Robin Friedman

Our work on mammalian sperm heterogeneity and sperm-level natural selection is now out in @ScienceMagazine: science.sciencemag.org/content/early/… We've added lots of new data and analysis since the @biorxivpreprint came out last year. I'll highlight the new findings here! (1/n)

🧵 (1/6) Two years ago, when I only started digging into the current state of aging research, I was much more optimistic about our progress. I read articles like Laura Deming's Longevity FAQ, which lists "95 things that make mice live longer", and thought: "Well, at least we have something that works for mice, right?" Boy, I was naive! Well, below is a list of findings that made me think we have almost nothing that reliably works on mice. The Longevity FAQ post: #95thingsthatmakemicelivelonger" target="_blank" rel="nofollow noopener">ldeming.com/longevityfaq#9….

In this preprint biorxiv.org/content/10.110… with @sindri_e we compared seven widely used methods for batch correction of single cell RNA-seq data. We found that all but one of the methods introduce batch effects when there are none. 1/N

@iskander 🙋‍♂️

Got ~20 more invites, let me know if you need one. My heuristic for who I send them to is I scroll through each person's feed and look for any sign of participation in or engagement with scholarly research of any kind.

Today #CZCellxGene is releasing the R package cellxgene.census — it gives access from R to Census, the largest standardized aggregation of single-cell data, composed of 33M+ cells and 60K genes. You can easily export slices to Seurat or @Bioconductor. 🧵⬇️ bit.ly/44Uq5pm

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 @elapertea @YuchenGe1 @JenniferLu717 biorxiv.org/content/10.110…

Ever analyze a scRNAseq dataset and wonder if a specific cell state has been seen before? And if so, where in the human body? Under what conditions? Well, now you can use our lightning fast SCimilarity search and foundational model for that! ⚡️🔎🧬 biorxiv.org/content/10.110… (1/11)

We are happy to share our latest work on #ambientRNA in single-cell and single-nucleus RNA-seq experiments, out now in @GenomeBiology! (1/7) link.springer.com/article/10.118…

(1/5) scfoundation, another single-cell foundation model tinyurl.com/2w468bzu 1- trained on 50M cells (biggest out there) 2- introduced read depth pretraining task (subsample counts and the predict the difference), more robust pretraining task imo compared to prev ones imo

Mind blown 🤯: It turns out that somatic cells turn *on* a regulator that increases mutation. This complex is turned off in the germline. WTF evolution.

It's frustrating reading comp bio articles these days because many keep falling into the same pitfalls. Hard to know if the method actually works, or whether they messed up the evaluation. Here are some issues I've seen recently (w/o names):

What a revolution in a very few yrs for cystic fibrosis patients! Such great news for those who made it to today, albeit tempered with regret for those who didn't. A genetic disease but the revolution isn't gene therapy. Pursuing gene therapy still worthwhile, maybe less urgent

RBPamp: Quantitative Modeling of Protein-RNA Interactions in vitro Predicts in vivo Binding bioRxiv biorxiv.org/cgi/content/sh…

Cancer #immunotherapy #DataScience resource of the week: #scRNAseq & #scTCRseq atlas of 400,000‼️T cells from 316 patients of 21 cancer types, derived from tumors, adjacent normal tissue, and peripheral blood.Half of data newly sequenced, half gathered from literature. 🧵(1/4)

"Why don't biotech co's open source their SW?" a.k.a. "Tech co's open source; let's be more like them" a.k.a. "Why is everyone I know rebuilding the same shit, over and over, instead of sharing?" 🧵

Meanwhile, the single cell field

Our review (with co-first authors Natalie Wolf and Djem Kissiov) of the roles of NK cells in immunity to cancer, and applications to immunotherapy of cancer, is out in Nature Reviews Immunology! nature.com/articles/s4157…

Why you can't use eQTLs to interpret GWAS hits: A story in 2 parts

@izabelcavassim @illumina Parabéns Izabel! Ótimo!

Dear Twitter friends, I am delighted to share that this week I will be starting a new position @illumina in SD as a Bioinformatics Scientist. I'd like to thank everyone that has contributed one way or another to this––special gratitude towards my direct and indirect supervisors

Excited to share our newest manuscript! We find that RNA localization mechanisms that send RNAs to a given subcellular structure in one cell type can *predictably* traffic RNAs in other cell types, even if they don't have that subcellular structure. biorxiv.org/content/10.110…

In 2018, we developed mux-seq and demuxlet to enable population-scale single-cell sequencing. Today, excited to share our paper in @ScienceMagazine where we deployed mux-seq to profile 1.2M immune cells from 162 lupus patients and 99 healthy controls: science.org/doi/full/10.11…. 1/n