SO timely! A short teaser preprint from a wonderful collab w/ ⁦Alex swarbrick⁩ lab. Full protocol available for in supporting material. snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profiling ⁦⁦⁦10x Genomics⁩ biorxiv.org/content/10.110…

Functional inference of gene regulation using single-cell multi-omics - ScienceDirect sciencedirect.com/science/articl…

The CFCE had a wonderful visit to the Franklin Park Zoo this weekend as part of the DFCI 75th anniversary! #DanaFarber75

Our prostate cancer cfDNA methylation profiling study is out Nature Communications, >200 patients, strong classifier for local disease and mets, methylation at GR related to immune signature and outcome. More to be discovered. Dataset available through EGA. rdcu.be/cYwNs

Super cool project from Johannes Köster’s group on making datavzrd = tool to create visual and interactive HTML reports from collections of CSV/TSV tables! #biodata22 🔗 github.com/koesterlab/dat…

New collaboration led by Carlo Palmieri with RCSI School of Pharmacy and Biomolecular Sciences Beaumont RCSI Cancer Centre EORG groups highlighting immune differences between breast cancer and brain mets and the potential importance of ARG2 expression in T-cell depletion and clinical outcome. sciencedirect.com/science/articl…

🕺🏿 OUT TODAY Nature Genetics 📰 Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1 🧑🏿‍🤝‍🧑🏼 Xavier Darzacq Robert Tjian, and team 👇 go.nature.com/3He5aVy

We are happy to share our manuscript describing the Regulatory Genomics Toolbox (RGT). RGT is a python framework for analysis of chromatin and regulatory genomics data as interval algebra, peak calling, motif matching and IO tinyurl.com/wfeccn4c

Comprehensive profiling of metastatic breast tumours at mutational, gene expression and methylation level. Lots of paired samples allowing tracking of cancer evolution nature.com/articles/s4301…

An allosteric pan-TEAD inhibitor blocks oncogenic YAP/TAZ signaling and overcomes KRAS G12C inhibitor resistance | Nature Cancer | Great work by ⁦⁦Genentech⁩ #ASCO23 nature.com/articles/s4301…

Clustering algorithms report clusters even when none exist. In single-cell RNA-Seq pipelines, novel cell types are often identified by clustering algorithms. Expanding on Kimes et al.'s work, we introduce significance analysis for single-cell RNA-Seq data: nature.com/articles/s4159…

Introducing CODAL: rdcu.be/dgCQF a powerful method for analyzing perturbations in cell state atlases constructed through single-cell RNA-seq and ATAC-seq analysis! See MIRA Python package at mira-multiome.readthedocs.io. #SingleCell #multiome #scRNAseq #scATACseq #ITCR

I am happy to communicate that SCENIC+ was published in Nature Methods. SCENIC+ is a workflow to infer enhancer-driven gene regulatory networks from scRNA-seq and scATAC-seq data. This work was done together with Carmen Bravo at Stein Aerts lab! 🧵1/9🧵 nature.com/articles/s4159…

So sad to say goodbye to Ruiyang who has done such fantastic work over the past year at the Dana-Farber! But we know we will continue to do great things in grad school Columbia University and NY Genome Center.

The Gray Foundation has awarded $25 million to 7 research teams, 5 of which are based in Greater Boston, to fight BRCA-related cancers. "Boston is number one in terms of cancer research,” Laurie Glimcher MD said. “It’s an unbelievable life sciences ecosystem.” bostonglobe.com/2023/08/10/bus…

So happy to have contributed to this very interesting study with the OserLab !