How Hi-C ignited the era of 3D genome biology. Nat Rev Genet (2023).

A GC-centered view of 3D genome organization. Current Opinion in Genetics & Development 2023, 78:102020. doi: 10.1016/j.gde.2022.102020


Genomic profiling identifies putative pathogenic alterations in NSCLC brain metastases. JTO Clin Res Rep. 2022;3:100435. doi: 10.1016/j.jtocrr.2022.100435

FRET-FISH probes chromatin compaction at individual genomic loci in single cells, Nat Commun 13, 6680 (2022). doi: 10.1038/s41467-022-34183-y

Deep learning-based tumor microenvironment segmentation is predictive of tumor mutations and patient survival in non-small-cell lung cancer. BMC Cancer 22, 1001 (2022). doi: 10.1186/s12885-022-10081-w

An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination
Sci Data 9, 400 (2022). doi: 10.1038/s41597-022-01508-x

The era of 3D and spatial genomics
Trends in Genetics (2022). doi: 10.1016/j.tig.2022.05.010

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH
Sci Data 9, 47 (2022). doi: 10.1038/s41597-022-01139-2

RNA gradients: Shapers of 3D genome architecture.
Curr Opin Cell Biol. 2022 Jan 5;74:7-12. doi: 10.1016/


Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1.
Mol Cell. 2021 Dec 16;81(24):5007-5024.e9. doi: 10.1016/j.molcel.2021.10.015

A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization.
Mol Cell. 2021 Dec 2;81(23):4907-4923.e8. doi: 10.1016/j.molcel.2021.10.017.

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 study
npj Breast Cancer 7, 144 (2021). doi: 10.1038/s41523-021-00352-3

Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas
Front. Oncol. 11:700568 (2021). doi: 10.3389/fonc.2021.700568

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance
Nat Commun 12, 3903 (2021). doi: 10.1038/s41467-021-24078-9


Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells
Nat Commun 11, 5445 (2020). doi: 10.1038/s41467-020-19011-5

Genome-wide detection of DNA double-strand breaks by in-suspension BLISS
Nature Protocols 2020;… doi: 10.1038/s41596-020-0397-2

Genome-Wide CRISPR Off-Target DNA Break Detection by the BLISS Method
Methods in Molecular Biology 2021;2162:261-281. doi: 10.1007/978-1-0716-0687-2_15

Colibactin DNA-damage signature indicates mutational impact in colorectal cancer
Nature Medicine 2020 Jun 1; 1546-170X doi: 10.1038/s41591-020-0908-2

GPSeq reveals the radial organization of chromatin in the cell nucleus
Nature Biotechnology 2020 May 25; 1546-1696 doi: 10.1038/s41587-020-0519-y

Radial Organization in the Mammalian Nucleus
Frontiers in Genetics 2020 Feb 12; 11, 33 doi: 10.3389/fgene.2020.00033


A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
Cell 2019 Dec 12;179 (7):1647-1660.e19. doi: 10.1016/J.CELL.2019.11.025.

CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples
Nat Commun. 2019 Oct 18;10(1):4732. doi: 10.1038/s41467-019-12570-2.

Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51
Cell Rep. 2019 Oct 15;29(3):560-572.e4. doi: 10.1016/j.celrep.2019.09.001.

Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations
Mol Cell. 2019; S1097-2765(19)30387-9. doi: 10.1016/j.molcel.2019.05.015.

Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations
Nat Genet. 2019. doi: 10.1038/s41588-019-0421-z.

Human skin long noncoding RNA WAKMAR1 regulates wound healing by enhancing keratinocyte migration
PNAS 2019; 116(19):9443-9452. doi: 10.1073/pnas.1814097116.

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture
Nat Commun. 2019; 10:1636. doi: 10.1038/s41467-019-09616-w.

Modeling double strand break susceptibility to interrogate structural variation in cancer
Genome Biology 2019; 20:28. doi: 10.1186/s13059-019-1635-1.


Endogenous DNA Double-Strand Breaks during DNA Transactions: Emerging Insights and Methods for Genome-Wide Profiling
Genes 2018 14;9(12). doi: 10.3390/genes9120632.

RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples
Commun. Biol. 2018; 1:209. doi: 10.1038/s42003-018-0218-0.

An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics
Methods Mol Biol. 2018;1766:303-333. doi: 10.1007/978-1-4939-7768-0_17. PMID: 29605860.

Genome-Wide Profiling of DNA Double-Strand Breaks by the BLESS and BLISS Methods.
Methods Mol Biol. 2018;1672:167-194. doi: 10.1007/978-1-4939-7306-4_14.


Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer.
Nat Commun. 2017 Aug 29;8(1):374. doi: 10.1038/s41467-017-00393-y.

Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer.
Nat Commun. 2017 Aug 9;8(1):228. doi: 10.1038/s41467-017-00244-w.

Engineered Cpf1 variants with altered PAM specificities.
Nat Biotechnol 2017 Jun 5. doi: 10.1038/nbt.3900

A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks.
Nat Commun 2017 May 31;8:15656. doi: 10.1038/ncomms15656

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks.
Nat Commun 2017 May doi: 10.1038/ncomms15058

Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress.
Blood 2017 Mar doi: 10.1182/blood-2016-06-725093


Massive and parallel expression profiling using microarrayed single-cell sequencing.
Nat Commun. 2016 Oct 14;7:13182. doi: 10.1038/ncomms13182

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction.
Nat Biotechnol. 2016 Jun 27. doi: 10.1038/nbt.3598

Combined inhibition of DDR1 and Notch signaling is a therapeutic strategy for KRAS-driven lung adenocarcinoma.
Nat Med. 2016 Mar;22(3):270-7. doi: 10.1038/nm.4041


Genome-wide maps of nuclear lamina interactions in single human cells.
Cell. 2015 Sep 24;163(1):134-47. doi: 10.1016/j.cell.2015.08.040

Integrated genome and transcriptome sequencing of the same cell.
Nat Biotechnol. 2015 Mar;33(3):285-9. doi: 10.1038/nbt.3129

Spatially resolved transcriptomics and beyond.
Nat Rev Genet. 2015 Jan;16(1):57-66. doi: 10.1038/nrg3832

For our previous publications go to:

Nicola’s publication


Magda’s publications