A very nice collaboration with the Szczurek and Beerenwinkel labs under the Computational ONcology TRaining Alliance Innovative Training (CONTRA) Network.…
Continue ReadingSIEVE: joint inference of single‑nucleotide
Genomic characterization of circulating tumor cells
Today out in Genomics! We found substantial differences in the mutational loads of CTC pools obtained using different CTC-capture methods.…
Continue ReadingOn the root of eukaryotes
We started this collaboration with the Katz lab and today is finally out! Using phylogenomics, we propose that the eukaryote…
Continue ReadingScalable single-cell phylogenies
Nice collaboration with Luay Nakhleh and Hamim Zafar labs on scalable single-cell phylogenetic inference: Phylovar: toward scalable phylogeny-aware inference of…
Continue Readingmini-review on single-cell DNA variant callers
https://doi.org/10.1016/j.csbj.2022.06.013 Here, we review current approaches for single-cell variant calling, emphasizing single nucleotide variants. We highlight their potential benefits and shortcomings…
Continue Readingphylogenetic origins of relapse using single-cell data
Our phylogenetic analysis of single cells exposes how, where and when malignant cells survive treatment in a personalized manner in…
Continue ReadingmtDNA single-cell paper
In CRC, mtDNA heteroplasmy mainly arises from differences among cells, but in some cases, the ancestral tumor cell can host…
Continue ReadingUnderstanding SARS-CoV-2 transmission
Together with colleagues at a local hospital, here we show that is not easy to figure out with just genomics…
Continue ReadingCellPhy paper
Finally out! ML inference of single-cell phylogenies https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02583-w Download CellPhy at: https://github.com/amkozlov/cellphy
Continue ReadingAECC grant: Microbiome as biomarker for CRC
We want to thank the Spanish Cancer Association (AECC) for awarding us a research grant to study the role of…
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