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ryansohny.bsky.social
Sohny
@ryansohny.bsky.social
75 followers 290 following 10 posts
PostDoc @Stergachislab UW |
Trying to become a scientist failing miserably for now
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Reposted by Sohny
daphnarothschild.bsky.social
Ribosomal RNA (rRNA) genes are found in hundreds of copies in the human genome.

Do sequence variations in these paralogs change the ribosome function? Yes!

I am excited to share our new preprint @mbarnalab @jkpritch in collaboration with Calico:
www.medrxiv.org/content/10.1...

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November 19, 2025 at 11:00 PM
Reposted by Sohny
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Sohny
clauswilke.com
A response to all the people who say "if your results depend on your random seed you have bigger problems."
blog.genesmindsmachines.com/p/random-see...
Random seeds and brown M&Ms
Your first mistake was assuming people actually understand how random numbers work.
blog.genesmindsmachines.com
October 23, 2025 at 4:48 PM
ryansohny.bsky.social
Delighted to announce that our consortium-wide paper demonstrating identification of cancer somatic genome alterations & epigenetic aberrations across traditionally intractable genomic regions (i.e., centromeres & telomeres) by leveraging personalized diploid genome assemblies is now up on bioRxiv.
biorxivpreprint.bsky.social bioRxivpreprint @biorxivpreprint.bsky.social · Oct 13
A telomere-to-telomere map of somatic mutation burden and functional impact in cancer https://www.biorxiv.org/content/10.1101/2025.10.10.681725v1
October 14, 2025 at 1:52 AM
Reposted by Sohny
biorxivpreprint.bsky.social
A telomere-to-telomere map of somatic mutation burden and functional impact in cancer https://www.biorxiv.org/content/10.1101/2025.10.10.681725v1
October 13, 2025 at 11:33 PM
Reposted by Sohny
aphillippy.bsky.social
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Reposted by Sohny
stevenstrogatz.com
My "Math, Revealed" series is freely available to anyone -- no paywall! -- in the thread below.
July 4, 2025 at 12:07 AM
Reposted by Sohny
smahtnetwrk.bsky.social
This upcoming #WorldEnvironmentDay, we’re highlighting how SMaHT is advancing science in ways that support both human health and sustainability.

By deepening our understanding of somatic mosaicism, SMaHT is helping to drive more precise diagnoses and support a more efficient healthcare system. 🌱🌍
June 3, 2025 at 4:02 PM
Reposted by Sohny
mollyprz.bsky.social
Now published in PNAS: www.pnas.org/doi/10.1073/...
May 23, 2025 at 6:39 PM
Reposted by Sohny
fubsyshabaroon.bsky.social
Apologies for getting a bit political on main tonight.

I think this cartoon sums it up.
January 20, 2025 at 10:10 PM
ryansohny.bsky.social
I freakin love what Liz has been doing.
January 18, 2025 at 1:58 AM
ryansohny.bsky.social
The president of South Korea has just been impeached.
December 14, 2024 at 8:10 AM
Reposted by Sohny
rebeccasolnit.bsky.social
Just a little reminder that the South Korean president who just declared martial law was elected two years ago on a wave of anti-feminist backlash. Misogyny is routinely part of the authoritarian package.

www.bbc.com/news/world-a...
Why misogyny is at the heart of South Korea's presidential elections
Disgruntled young men who resent feminism are the focus of candidates vying to be president.
www.bbc.com
December 3, 2024 at 6:11 PM
Reposted by Sohny
biorxiv-genomic.bsky.social
Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing https://www.biorxiv.org/content/10.1101/2024.11.06.622310v1
Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing https://www.biorxiv.org/content/10.1101/2024.11.06.622310v1
Gene regulation is mediated by the co-occupancy of numerous proteins along individual chromatin fibe
www.biorxiv.org
November 7, 2024 at 8:36 AM