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Ilya Ruvinsky

@ruvinskyilya.bsky.social
336 followers 295 following 69 posts

Lots: dev bio, neuro, social signals, worms. Some: comments re practice of science, art, nature. Occasionally: something funny.

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Ilya Ruvinsky @ruvinskyilya.bsky.social · 13/02/2025
Dear @dev-journal.bsky.social, do you know what makes your claim of "format-free submission" a LOT less credible? Having in place ridiculously arcane formatting rules for submission! This must change!
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Sri Kosuri @srikosuri.bsky.social · 08/02/2025
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 24/01/2025
100% this experience on multiple previous occasions. Sharing in the worm community is outstanding!
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 16/01/2025
Easy choice! This is incredible.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 15/01/2025
What makes you say that the "to-be-ignored" reviews are on average detrimental to the system?
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 15/01/2025
Here's something astounding: www.nature.com/articles/s41...
nature.com
De novo designed proteins neutralize lethal snake venom toxins - Nature
Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 14/01/2025
Strongly endorse:
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 13/01/2025
It always is!
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 13/01/2025
Matt, it really was a fund read. A nice piece of classical genetic analysis that calls on diverse data types for support. What not to like? Plus the writing - "With a bit of tedious book keeping..." Dude! 👌
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 12/01/2025
A nice piece of work by @wormsrock.bsky.social. Highly recommend! academic.oup.com/genetics/art...
academic.oup.com
Parental-effect gene-drive elements under partial selfing, or why do Caenorhabditis genomes have hyperdivergent regions?
Abstract. Self-fertile Caenorhabditis nematodes carry a surprising number of Medea elements, alleles that act in heterozygous mothers and cause death or de
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 09/01/2025
You should try it at school drop off/pick up more often. Just sayin'
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 09/01/2025
I suspect all of us had reviews like this. Conservation is NOT a review criterion at the NIH. No harm in pointing that out. A larger problem is the insane reliance on proposals to decide what should be funded. I would trade OA publishing and players to be named later, for the system to change.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 08/01/2025
"Primarily" is a high standard to match, but I thought this study was cool. www.nature.com/articles/s41...
nature.com
Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection - Nature Microbiology
A secondary metabolite sensitizes competitor Bacillus subtilis to a wide panel of lytic phages by sequestering iron and preventing the activation of Spo0A.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 03/01/2025
It depends on what the meaning of the word "species" is. (just a reminder... Funny sayings by famous people for 100)
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 02/01/2025
Care to estimate the relative frequency of these four categories in 2024? Also, how about A, B, C for Category 4 (Huge, Medium, Minor)?
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 02/01/2025
journals.plos.org/plosbiology/...
journals.plos.org
Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue
Although human neural organoids are commonly used to study brain development, it is unclear how well they replicate the biology of primary tissue. These authors conduct a meta-analysis to compare over...
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 22/12/2024
!
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 20/12/2024
I am a little more positive re peer review, though I largely agree with you. But... because the current situation is unsatisfying does not mean it won't get worse if we scrap journals/review. We have recent experience - changes that were supposed to improve likely contributed to making things worse
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 20/12/2024
When one is convinced that one is right, one tends to consider evidence contradicting one's conviction to be less relevant.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 20/12/2024
Best and right-est.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 20/12/2024
Are the data consistent with this take? In the 20 years of OA evangelism, the costs (per paper and overall) to investigators increased. The publishing ecosystem seems less healthy than 2-3 decades ago. Unintended consequences are a powerful force. Publishers love the current situation. Should we?
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 20/12/2024
Sharp. Thoughtful. Insightful. Probably the best thing you will read about academic publishing today, this week, this month, or this year. DO IT!
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 18/12/2024
This clean and this empty?
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Reposted by Ilya Ruvinsky
The Map Center @mapcenter.com · 17/12/2024
Hi. I'm Andrew. I own New England's oldest map store because last year I moved across the country after an old guy retired and gave it to me Willy Wonka-style. Visit my store in Rhode Island. www.mapcenter.com
A nerd in a teal sweater holding a stack of books about railroads in front of a wall of framed maps.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 16/12/2024
Stress is bad. Several different stresses can be too much. A relatable experience. @currentbiology.bsky.social www.cell.com/current-biol...
cell.com
Combining multiple stressors blocks bacterial migration and growth
Here, Sharma et al. use microfluidics to simultaneously provide a physical stressor (shear flow) and a chemical stressor (H2O2) to the human pathogen Pseudomonas aeruginosa. The replenishing power of shear flow increases H2O2 effectiveness 50-fold, allowing natural levels of H2O2 to block bacterial migration and growth.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 16/12/2024
@currentbiology.bsky.social does it again! Our environments are considerably more complex than we typically think. Is it really so surprising that there are broad swaths of biology we don't even know about, let alone don't know how to interpret? www.cell.com/current-biol...
cell.com
Latitudinal gradients in air density create invisible topography at sea level, affecting animal flight costs
Air density affects the costs of animal flight. This is well-established for flight at high altitude. Shepard et al. show that changes in air density cause regional differences in flight costs at sea level due to latitudinal temperature gradients. They discuss the implications for species distributions and for global change.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 16/12/2024
The chocolate shriveled in the Buffalo cold if you ask me.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 16/12/2024
'tis the bagels.
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eric lai @lucksmith.bsky.social · 11/12/2024
Natasha Staller and Gary Ruvkun, from yesterday's ceremony with the King of Sweden! 🏆
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 13/12/2024
Considering their evidently chimeric nature, mermaids are plausibly produced via hybridization between distantly related species. If so, they likely don't produce live offspring. Unless rarely via arcane partheno- or gynogenesis. This implies extreme longevity, ongoing hybridization, or both.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 13/12/2024
CN(G)S
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 12/12/2024
I agree that these are serious concerns. To me, the answer to "is it worth it?" strongly depends on whether the assertion "papers get better… but not by much" is true. Do we actually have serious estimates?
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 12/12/2024
More true in some parts of the country than in others.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 12/12/2024
This describes the process pretty well.
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 12/12/2024
Is 1/3 estimate due to going to "fancy" journals? In my experience, the average time in review (particularly considering bouncing from one journal to another) is well correlated with how fancy the first place of submission is. So there is value in IF - it's a predictor of time in review.
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John Doench @johndoench.bsky.social · 12/12/2024
We could also have PI fantasy league. +5 points for a glam mag publication, -2 for a Not Discussed R01 application, etc etc. I will workshop this idea in order to find a scoring scheme that alienates everyone on the planet.
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Neil Renic @ncrenic.bsky.social · 10/12/2024
Just had an idea
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Ariel Chipman @chipman-lab.bsky.social · 11/12/2024
New preprint just dropped. This is the first of my "sabbatical papers" - conceptual/synthetic papers trying to address broader questions of body-plan evolution. 1/5 ecoevorxiv.org/repository/v...
ecoevorxiv.org
The Development and Evolution of Arthropod Tagmata
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 10/12/2024
As the Nobel Award Ceremony is about to begin, what a valuable lesson was reminded to us all by the lectures given by Victor Ambros and Gary Ruvkun - some of the best science is done in the spirit of curiosity-driven research and genuine collaboration with friends and colleagues. www.nobelprize.org
nobelprize.org
The official website of the Nobel Prize - NobelPrize.org
Nobel Prize award ceremony
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 06/12/2024
Great study, Ethan! Congratulations!
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 06/12/2024
Neurons regulate the germline @odedrechavi.bsky.social @bjornschumacher.bsky.social Impressive!
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 06/12/2024
Turns out parental brains are thinking about offspring. @odedrechavi.bsky.social @bjornschumacher.bsky.social @meital.bsky.social Impressive!
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 06/12/2024
www.cnn.com/science/aust...
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 05/12/2024
Connectomes of synaptic wiring represent remarkable scientific achievements and are useful research tools. That said, much activity in the nervous system occurs via nonsynaptic signaling that is not represented in connectomes. Check out this review: www.sciencedirect.com/science/arti...
sciencedirect.com
Nonsynaptic encoding of behavior by neuropeptides
A basic tenet of neuroscience is that animal behavior is generated by neural circuits that operate through synaptic transmission. On top of this synap…
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 05/12/2024
That was too close for comfort 😅
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 05/12/2024
1. This does not apply to me because I am an efficient writer 2. Oh no
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Binyam Mogessie ቢንያም ሞገሴ @binyammogessie.bsky.social · 29/11/2024
Chromosome segregation errors are common in the early stages of human embryonic development. Read here our open access commentary on three recent studies of spindle architecture and positioning features that could provide insights into why early embryos are predisposed to aneuploidy. rdcu.be/d1TgG
rdcu.be
On the origin of mitosis-derived human embryo aneuploidy
Nature Communications - Chromosome segregation errors are common in the early stages of human embryonic development. By examining the first mitotic divisions of human embryos using live cell...
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 28/11/2024
Nice piece, @javierapfeld.bsky.social
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Ilya Ruvinsky @ruvinskyilya.bsky.social · 28/11/2024
Wait until people discover that same is true of Peru. Being equatorial is just not what it's cracked up to be.
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