraham, Alex; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario.

Nat Methods ; 18(10): 1266, 2021 Oct.

Article in English | MEDLINE | ID: mdl-34480161

8.

Extensive folding variability between homologous chromosomes in mammalian cells.

Irastorza-Azcarate, Ibai; Kukalev, Alexander; Kempfer, Rieke; Thieme, Christoph J; Mastrobuoni, Guido; Markowski, Julia; Loof, Gesa; Sparks, Thomas M; Brookes, Emily; Natarajan, Kedar Nath; Sauer, Stephan; Fisher, Amanda G; Nicodemi, Mario; Ren, Bing; Schwarz, Roland F; Kempa, Stefan; Pombo, Ana.

bioRxiv ; 2024 May 10.

Article in English | MEDLINE | ID: mdl-38766012

9.

GIInger predicts homologous recombination deficiency and patient response to PARPi treatment from shallow genomic profiles.

Pozzorini, Christian; Andre, Gregoire; Coletta, Tommaso; Buisson, Adrien; Bieler, Jonathan; Ferrer, Loïc; Kempfer, Rieke; Saintigny, Pierre; Harlé, Alexandre; Vacirca, Davide; Barberis, Massimo; Gilson, Pauline; Roma, Cristin; Saitta, Alexandra; Smith, Ewan; Consales Barras, Floriane; Ripol, Lucia; Fritzsche, Martin; Marques, Ana Claudia; Alkodsi, Amjad; Marin, Ray; Normanno, Nicola; Grimm, Christoph; Müllauer, Leonhard; Harter, Philipp; Pignata, Sandro; Gonzalez-Martin, Antonio; Denison, Ursula; Fujiwara, Keiichi; Vergote, Ignace; Colombo, Nicoletta; Willig, Adrian; Pujade-Lauraine, Eric; Just, Pierre-Alexandre; Ray-Coquard, Isabelle; Xu, Zhenyu.

Cell Rep Med ; 4(12): 101344, 2023 12 19.

Article in English | MEDLINE | ID: mdl-38118421

10.

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.

McGarvey, Alison C; Kopp, Wolfgang; Vucicevic, Dubravka; Mattonet, Kenny; Kempfer, Rieke; Hirsekorn, Antje; Bilic, Ilija; Gil, Marine; Trinks, Alexandra; Merks, Anne Margarete; Panáková, Daniela; Pombo, Ana; Akalin, Altuna; Junker, Jan Philipp; Stainier, Didier Y R; Garfield, David; Ohler, Uwe; Lacadie, Scott Allen.

Cell Genom ; 2(1): 100083, 2022 Jan 12.

Article in English | MEDLINE | ID: mdl-36777038

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