Jonas Koeppel

@JonasKoeppel

EMBO postdoctoral fellow | Shendure & Pinglay labs @UW Trying to understand and engineer our wonderfully weird genomes 🧬

865Followers

654Following

262Posts total

44.6KViews on collected posts

Growth & engagement

How the posts we collected actually performed: views and reaction rate post by post, what the audience did with them, and where the follower count goes.

Views per post

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679

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Last 14 collected posts, oldest on the left. The scale is logarithmic: one post can outrun the rest a hundred times over.

Engagement rate per post

0.80%3 Jun

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Reactions — likes, reposts, replies and quotes — divided by views.

What the audience does

Likes57.8%273 in total

Reposts15.3%72 in total

Replies5.7%27 in total

Quotes1.5%7 in total

Bookmarks19.7%93 in total

Share of every reaction we collected for this account. Replies mean argument, reposts mean endorsement, bookmarks mean the post was worth keeping.

The follower curve appears once this account has two daily snapshots — we take one a day, and this one is on its first.

Latest posts

@JonasKoeppel @sudpinglay @JShendure Exciting to see you followed up on something we tried to dissect already while ago. https://t.co/T7pxyDAy4p 200 views · 2 likes · 0 reposts · 1 replies 04 Jun 2026 20/n Of course, viability in one near-haploid cell line is a narrow definition of essentiality. The exciting next step is to apply Shred-seq across diverse cell types, including pluripotent stem cells and differentiation systems 405 views · 1 likes · 0 reposts · 1 replies 03 Jun 2026 22/n On a personal note, I’ll soon start an independent research group in the Genome Biology Unit at EMBL Heidelberg. If you enjoy this type of work and want to engineer genomes at the largest scale, please reach out! https://t.co/PZtPj6fnrE https://t.co/XMH6FH4dJQ 3.9K views · 55 likes · 11 reposts · 2 replies 03 Jun 2026 21/n This has been a really fun project to work on. Huge thanks to all co-authors, collaborators, and everyone who helped along the way: @sudpinglay @JShendure, Aidan Keith, @ssgriz, @chen_peixi, Riza Daza, @fquaisar1, Eleftheria Anastasia, Zihao Song 679 views · 0 likes · 0 reposts · 1 replies 03 Jun 2026 19/n See the fantastic perspective by @sudpinglay, also out today! https://t.co/gi7F9Ly37Q 438 views · 1 likes · 0 reposts · 1 replies 03 Jun 2026 18/n Overall, we think Shred-seq opens the door to genome-wide deletion scanning at high resolution. Once we can empirically define which sequences are required for survival in defined contexts, we can design minimal human genomes 414 views · 0 likes · 0 reposts · 1 replies 03 Jun 2026 17/n. We envision that large data sets matching tens of thousands of deletions to viability and expression changes will be ideal to train/benchmark the next generation of genomic AI models, which are currently bottlenecked by the paucity, relatedness, and bias of natural genomes 404 views · 3 likes · 0 reposts · 1 replies 03 Jun 2026 14/n A major advantage of phage-promoter genotyping is that the genotype is transcribed into RNA. That means Shred-seq should, in principle, be compatible with single-cell RNA-seq, linking specific deletions to transcriptomes in the same cells 426 views · 1 likes · 0 reposts · 1 replies 03 Jun 2026 15/n Making this work required several tweaks. For example, in situ T7 transcripts are not naturally polyadenylated, so we adapted the workflow to polyadenylate T7-derived transcripts and capture them alongside endogenous mRNAs. Details are in the manuscript https://t.co/q0iJ7IuG 452 views · 2 likes · 0 reposts · 1 replies 03 Jun 2026 16/n It worked! For example, we recovered an allelic deletion series where some deletions overlap RBM3 while others spare it. In single-cell transcriptomes, only the RBM3-overlapping deletions reduced RBM3 expression, giving a clean genotype-phenotype link https://t.co/9QgTgbusvZ 452 views · 3 likes · 0 reposts · 1 replies 03 Jun 2026 13/n Coming back to the original question: How much of the human genome is dispensable for the growth of a haploid cell line? Somewhere between 50-96%! Running Shred-seq at higher coverage should further narrow that empirical bound https://t.co/trgBXAr5O5 475 views · 3 likes · 0 reposts · 2 replies 03 Jun 2026 12/n For example, surviving deletions at this locus are depleted of deletions that intersect WDR3, an essential gene. Generally, Shred-seq lets us identify constrained loci by looking for places where the surviving deletion profile deviates from expected Cas3 distribution https:/ 459 views · 1 likes · 0 reposts · 1 replies 03 Jun 2026 11/n Beyond global trends, deletion scans allow us to look at locus-specific essentiality. If unselected deletions follow a baseline length distribution, then post-selection distortions of that distribution can reveal regions under constraint without relying on prior annotations 456 views · 1 likes · 1 reposts · 1 replies 03 Jun 2026 10/n Is this all just avoidance of essential coding genes? Not entirely. Even when we restricted the analysis to noncoding deletions, surviving deletions were depleted from active chromatin and enriched in inactive chromatin features https://t.co/XVtVvbccr3 498 views · 3 likes · 0 reposts · 1 replies 03 Jun 2026 9/n Surviving deletions are depleted not only for essential protein-coding exons, but also for active, conserved, and mutation-constrained sequences. We even see a signal for lncRNAs (using a dataset generated by @nevillesanjana lab) https://t.co/5eg2dhtxeW 567 views · 4 likes · 1 reposts · 1 replies 03 Jun 2026 8/n Because we generate the deletions experimentally, we can compare variants shortly after editing, before strong selection, to variants that survive weeks of growth in culture. This gives a direct way to quantify purifying selection on deletions in coding and non-coding regions 555 views · 2 likes · 1 reposts · 1 replies 03 Jun 2026 7/n After lots of optimizations, we managed to make this really high throughput (gigabase-scale): We induced > 36k deletions between 1-500 kb that sum up to 2.55 Gb, and scanned ~14% of the human genome https://t.co/p0yGdNxkYe 622 views · 4 likes · 1 reposts · 1 replies 03 Jun 2026 3/n But not just any deletions. Ideally, we wanted deletion scans: many overlapping deletions of different lengths starting from defined sites. Such an allelic series should make it possible to identify where essential genomic regions begin and end with high resolution. https://t 958 views · 3 likes · 1 reposts · 1 replies 03 Jun 2026 5/n Making deletions is only half the problem. The harder question is how to read out thousands of unpredictable deletion junctions at high throughput. For this, we took inspiration from phage-promoter-based genotyping developed by @sudpinglay, @XiaoyiLi10, and others 637 views · 3 likes · 1 reposts · 1 replies 03 Jun 2026 4/n There is a CRISPR system that does exactly that! CRISPR-Cas3 can be targeted to any DNA sequence using a crRNA. Once there, it starts chewing up DNA, leaving large deletions in its wake! Fantastic pioneering work by the Yan Zhang lab and @TanRenke https://t.co/2dScCItFQr 717 views · 6 likes · 1 reposts · 1 replies 03 Jun 2026 2/n For two decades, genome-wide screens in human cells overwhelmingly confined themselves to the disruption of protein-coding genes, leaving the remaining non-coding 98% of the genome largely unexplored by direct perturbation 1.1K views · 3 likes · 1 reposts · 1 replies 03 Jun 2026 1/n What fraction of the human genome is essential for cellular viability? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay @JShendure https://t.co/rTO1MyFv3q h 29.7K views · 172 likes · 53 reposts · 4 replies 03 Jun 2026

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