bioRxiv
2026Tumour evolution as ground truth for cancer whole-genome sequencing
10.64898/2026.06.09.731105
Publications
Publications from the Caravagna Lab
Outputs · Publications
Our scientific record.
A live publication list drawn from Giulio Caravagna’s Google Scholar profile. Citation counts reflect Scholar and may change over time.
The laboratory was established in 2020; earlier publications reflect the PI’s PhD and postdoctoral research.
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Research selected by the laboratory.
bioRxiv
2025Timing and clustering co-occurring genome amplifications in cancers
10.1101/2025.03.31.646456
Genome Biology
2025MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles
10.1186/s13059-025-03530-9
Genome Biology
2025BASCULE: bayesian inference and clustering of mutational signatures leveraging biological priors
10.1186/s13059-025-03835-9
Genome Biology
2024Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc
10.1186/s13059-024-03170-5
Nature Communications
2026Scalable, fast and accurate differential gene expression testing from millions of cells of multiple patients
10.1038/s41467-026-74451-9
Nature Communications
2024Clinical application of tumour-in-normal contamination assessment from whole genome sequencing
10.1038/s41467-023-44158-2
Annals of Oncology
2023Clonal KEAP1 mutations with loss of heterozygosity share reduced immunotherapy efficacy and low immune cell infiltration in lung adenocarcinoma
10.1016/j.annonc.2022.12.002
bioRxiv
2024A high-throughput 3D culture microfluidic platform for multi-parameter phenotypic and omics profiling of patient-derived organoids
10.1101/2024.12.28.630600
Cancer discovery
2026Negative selection maintains grossly altered but broadly stable karyotypes in metastatic colorectal cancer
10.1158/2159-8290.cd-24-0813
Cancer Research
2025Epigenetic Heritability of Cell Plasticity Drives Cancer Drug Resistance through a One-to-Many Genotype-to-Phenotype Paradigm
10.1158/0008-5472.can-25-0999
Cancer Research
2023Tumor evolution and immune microenvironment dynamics define response to neoadjuvant treatment of esophageal adenocarcinoma
10.1158/1538-7445.am2023-4539
Clinical Cancer Research
2026Clinical significance of EGFR amplification in patients with EGFR-mutated metastatic non-small cell lung cancer receiving first-line osimertinib
10.1158/1078-0432.ccr-26-0924
Clinical Cancer Research
2024Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
10.1158/1078-0432.ccr-24-0626
Nature
2024The genomic landscape of 2,023 colorectal cancers
10.1038/s41586-024-07747-9
Nature
2024Long-term lineage commitment in haematopoietic stem cell gene therapy
10.1038/s41586-024-08250-x
Nature Biotechnology
2022Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin
10.1038/s41587-021-01031-1
Nature Cancer
2025Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of esophageal adenocarcinoma
10.1038/s43018-025-00955-w
Nature communications
2025Genomic landscape of diffuse glioma revealed by whole genome sequencing
10.1038/s41467-025-59156-9
Nature communications
2025Early tolerance and late persistence as alternative drug responses in cancer
10.1038/s41467-024-54728-7
Nature Communications
2023Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions
10.1038/s41467-023-39313-8
Nature Genetics
2024Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer
10.1038/s41588-024-01777-9
Nature Genetics
2020Subclonal reconstruction of tumors by using machine learning and population genetics
10.1038/s41588-020-0675-5
Nature Methods
2018Detecting repeated cancer evolution from multi-region tumor sequencing data
10.1038/s41592-018-0108-x
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