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Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization cell.com/cell/fulltext/…

Cancer cell models, derived from patients in NCI-supported clinical trials, are available to the cancer research community. Learn more: pdmr.cancer.gov

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries [Laura Wiehle Graeme Thorn Güenter Raddatz Chris Clarkson DKFZ Epigenetics Karsten Rippe Achim Breiling Teif Lab] genome.cshlp.org/content/early/… 5hmC loss > nuc gain > CTCF loss > 5mC spreading > gene↓

Normal cell populations may not be as “normal” as once thought; a new Science study finds that somatic #mutations—including #genes associated with #cancer risk—arise in virtually every type of normal #tissue in the #human body. ($) fcld.ly/ree84z6

Our open-access paper in PLOS Biology on analysis validation and #simulation as a way to improve reproducibility of results journals.plos.org/plosbiology/ar… #datascience #informatics #bioinformatics

Robot unhappy hour. By T⚽️m Chitty™ ☆ with CartoonStock wired.trib.al/9v57fxh

Dear celebrities, #JurgenKlopp has a suggestion about how to give health advice. Sum: don't. #coronavirus

Happy to share our latest study on site-specific turnover of DNA methylation: nature.com/articles/s4146… Genomic maps of DNA methylation, while informative about genome activity and cell state, provide only a freeze frame and do not reveal the dynamics of DNA methylation.

The last portion of my graduate work, highlighting mesothelin-associated biology buried within patient tumor tissue datasets, is out today: nature.com/articles/s4138… #histoepigenetics histoepigenetic

9 months after presenting #ASHG19 the paper is finally out! Congrats Eugene Lurie for your amazing work on grouping human tumors by cancer cell intrinsic expression! Check out how MSLN and AKT are related in #PDAC #PancreaticCancer #openaccess rdcu.be/b5nTl

Nearly every human gene can be linked to cancer based on existing literature and if not, it will be. sciencedirect.com/science/articl…

This blog post by Paul Agapow written 5 years ago is very much on point, and (sadly) still relevant. agapow.net/science/comput…

PERFECT! journals.plos.org/plosbiology/ar…

Let’s talk about proteins whose abundance generally does not correlate the abundance of the transcripts that templates them. Give examples.

A cartoon by Colin Tom. #NewYorkerCartoons

We’re excited to share our preprint on spatial organization in glioblastoma: doi.org/10.1101/2023.0…. We combine spatial transcriptomics (Visium) and proteomics (CODEX) to reveal a five-layer organization of cellular states and highlight a role of hypoxia as tissue organizer. 1/

Lymphatic-localized Treg-mregDC crosstalk limits antigen trafficking and restrains anti-tumor immunity: Cancer Cell cell.com/cancer-cell/fu…

3) Yet in my past 25 years as a computational biologist I have repeatedly seen some of the best, most technically gifted and intellectually deep, bench biologists treat computationally differently. Any computational result that supports a claim they wish to make is sufficient ->

Are metastatic #cancers more like their normal origin or target tissues? Our work in Science Advances systematically compares the #transcriptomics of primary and metastatic #tumors to healthy tissues in a #PanCancer, genome-wide manner! #metastasis 🧵1/10 shorturl.at/Uc4xx

This is a fantastic #OpenAccess review in Cell Genomics! scTrends: A living review of commercial single-cell and spatial 'omic technologies Perfect for that overview for your trainees. Find link below.