Alex Pollen

Perspective outlining multiple entry points for studying the molecular basis of human brain evolution with @TylerFair_ sciencedirect.com/science/articl…

Interested in single cell genomics but need help getting started? Come to my lab's 10th (!) Single Cell Genomics Day on 6/12 Talks include Aviv Regev @anshulkundaje @junyue_cao @xinjin + (many) more + @ATJCagan illustrations! Free Youtube livestream at satijalab.org/scgd

Form follows function, or function dictates form? 📢Preprint: we build Perturb-CLEAR, in vivo screen of neuroanatomy! Disease perturbations produce selective morphology-RNA changes that RNA impact alone cannot predict. Was led by the invincible @BoliWu! biorxiv.org/content/10.648…

New preprint on Detectrons from @jihoon_han_phd! These are programmable biosensors for RNAs that produce DNA barcodes in the presence of their target RNA. Check out Jihoon's quoted thread for more: biorxiv.org/content/10.648…

NEXT TUE: DDD seminar, Feb. 17, 2026 @ 1PM Eastern US: Dr. Annerieke Sierksma (Dr. Bart De Strooper's @BStrooper group @ KU Leuven) present "Polygenic risk for Alzheimer’s disease shapes microglial inflammatory and antigen-presentation programs in vivo". carlocolantuoni.org/seminar

Today I'd like to honor the memory of my mentor and friend, Roger Tsien, born 1952 February 1. Today would have been Roger's 74th birthday. Most know Roger for his 2008 Chemistry Nobel Prize with Shimomura and Chalfie. Roger made GFP into the versatile imaging method it is now.

Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element biorxiv.org/content/10.648…

Excited to share work I contributed to during my UCSF postdoc with amazing colleagues, including Dr. Tianzhi Wu & Dr. Jingjing Li! @Kriegsteinlab @jingjingSF @UCSFstemcell ❤️ nature.com/articles/s4158…

10/ Thanks to @lessi_manuel for highlighting a preprint of the study prelights.biologists.com/highlights/dis…

9/ We hope our study will provide a framework for functionally studying how disease and evolution shape human cortical development.

1/ Our new study, led by @ding5066, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification nature.com/articles/s4158…

New preprint on technologies to scale up CRISPR screens. We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells. We also introduce an approach for cloning lentiviral libraries with billions of elements.

@TommyVierbuchen shared his work with us today: "A pluripotent stem cell platform for in vitro systems genetics studies of mouse brain development", see the recording at: youtube.com/playlist?list=… (more info at carlocolantuoni.org/seminar)

@MysmtpT5035 @anshulkundaje For pooled processing experiments of multiple individuals, CellBouncer (from @nkschaefer87) uses transcript polymorphisms that mismatch a cell's individual assignment as a ground truth for identifying and removing ambient RNA biorxiv.org/content/10.110…

@anshulkundaje CellBender from the Broad is a great tool and it generates a report to monitor and adapt as desired. It also helped our lab notice a huge issue with the exp protocol we were doing.

Does anyone have or know of robust automated adaptive approaches to filtering cells after mapping sc/snRNA-seq data. In my experience, this is a major manual bottleneck where thresholds are selected in rather arbitrary ways. There must be a better way, maybe even with AI agents?