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Sergey Kryazhimskiy

@skryazhi.bsky.social
1.6K followers 481 following 315 posts

Work in progress | Evolution | Ecology | Systems Biology | Experiments | Theory | Running a lab @ucsdbiosciences | sklab.science | thoughtsforbreakfast.wordpress.com

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Reposted by Sergey Kryazhimskiy
Claus Wilke @clauswilke.com · 10h
Implementing oral exams at scale. The paper describes oral exams for hundreds of students, 5 min. each over zoom, administered by graduate TAs. My thoughts: It's doable but not easy. 5 min. is super short, yet it's tough for the TAs do to ~100 exams. www.tandfonline.com/doi/full/10....
tandfonline.com
Implementing Oral Exams at Scale: Experiences from Graduate Student Instructors
This paper describes the implementation of oral exams, a more authentic and potentially more informative form of assessment than written exams, at a large scale (over 600 students), in the context ...
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Reposted by Sergey Kryazhimskiy
Nigel Goldenfeld @nigelgoldenfeld.bsky.social · 04/10/2026
#Prop38 #California Clear reporting from @sandiegouniontribune.com "Critics view the legislation as a Trojan horse: while promising transformative medical breakthroughs, it will channel billions in state funding to a newly created institute that currently has no scientists or researchers."
sandiegouniontribune.com
San Diego research institutions aren’t talking about Prop. 38, even though they stand to receive billions
Californians to decide if they want the state to borrow $8.4 billion to support research that aims to deliver cures for cancer, Alzheimer’s and heart disease “in our lifetime.”
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Kristian G. Andersen @kgandersen.bsky.social · 03/10/2026
"The future depends on wisdom that Silicon Valley lacks" That's exactly right - a critical read on the future of AI (safety): www.theatlantic.com/technology/2...
theatlantic.com
I Quit OpenAI Because Its Culture Is Broken
The industry’s approach to safety will guarantee more failures unless something changes.
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Will Ratcliff @wcratcliff.bsky.social · 30/09/2026
Application review for the GRC in Microbial Population Biology will start October 15th! Please apply before then if you are keen on coming. www.grc.org/microbial-po...
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Reposted by Sergey Kryazhimskiy
Pleuni Pennings @pleunipennings.bsky.social · 29/09/2026
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...
abetterscientist.wordpress.com
Postdoc position on drug resistance evolution in Montpellier, France
I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…
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Reposted by Sergey Kryazhimskiy
Will Ratcliff @wcratcliff.bsky.social · 28/09/2026
New paper out with @kaylastoy.bsky.social: academic.oup.com/evlett/advan...
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Reposted by Sergey Kryazhimskiy
Richard Lenski @relenski.bsky.social · 22/09/2026
"Philosophy of Biology: The power of theory in the life sciences" elifesciences.org/articles/112... @zdblount.bsky.social shared this thought-provoking paper with the lab group.
elifesciences.org
Philosophy of Biology: The power of theory in the life sciences
Theory can help address cell and molecular biology’s major challenges, particularly those arising from large omics datasets.
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Reposted by Sergey Kryazhimskiy
Maitreya Dunham @maitreya.bsky.social · 17/09/2026
One fun thing at the Botstein symposium was being reminded of this great article about the novelist Jeffrey Eugenides visiting the lab to get some "spice" for The Marriage Plot. I can literally hear David say "I have here a novelist” when he brings him into the lab. www.nytimes.com/2012/02/14/s...
nytimes.com
The Scientist Was a Figment, but His Work Was Real (Gift Article)
Jeffrey Eugenides’s new novel, “The Marriage Plot,” has scenes describing yeast genetic studies that ring so true, many assume that researchers had to have given him some in-depth help.
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Will Ratcliff @wcratcliff.bsky.social · 15/09/2026
1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...
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Reposted by Sergey Kryazhimskiy
Anne Applebaum @anneapplebaum.wsocial.eu · 14/09/2026
Your regular reminder: If the Russians stop fighting, the war ends. If the Ukrainians stop fighting, their land will be occupied, their leaders will be killed, their history and language will be erased, their children will be kidnapped to serve Russia.
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Reposted by Sergey Kryazhimskiy
Graham Coop @gcbias.bsky.social · 10/09/2026
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
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Kristian G. Andersen @kgandersen.bsky.social · 10/09/2026
Take a look at the examples Antrophic provides for research that they blocked, and it's immediately clear almost much all of it is just basic research - but research that has gotten scary-sounding names via the media. An example, put Ebola genomes into Claude Science and ask for a TMRCA > blocked!
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
Check out the awesome read the docs here: accusnv.readthedocs.io/en/latest/ And the paper here: genome.cshlp.org/content/earl... Github here: github.com/liaoherui/Ac... Downstream analyses can be refined using either command line or notebook options.
accusnv.readthedocs.io
AccuSNV — AccuSNV documentation
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Will Shoemaker @shoestrapped.bsky.social · 04/09/2026
Self-reposting (re-skeeting?) as I may be teaching this sooner than expected.
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Sergey Kryazhimskiy @skryazhi.bsky.social · 01/09/2026
Question for evolutionary biologists. Am I missing something or are Fisher's geometric model and Simpson's adaptive landscape model exactly the same thing? And why has nobody said so? If you know a paper that makes this point even tangentially, pls let me know. #evolution #popgen #quantgen
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Christian Kost @kostchristian.bsky.social · 24/08/2026
Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb
nature.com
Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology
Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...
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Reposted by Sergey Kryazhimskiy
Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
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SeppeKuehnLab @seppekuehnlab.bsky.social · 29/06/2026
New paper out today in Nature Microbiology: "Epistatic interactions inform rational design of synthetic microbial communities for bioremediation." 🧵https://www.nature.com/articles/s41564-026-02386-4 @kiseokmicro.bsky.social @nitmb.bsky.social
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Sean Carroll @seanmcarroll.bsky.social · 20/08/2026
Thing I didn’t anticipate about living through civilizational decline is how many people responsible for the decline would be loudly convinced they were saving civilization.
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Glen Dsouza @nonresidentdesi.bsky.social · 10/08/2026
📣 We’re hiring a postdoc for @hot-mes-asu.bsky.social ! 🦠🔬 We’re looking for someone excited about microbial interactions, ecology & evolution, and using molecular genetics and microfluidics to understand microbial communities. Come do fun science with us! apply.interfolio.com/190859
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Will Ratcliff @wcratcliff.bsky.social · 03/08/2026
So, bluesky, where is the discussion of the absolute insane things AI is doing in the realm of mathematics? It seems like we're nearly at the inflection point where the models are as good as human domain experts, and soon may well be better. Is that discourse only happening on twitter?
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Megan Behringer @megbehri.bsky.social · 05/08/2026
New Preprint 🚨: Led by Ph.D student, Ashlynn Bruder, we explore how feast/famine cycles in our LTRS system influence temporal selection on new mutations. Reconstruction of mutations reveals environment-dependent epistasis + increased fitness during both feast and famine conditions. Summary Fig ⬇️
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Reposted by Sergey Kryazhimskiy
Elena Litchman @elenalitchman.bsky.social · 04/08/2026
Interested in doing a postdoc in plankton ecology, on topics of community assembly, trait-based ecological resilience, stressor interactions, harmful algal blooms and others? Contact me to discuss developing a proposal for MSU's EEB Presidential Postdoc Fellowship (Nov 1 application deadline).
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Reposted by Sergey Kryazhimskiy
C. Brandon Ogbunu @cbo.bsky.social · 04/08/2026
🚨NEW PAPER 🚨 "Deconstructing empirical fitness seascapes across scales of granularity" published in #G3 (@genetics-gsa.bsky.social) 1/2 The fitness landscape has been among the most influential instruments in evolutionary theory for nearly a century. But we often treat them as fixed and static.
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Christian Landry @christianlandry.bsky.social · 04/08/2026
Our latest contribution on #regulatoryevolution in which we show that the shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations. Led by @simonaube.bsky.social www.nature.com/articles/s41...
nature.com
The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations - Nature Ecology & Evolution
Saturation mutagenesis of the FCY1 promoter in budding yeast shows that adaptation to 5-fluorocytosine is not accessible through single cis-regulatory mutations, despite large mutational effects on pr...
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Chris Adami @chrisadami.bsky.social · 03/08/2026
Call for Presidential Postdoctoral Fellows in Evolution, Ecology, and Behavior (EEB) is open at Michigan State University. If you are interested in working with me, we can craft a proposal together. careers.msu.edu/jobs/postdoc...
careers.msu.edu
Postdoctoral Scholar-Fixed Term - East Lansing, Michigan, United States
Working/Functional Title Presidential Postdoctoral Fellow Position Summary We encourage applications from candidates in any early career stage, from finishing Ph.D. students to current postdoctoral sc...
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Reposted by Sergey Kryazhimskiy
Joshua Weitz @joshuasweitz.bsky.social · 03/08/2026
60,000+ comments on OMB’s proposal to politicize grants. The lesson: speak up. It makes a difference & it’s not over yet. 🎁 wapo.st/44YL4t1
WP story by Riley Beggin

Senate aims to block White House from gaining new power over science funding

https://wapo.st/44YL4t1
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Princess Vimentin PhD | Cancer Biologist @princess-vimentin.bsky.social · 02/08/2026
Yaaas! Good news on a Sunday! The senate moves to temporarily ban the OMB proposal that would allow political appointees in charge of approving federal grants, especially #NIH grants. Recall that the OMB rule yielded 500k comments, 95% of them against it. 🧪 www.politico.com/news/2026/08...
politico.com
Senate finalizes funding patch that would block Trump’s grant overhaul
Language is included to delay the president’s move to put political appointees in charge of grant approval.
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bioRxivpreprint @biorxivpreprint.bsky.social · 30/07/2026
The latent simplicity of microbial ecological interactions www.biorxiv.org/content/10.64898/20…
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Reposted by Sergey Kryazhimskiy
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 30/07/2026
We already do this and companies who want them are happy to pay for PhD student interns. Why do precious and limited NSF funds need to be deployed for this? Most PhD student pursue industry jobs anyways - that has always been true. Use NSF funds to support basic science that industry wont support!
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Arseny Khakhalin @khakhalin.bsky.social · 29/07/2026
Anecdotally Putin's Russia went for a new sweeping wave of repressions. Friends of friends and distant relatives are getting arrested, or warned that they will get arrested within a week, unless they flee abroad. Savings and real estate confiscated. Not sure why, but suddenly cracking down some more
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Reposted by Sergey Kryazhimskiy
Ran Blekhman @blekhman.bsky.social · 26/07/2026
Everyone says AI will accelerate science. I don't think it will -- at least not in biology, and at least not soon. New post where I explain why, and how the productivity paradox can be resolved: blekhman.substack.com/p/why-ai-wil...
blekhman.substack.com
Why AI will not speed up science (yet)
You can see AI everywhere except in the productivity statistics
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Revolving Door Project @revolvingdoordc.bsky.social · 24/07/2026
🚨 The Department of Energy admitted that Russell Vought cancelled hundreds of grants in October 2025 "based solely on the political identity of the grant recipient's state." It is long overdue—Democrats MUST move to impeach Vought, and Blue State Republicans need to answer for their complicity.
nytimes.com
Trump Administration Admits Canceling Grants to States That Did Not Vote for Him
Federal officials said in court documents that they halted billions of dollars in funding for energy projects to states “based solely” on whether they backed President Trump in the 2024 election.
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Jenna Norton @jenna-m-norton.bsky.social · 24/07/2026
Another damning admission on the Trump administration’s weaponization of government: the administration terminated grants of perceived political enemies. We all knew this was happening, but the admission and documentation in court is validating. www.nytimes.com/2026/07/24/b...
nytimes.com
Trump Administration Admits Canceling Grants to States That Did Not Vote for Him (Gift Article)
Federal officials said in court documents that they halted billions of dollars in funding for energy projects to states “based solely” on whether they backed President Trump in the 2024 election.
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Justin Hendrix @justinhendrix.bsky.social · 24/07/2026
A ‘golden age’ for whom? Cole Donovan argues that White House Office of Science and Technology Policy director Michael Kratsios' new report on the future of American science is cover for reallocating funding to the administration's friends—the big AI firms and hyperscalers.
techpolicy.press
OSTP Vision for Science is a ‘Golden Age’ for Corporations
"Science: A New Golden Age" tries to reframe the conversation away from the ongoing destruction of American science, writes Cole Donovan.
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Carl T. Bergstrom @carlbergstrom.com · 23/07/2026
1. The new Trump / Kratsios plan for US science appears explicitly designed to destroy US universities. Diverting money to tech donors is probably just a bonus. Gift link.
nytimes.com
Trump’s Plan for Science: More Money for A.I., Less for Universities (Gift Article)
Michael Kratsios, President Trump’s science adviser, proposed overhauling how the government funds research. Democrats said Mr. Trump’s actions had weakened science.
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Christopher Webb @cwebbonline.com · 19/07/2026
PURE EVIL Stephen Miller’s worldview in one video clip. "I think the ideal solution would be to cut off their fingers. I don't think it's necessary to kill them entirely. We're not a barbaric people. We respect life. Therefore, torture is the way to go. Because tortured people can live.”
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Javi Ibarrondo @jibarrondo.bsky.social · 15/07/2026
Editorial and peer review dynamics at elite general science journals | Science Advances www.science.org/doi/10.1126/... 🧪
science.org
Editorial and peer review dynamics at elite general science journals
Analyses of deidentified data reveal complex interactions that quantify success at elite general science journals.
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Jenna Norton @jenna-m-norton.bsky.social · 13/07/2026
I submitted my comment on the proposed OMB rule. Sharing here to the extent it’s useful. Today is the last day to comment. If you have not yet commented, please do! substack.com/@jennanorton...
substack.com
A Public Comment on Proposed Rule: Regulation for Federal Financial Assistance
Docket: OMB-2026-0034, Submitted by: Jenna M Norton, PhD, MPH in a personal capacity
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Glen Dsouza @nonresidentdesi.bsky.social · 12/07/2026
Excited to share that I've been awarded a 5-year NIH MIRA (R35) from the National Institute of General Medical Sciences! The lab is growing! We're recruiting postdocs and research techs interested in microbial ecology, quantitative microscopy, microfluidics, and molecular biology. Please share!
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Sergey Kryazhimskiy @skryazhi.bsky.social · 12/07/2026
Working on my comment now. This tool is useful, but there is a mistake with at least one paragraph citation. It is §200.461 that refers to publication costs not §200.405.
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Genetics Society of America @genetics-gsa.bsky.social · 09/07/2026
The proposed OMB "Regulation for Federal Financial Assistance" could fundamentally change how federal research funding is awarded and managed. Learn more in our blog: buff.ly/AazbsEG Make use of a great tool by APS: buff.ly/gRnlJCT ✍️ Submit your comments by July 13!
buff.ly
OMB Proposed Revision to Uniform Guidance
Submit a comment on OMB’s proposed revision to uniform guidance by July 13
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lessergoldfinch.bsky.social @lessergoldfinch.bsky.social · 09/07/2026
Still working on my public comment but this @standupforscience.net tool made it really easy for me to contact my members of Congress about the Voght rule to destroy the scientific enterprise: fight2win.standupforscience.net?utm_source=o...
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Sergey Kryazhimskiy @skryazhi.bsky.social · 08/07/2026
Just visited Cambridge, UK, for the first time (as a tourist). Beautiful town! And so much amazing history. As a scientist, it gave me goosebumps to pass by the Cavendish laboratory. It's remarkable how many discoveries happened in this one building! www.phy.cam.ac.uk/about/our-hi...
phy.cam.ac.uk
Our history - Cavendish Laboratory Department of Physics
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Christian Kost @kostchristian.bsky.social · 08/07/2026
Happy to announce that a new opinion paper of our group just came out: A conceptual framework to dissect emergent functions in microbial communities with @swagatika.bsky.social @sharvari27.bsky.social @anjanaprasad.bsky.social @palshubharthi.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
A conceptual framework to dissect emergent functions in microbial communities
Microbial communities play vital roles in diverse ecosystems and are key drivers of numerous industrial or health-related applications. In many cases,…
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Casey terHorst @ecoevolab.bsky.social · 29/06/2026
Although Priyanga was fired, the story very much continues for her as she is struggling to make ends meet without a job or prospects. She recently sold her home to move into a small apartment in LA. She made some mistakes...but the punishment so far exceeds the "crime" (see: gender and race)
linkedin.com
UCLA's Most Decorated Ecologist Just Got Fired : Here's the sequence
In January of 2025, at the ICTP ICTS winter school at NCBS, Priyanga Amarasekare offered to take me and a few other students out for my birthday. She didn't have to do that.
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Claus Wilke @clauswilke.com · 25/06/2026
People always say "tell a story" but then don't explain how to do so! How is that helping? If we knew how to tell a story we wouldn't need the advice in the first place. 1/
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Sergey Kryazhimskiy @skryazhi.bsky.social · 23/06/2026
Cause exponential growth
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Mike Levin @mikelevin.org · 23/06/2026
Seen here in San Diego: “He Can’t Even Win A War Against Algae” 😂
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David Ho @davidho.bsky.social · 22/06/2026
François Primeau, a UC Irvine professor, developed mathematical and computational ocean models that helped us understand the ocean's role in global climate. He was killed on his bike by someone driving a car. 🌊
cbsnews.com
Orange County bicyclist fatally struck by hit-and-run driver in Santa Ana
It happened at around 6:15 p.m. Friday near the intersection of Standard Avenue and Warner Avenue, Santa Ana Police Department officers said in a news release shared on social media.
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