Enhancers dysfunction in the 3D genome of cancer cells by Giulia Della Chiara, Carlos Jiménez, Mohit Virdi, Nicola Crosetto, Nicola Crosetto, Nicola Crosetto, Magda Bienko, Magda Bienko, Magda Bienko

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Radial Organization in the Mammalian Nucleus by Nicola Crosetto, Magda Bienko

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Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas by Luuk Harbers, Luuk Harbers, Federico Agostini, Federico Agostini, Marcin Nicos, Dimitri Poddighe, Dimitri Poddighe, Magda Bienko, Magda Bienko, Nicola Crosetto, Nicola Crosetto

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The Role of Intratumor Heterogeneity in the Response of Metastatic Non-Small Cell Lung Cancer to Immune Checkpoint Inhibitors by Marcin Nicoś, Marcin Nicoś, Paweł Krawczyk, Nicola Crosetto, Janusz Milanowski

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Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51 by Idit Hazan, Jonathan Monin, Britta A.M. Bouwman, Nicola Crosetto, Rami I. Aqeilan

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FuseFISH: Robust Detection of Transcribed Gene Fusions in Single Cells by Stefan Semrau, Nicola Crosetto, Magda Bienko, Marina Boni, Paolo Bernasconi, Roberto Chiarle, Alexander van Oudenaarden

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Modeling double strand break susceptibility to interrogate structural variation in cancer by Tracy J. Ballinger, Britta A. M. Bouwman, Reza Mirzazadeh, Silvano Garnerone, Nicola Crosetto, Colin A. Semple

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An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination by Roberto Ballarino, Britta A. M. Bouwman, Federico Agostini, Luuk Harbers, Constantin Diekmann, Erik Wernersson, Magda Bienko, Nicola Crosetto

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FRET-FISH probes chromatin compaction at individual genomic loci in single cells by Ana Mota, Szymon Berezicki, Erik Wernersson, Luuk Harbers, Xiaoze Li-Wang, Katarina Gradin, Christiane Peuckert, Nicola Crosetto, Magda Bienko

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Deep learning-based tumor microenvironment segmentation is predictive of tumor mutations and patient survival in non-small-cell lung cancer by Alicja Rączkowska, Iwona Paśnik, Michał Kukiełka, Marcin Nicoś, Magdalena A. Budzinska, Tomasz Kucharczyk, Justyna Szumiło, Paweł Krawczyk, Nicola Crosetto, Ewa Szczurek

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Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer by Ruli Gao, Charissa Kim, Emi Sei, Theodoros Foukakis, Nicola Crosetto, Leong-Keat Chan, Maithreyan Srinivasan, Hong Zhang, Funda Meric-Bernstam, Nicholas Navin

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CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples by Xiaolu Zhang, Silvano Garnerone, Michele Simonetti, Luuk Harbers, Marcin Nicoś, Reza Mirzazadeh, Tiziana Venesio, Anna Sapino, Johan Hartman, Caterina Marchiò, Magda Bienko, Nicola Crosetto

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iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture by Eleni Gelali, Gabriele Girelli, Masahiro Matsumoto, Erik Wernersson, Joaquin Custodio, Ana Mota, Maud Schweitzer, Katalin Ferenc, Xinge Li, Reza Mirzazadeh, Federico Agostini, John P. Schell, Fredrik Lanner, Nicola Crosetto, Magda Bienko

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BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks by Winston X. Yan, Reza Mirzazadeh, Silvano Garnerone, David Scott, Martin W. Schneider, Tomasz Kallas, Joaquin Custodio, Erik Wernersson, Yinqing Li, Linyi Gao, Yana Federova, Bernd Zetsche, Feng Zhang, Magda Bienko, Nicola Crosetto

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A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks by Fabio Iannelli, Alessandro Galbiati, Ilaria Capozzo, Quan Nguyen, Brian Magnuson, Flavia Michelini, Giuseppina D’Alessandro, Matteo Cabrini, Marco Roncador, Sofia Francia, Nicola Crosetto, Mats Ljungman, Piero Carninci, Fabrizio d’Adda di Fagagna

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CDK12 controls transcription at damaged genes and prevents MYC-induced transcription-replication conflicts by Laura Curti, Sara Rohban, Nicola Bianchi, Ottavio Croci, Adrian Andronache, Sara Barozzi, Michela Mattioli, Fernanda Ricci, Elena Pastori, Silvia Sberna, Simone Bellotti, Anna Accialini, Roberto Ballarino, Nicola Crosetto, Mark Wade, Dario Parazzoli, Stefano Campaner

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Author Correction: scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells by Jinxin Phaedo Chen, Constantin Diekmann, Honggui Wu, Chong Chen, Giulia Della Chiara, Enrico Berrino, Konstantinos L. Georgiadis, Britta A. M. Bouwman, Mohit Virdi, Luuk Harbers, Sara Erika Bellomo, Caterina Marchiò, Magda Bienko, Nicola Crosetto

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scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells by Jinxin Phaedo Chen, Constantin Diekmann, Honggui Wu, Chong Chen, Giulia Della Chiara, Enrico Berrino, Konstantinos L. Georgiadis, Britta A. M. Bouwman, Mohit Virdi, Luuk Harbers, Sara Erika Bellomo, Caterina Marchiò, Magda Bienko, Nicola Crosetto

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Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility stud... by Ioannis Zerdes, Michele Simonetti, Alexios Matikas, Luuk Harbers, Balazs Acs, Ceren Boyaci, Ning Zhang, Dimitrios Salgkamis, Susanne Agartz, Pablo Moreno-Ruiz, Yalai Bai, David L. Rimm, Johan Hartman, Artur Mezheyeuski, Jonas Bergh, Nicola Crosetto, Theodoros Foukakis

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Cytokine Profiling of End Stage Cancer Patients Treated with Immunotherapy by Marco Carlo Merlano, Andrea Abbona, Matteo Paccagnella, Antonella Falletta, Cristina Granetto, Vincenzo Ricci, Elena Fea, Nerina Denaro, Fiorella Ruatta, Anna Merlotti, Oscar Bertetto, Nicola Crosetto, Danilo Galizia, Marco Basiricò, Loretta Gammaitoni, Dario Sangiolo, Massimo Aglietta, Ornella Garrone

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