Selected publications
2024
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images. Nat Methods. doi: 0.1038/s41592-024-02294-7
High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue. Nat Commun. doi: 10.1038/s41467-024-47664-z
scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells. Nat Commun. doi: 10.1038/s41467-024-45972-y
2023
How Hi-C ignited the era of 3D genome biology. Nat Rev Genet. doi: 10.1038/s41576-023-00583-z
2022
Genomic Profiling Identifies Putative Pathogenic Alterations in NSCLC Brain Metastases. JTO Clin Res Rep. doi: 10.1016/j.jtocrr.2022.100435
FRET-FISH probes chromatin compaction at individual genomic loci in single cells. Nat Commun. doi: 10.1038/s41467-022-34183-y
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. doi: 10.1038/s41523-021-00352-3
2021
Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas. Front Oncol. doi: 10.3389/fonc.2021.700568
COVseq is a cost-effective wokflow for mass-scale SARS-CoV-2 genomic surveillance. Nat Commun. doi: 10.1038/s41467-021-24078-9
2020
Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc. doi: 10.1038/s41596-020-0397-2
GPSeq reveals the radial organization of chromatin in the cell nucleus. Nat Biotechnol. doi: 10.1038/s41587-020-0519-y
2019
CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples. Nat Commun. doi: 10.1038/s41467-019-12570-2
Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations. Mol Cell. doi: 10.1016/j.molcel.2019.05.015
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. Nat Commun. doi: 10.1038/s41467-019-09616-w
2018
RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples. Commun Biol. doi: 10.1038/s42003-018-0218-0
2017
BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nat Commun. doi: 10.1038/ncomms15058
Quantification of HER2 and estrogen receptor heterogeneity in breast cancer by single-molecule RNA fluorescence in situ hybridization. Oncotarget. doi:
Older
Spatially resolved transcriptomics and beyond. Nat Rev Genet. 2015. doi: 10.1038/nrg3832
FuseFISH: robust detection of transcribed gene fusions in single cells. Cell Rep. 2014. doi: 10.1016/j.celrep.2013.12.002
Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods. 2013. doi: 10.1038/nmeth.2408
A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nat Methods. 2013. doi: 10.1038/nmeth.2306