Major, fatal errors found in the data and methods of a 2020 paper in nature, including millions of reads mis-identified as bacteria. The "cancer microbiome" in this study was simply not there. @abrahamgihawi Mihaela Pertea Yuchen Ge Jen Lu biorxiv.org/content/10.110…

ggcoverage: an R package to visualize and annotate genome coverage for various NGS data bmcbioinformatics.biomedcentral.com/articles/10.11…

Cell type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells biorxiv.org/content/10.110…

The second annual Spatial Biology Workshop is just two weeks away! This free event will showcase the power of spatial techniques to answer biological questions. We'll be showcasing new methods for data generation and analysis, as well as the novel findings they enable (1/x)

how did long DNA molecules - 100 times longer than those usually sequenced in cancer - help us solve a paradox about BRCA deficiency? read all about in our paper, out in nature today nature.com/articles/s4158… 👇🧵 1/

Our latest paper: measurement of cancer evolutionary dynamics at massive scale, using just a methylation array on bulk DNA. Find evolutionary dynamics strongly determine clinical outcomes in lymphoid cancers. Fab collab with Inaki Martin & Martí Duran-Ferrer, & led by Calum Gabbutt. A🧵⬇️

We have just updated our database of (496!) funding opportunities for early-career researchers/faculty. For each entry, we provide link, $ amount, deadline, eligibility criteria. Download this database for free here: research.jhu.edu/rdt/funding-op…

Beyond excited to see this paper out. Most satisfying paper reproducing lung adeno to small-cell transformation in experimental model. Key players: EGFR, TP53, RB1, PIK3CA/PTEN, and MYC. Huge congratulations to Eric Gardner, Ashley Laughney, and the team! science.org/doi/10.1126/sc…

I'm super excited to share Nimbus, our algorithm for automatic classification of cellular marker expression in multiplexed image data! Nimbus is a pretrained deep learning model that works out of the box across panels with any combination of markers (1/x) biorxiv.org/content/10.110…

Open #PhD position in my lab Human Technopole in Milan together with Politecnico di Milano. #DataScience for cancer evolution. Use #MachineLearning methods to analyse and interpret cancer single cell data and understand how to design better treatments. Join us!

Does cancer #evolution & intra-tumour heterogeneity predict long-term relapse? We tested the evolutionary paradigm in prostate cancer clinical trials with long follow-up, combining genomics with digital histopathology: nature.com/articles/s4301…

We are pleased that our analyses on somatic mitochondrial DNA mutations (mosaicism) in normal human cells are published! Great work Jisong An. nature.com/articles/s4158…

Peter Campbell leaves the Sanger Institute at the end of the year to become Quotient's CSO. A mentor and one of my favourite scientists. His foundational, profound and creative contributions to cancer genomics and somatic evolution have truly shaped those fields. [1/7]

I am delighted that my company (Inocras) shows the utility of whole-genome sequencing in real-world oncology! A prospective study with Ajou Univ. Hospital. nature.com/articles/s1227…

It was fantastic scientific event. I gained valuable insights into cancer research and connected with peers for discussions. Many thanks to @NCICancerBio and the organizing committee. #NCI_JI_2024

🧬Excited to share highlights from our latest publication demonstrating preservation of clinical utility with whole genome sequencing (WGS) data generated from routine FFPE cancer biopsies! 🧵#CancerGenomics Serena Nik-Zainal Early Cancer Institute, University of Cambridge @MedGen_UOC nature.com/articles/s4146…

The Curtis Lab’s latest study on the genomic architecture of breast cancer from the pre-invasive to metastatic setting is now out in Nature! nature.com/articles/s4158…

Super excited to introduce QUICHE (Quantitative InterCellular Niche Enrichment) - a statistical method that can be used to discover local cellular niches differentially enriched in spatial regions, longitudinal samples, or clinical patient groups :) (1/10) biorxiv.org/content/10.110…

I’m super excited to share what I’ve been working on for the last (many) years: a spatial + genomic + transcriptomic characterization of how the breast cancer microenvironment evolves through immunotherapy! (1/x) biorxiv.org/content/10.110…

I am honored to be part of this fellowship and look forward to engaging with experts.