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1.

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.

Kim, Charissa; Gao, Ruli; Sei, Emi; Brandt, Rachel; Hartman, Johan; Hatschek, Thomas; Crosetto, Nicola; Foukakis, Theodoros; Navin, Nicholas E.

Cell ; 173(4): 879-893.e13, 2018 05 03.

Article in English | MEDLINE | ID: mdl-29681456

2.

Compartmentalizing damaged DNA: A double-edged sword.

Georgiades, Emily; Crosetto, Nicola; Bienko, Magda.

Mol Cell ; 84(1): 12-13, 2024 Jan 04.

Article in English | MEDLINE | ID: mdl-38181754

3.

Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1.

Wiegard, Anika; Kuzin, Vladislav; Cameron, Donald P; Grosser, Jan; Ceribelli, Michele; Mehmood, Rashid; Ballarino, Roberto; Valant, Francesco; Grochowski, Radoslaw; Karabogdan, Ivana; Crosetto, Nicola; Lindqvist, Arne; Bizard, Anna Helene; Kouzine, Fedor; Natsume, Toyoaki; Baranello, Laura.

Mol Cell ; 81(24): 5007-5024.e9, 2021 12 16.

Article in English | MEDLINE | ID: mdl-34767771

4.

A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization.

Zampetidis, Christos P; Galanos, Panagiotis; Angelopoulou, Andriani; Zhu, Yajie; Polyzou, Aikaterini; Karamitros, Timokratis; Kotsinas, Athanassios; Lagopati, Nefeli; Mourkioti, Ioanna; Mirzazadeh, Reza; Polyzos, Alexandros; Garnerone, Silvano; Mizi, Athanasia; Gusmao, Eduardo G; Sofiadis, Konstantinos; Gál, Zita; Larsen, Dorthe H; Pefani, Dafni-Eleftheria; Demaria, Marco; Tsirigos, Aristotelis; Crosetto, Nicola; Maya-Mendoza, Apolinar; Papaspyropoulos, Angelos; Evangelou, Konstantinos; Bartek, Jiri; Papantonis, Argyris; Gorgoulis, Vassilis G.

Mol Cell ; 81(23): 4907-4923.e8, 2021 12 02.

Article in English | MEDLINE | ID: mdl-34793711

5.

Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

Wernersson, Erik; Gelali, Eleni; Girelli, Gabriele; Wang, Su; Castillo, David; Mattsson Langseth, Christoffer; Verron, Quentin; Nguyen, Huy Q; Chattoraj, Shyamtanu; Martinez Casals, Anna; Blom, Hans; Lundberg, Emma; Nilsson, Mats; Marti-Renom, Marc A; Wu, Chao-Ting; Crosetto, Nicola; Bienko, Magda.

Nat Methods ; 2024 Jun 06.

Article in English | MEDLINE | ID: mdl-38844629

6.

Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations.

Gothe, Henrike Johanna; Bouwman, Britta Annika Maria; Gusmao, Eduardo Gade; Piccinno, Rossana; Petrosino, Giuseppe; Sayols, Sergi; Drechsel, Oliver; Minneker, Vera; Josipovic, Natasa; Mizi, Athanasia; Nielsen, Christian Friberg; Wagner, Eva-Maria; Takeda, Shunichi; Sasanuma, Hiroyuki; Hudson, Damien Francis; Kindler, Thomas; Baranello, Laura; Papantonis, Argyris; Crosetto, Nicola; Roukos, Vassilis.

Mol Cell ; 75(2): 267-283.e12, 2019 07 25.

Article in English | MEDLINE | ID: mdl-31202576

7.

The era of 3D and spatial genomics.

Bouwman, Britta A M; Crosetto, Nicola; Bienko, Magda.

Trends Genet ; 38(10): 1062-1075, 2022 10.

Article in English | MEDLINE | ID: mdl-35680466

8.

What determines the specificity and outcomes of ubiquitin signaling?

Ikeda, Fumiyo; Crosetto, Nicola; Dikic, Ivan.

Cell ; 143(5): 677-81, 2010 Nov 24.

Article in English | MEDLINE | ID: mdl-21111228

9.

Deep learning-based tumor microenvironment segmentation is predictive of tumor mutations and patient survival in non-small-cell lung cancer.

Raczkowska, Alicja; Pasnik, Iwona; Kukielka, Michal; Nicos, Marcin; Budzinska, Magdalena A; Kucharczyk, Tomasz; Szumilo, Justyna; Krawczyk, Pawel; Crosetto, Nicola; Szczurek, Ewa.

BMC Cancer ; 22(1): 1001, 2022 Sep 21.

Article in English | MEDLINE | ID: mdl-36131239

10.

Discovering CRISPR-Cas off-target breaks.

Jiménez, Carlos; Crosetto, Nicola.

Nat Methods ; 20(5): 641-642, 2023 05.

Article in English | MEDLINE | ID: mdl-37024652

11.

Spatially resolved transcriptomics and beyond.

Crosetto, Nicola; Bienko, Magda; van Oudenaarden, Alexander.

Nat Rev Genet ; 16(1): 57-66, 2015 01.

Article in English | MEDLINE | ID: mdl-25446315

12.

Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress.

Shi, Wei; Vu, Therese; Boucher, Didier; Biernacka, Anna; Nde, Jules; Pandita, Raj K; Straube, Jasmin; Boyle, Glen M; Al-Ejeh, Fares; Nag, Purba; Jeffery, Jessie; Harris, Janelle L; Bain, Amanda L; Grzelak, Marta; Skrzypczak, Magdalena; Mitra, Abhishek; Dojer, Norbert; Crosetto, Nicola; Cloonan, Nicole; Becherel, Olivier J; Finnie, John; Skaar, Jeffrey R; Walkley, Carl R; Pandita, Tej K; Rowicka, Maga; Ginalski, Krzysztof; Lane, Steven W; Khanna, Kum Kum.

Blood ; 129(18): 2479-2492, 2017 05 04.

Article in English | MEDLINE | ID: mdl-28270450

13.

Regulation of translesion synthesis DNA polymerase eta by monoubiquitination.

Bienko, Marzena; Green, Catherine M; Sabbioneda, Simone; Crosetto, Nicola; Matic, Ivan; Hibbert, Richard G; Begovic, Tihana; Niimi, Atsuko; Mann, Matthias; Lehmann, Alan R; Dikic, Ivan.

Mol Cell ; 37(3): 396-407, 2010 Feb 12.

Article in English | MEDLINE | ID: mdl-20159558

14.

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

Bienko, Magda; Crosetto, Nicola; Teytelman, Leonid; Klemm, Sandy; Itzkovitz, Shalev; van Oudenaarden, Alexander.

Nat Methods ; 10(2): 122-124, 2013 Feb.

Article in English | MEDLINE | ID: mdl-23263692

15.

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.

Crosetto, Nicola; Mitra, Abhishek; Silva, Maria Joao; Bienko, Magda; Dojer, Norbert; Wang, Qi; Karaca, Elif; Chiarle, Roberto; Skrzypczak, Magdalena; Ginalski, Krzysztof; Pasero, Philippe; Rowicka, Maga; Dikic, Ivan.

Nat Methods ; 10(4): 361-5, 2013 Apr.

Article in English | MEDLINE | ID: mdl-23503052

16.

scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.

Chen, Jinxin Phaedo; Diekmann, Constantin; Wu, Honggui; Chen, Chong; Della Chiara, Giulia; Berrino, Enrico; Georgiadis, Konstantinos L; Bouwman, Britta A M; Virdi, Mohit; Harbers, Luuk; Bellomo, Sara Erika; Marchiò, Caterina; Bienko, Magda; Crosetto, Nicola.

Nat Commun ; 15(1): 1768, 2024 Feb 27.

Article in English | MEDLINE | ID: mdl-38409079

17.

High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.

Zhang, Ning; Harbers, Luuk; Simonetti, Michele; Diekmann, Constantin; Verron, Quentin; Berrino, Enrico; Bellomo, Sara E; Longo, Gabriel M C; Ratz, Michael; Schultz, Niklas; Tarish, Firas; Su, Peng; Han, Bo; Wang, Wanzhong; Onorato, Sofia; Grassini, Dora; Ballarino, Roberto; Giordano, Silvia; Yang, Qifeng; Sapino, Anna; Frisén, Jonas; Alkass, Kanar; Druid, Henrik; Roukos, Vassilis; Helleday, Thomas; Marchiò, Caterina; Bienko, Magda; Crosetto, Nicola.

Nat Commun ; 15(1): 3475, 2024 Apr 24.

Article in English | MEDLINE | ID: mdl-38658552

18.

Regulation of ubiquitin-binding proteins by monoubiquitination.

Hoeller, Daniela; Crosetto, Nicola; Blagoev, Blagoy; Raiborg, Camilla; Tikkanen, Ritva; Wagner, Sebastian; Kowanetz, Katarzyna; Breitling, Rainer; Mann, Matthias; Stenmark, Harald; Dikic, Ivan.

Nat Cell Biol ; 8(2): 163-9, 2006 Feb.

Article in English | MEDLINE | ID: mdl-16429130

19.

A GC-centered view of 3D genome organization.

Bouwman, Britta Am; Crosetto, Nicola; Bienko, Magda.

Curr Opin Genet Dev ; 78: 102020, 2023 02.

Article in English | MEDLINE | ID: mdl-36610373

20.

Enhancers dysfunction in the 3D genome of cancer cells.

Della Chiara, Giulia; Jiménez, Carlos; Virdi, Mohit; Crosetto, Nicola; Bienko, Magda.

Front Cell Dev Biol ; 11: 1303862, 2023.

Article in English | MEDLINE | ID: mdl-38020908

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