iiinova — where your digital self keeps evolving

Reposted by Shawn Costello

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 30/05/2026

Amplicon/Protein Bead Display enables quantitative in vitro biochemistry at scale www.biorxiv.org/content/10.64898/20…

Reposted by Shawn Costello

Gina El Nesr @ginaelnesr.bsky.social · 28/04/2026

Excited to report the first zero-shot designed, de novo enzyme catalyzing two of the most energetically demanding reactions in biology—phosphomonoester and phosphodiester hydrolysis—with catalytic efficiencies comparable to natural enzymes! 🚀 /🧵 @stanfordbiosci.bsky.social @simonduerr.eu

1205

Reposted by Shawn Costello

Kenneth Loi @kenjmloi.bsky.social · 27/04/2026

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

7448197

Reposted by Shawn Costello

Alex Crits-Christoph @acritschristoph.bsky.social · 27/04/2026

oh that's very very cool:

13410

Reposted by Shawn Costello

Jamie Cate @jhdcate.bsky.social · 27/04/2026

The best thing since *before* sliced bread... VIPRs. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...

biorxiv.org

14319

Reposted by Shawn Costello

Magnus Kjærgaard @proteinmagnus.bsky.social · 10/04/2026

A word of caution for protein designers: Thermostability is used as a proxy for other types of stability that are more closely related to equilibrium stability. A high thermal stability does not necessarily translate into a high equilibrium stability. /biophysicist rant over

151

Reposted by Shawn Costello

Magnus Kjærgaard @proteinmagnus.bsky.social · 10/04/2026

Why are de novo designed proteins so extremely thermostable? We try to answer this question by dissecting the thermodynamics of unfolding of mini-binders emerging from our protein design pipeline – and establish a convenient GUI for data analysis in the process. doi.org/10.64898/202...

Graphical abstract for pre-print showing a) theoretical model for thermostability, b) a GUI based analysis platform, c) protein denaturation data of mini-binders assessed by nanoDSF and d) a correlation plot that shows the de novo designed mini-binders have a much lower deltaCp than expected for a protein of their size.

34111

Reposted by Shawn Costello

matt-dejong.bsky.social @matt-dejong.bsky.social · 27/02/2026

First preprint of the @pollyfordyce.bsky.social and @dunnlab.bsky.social collaboration! We used high-throughput microfluidics for sequence-strength mapping at the single-molecule level. Our new tech allowed us to discover a fundamental nonequilibrium property of multivalent systems. 1/13

1179

Reposted by Shawn Costello

Polly Fordyce @pollyfordyce.bsky.social · 02/03/2026

Have you ever wanted to do single-molecule biophysics in high-throughput? @matt-dejong.bsky.social (amazing joint grad student with @dunnlab.bsky.social) invented a way & measured >100,000 single molecules across 241 different sequences. (1/3) www.biorxiv.org/content/10.6...

biorxiv.org

2247

Reposted by Shawn Costello

alex jaffe @alexjaf.bsky.social · 06/04/2026

🚨 preprint alert! check out our new pub on an unusual summer flu outbreak among shorebirds traced with targeted metagenomic sequencing of wastewater. more like this coming soon from our team at @wastewaterscan.bsky.social !

183

Reposted by Shawn Costello

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 26/02/2026

Engineering the mechanosensitivity of single DNA molecules via high-throughput microfluidic force spectroscopy www.biorxiv.org/content/10.64898/20…

021

Reposted by Shawn Costello

Mara Wilson @marawilson.bsky.social · 28/01/2026

Imagine having Bruce Springsteen AND Billy Bragg release songs about how much you fucking suck and how much the people fighting you rule you within the same 48 hours

5569961413

Reposted by Shawn Costello

asamelson @asamelson.bsky.social · 28/01/2026

After a long review process, I'm excited that our paper is finally in print: www.cell.com/cell/fulltex... TL;DR: We use CRISPR screens in iPSC-derived neurons to find a new tau E3 ligase and a relationship between oxidative stress, the proteasome, and tau proteolytic fragments. More below 👇

cell.com

CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis

CRISPR screens in iPSC-derived neurons reveal that the E3 ubiquitin ligase CRL5SOCS4 ubiquitinates tau, that CUL5 expression is correlated with resilience in human Alzheimer’s disease, and that electr...

23811

Reposted by Shawn Costello

Ami Fields-Meyer @fieldsmeyer.com · 25/01/2026

I wrote the speech I *wish* Chuck Schumer would give tonight - as an actual opposition leader. Here it is: "My fellow Americans: At this hour, an unrestrained force of militarized and violent federal officers is carrying out a project of ethnic cleansing in the streets of American cities." 1/14

16711293

Reposted by Shawn Costello

Rasmus Hartmann-Petersen @rhp-lab.bsky.social · 16/01/2026

New preprint! Led by @sarahgersing.bsky.social we map how 7,500+ variants in glucokinase (GCK) affect binding to GKRP and disentangle this from stability. We now have activity, abundance, and interaction scores for 7,128 GCK variants - a resource for understanding phenotypes and glucose homeostasis.

0166

Reposted by Shawn Costello

Alex Crits-Christoph @acritschristoph.bsky.social · 17/01/2026

when that guy who said he'd make the figure for the group project really lets you down

2214

Reposted by Shawn Costello

Hannah Wayment-Steele @hkws.bsky.social · 23/05/2025

The W-S lab is seeking to hire a research scientist! This person will lead wet-lab innovations in our team as we combine AI and experiments to understand and design dynamics! Thanks for sharing/RTs! jobs.wisc.edu/jobs/scienti...

jobs.wisc.edu

Scientist and Lab Operations Coordinator - Madison, Wisconsin, United States

Job Summary: The Wayment-Steele Lab seeks a Research Scientist to lead experimental operations within our highly interdisciplinary team, integrating both computational "dry" and experimental "wet" l...

01214

Reposted by Shawn Costello

Alex Crits-Christoph @acritschristoph.bsky.social · 24/12/2025

All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

Figure 2. Himar1 transposon variant screen on a cohort of 92 bacterial species.

18432

Reposted by Shawn Costello

dirt of the looming dawn @upfromsumdirt.blacksky.app · 23/12/2025

wendell berry QUESTIONNAIRE

Questionnaire
by Wendell Berry

How much poison are you willing
to eat for the success of the free
market and global trade? Please
name your preferred poisons.

For the sake of goodness, how much
evil are you willing to do?
Fill in the following blanks
with the names of your favorite
evils and acts of hatred

What sacrifices are you prepared
to make for culture and civilization?
Please list the monuments, shrines,
and works of art you would
most willingly destroy

In the name of patriotism and
the flag. how much of our beloved
land are vou willing to desecrate?
List in the following spaces
the mountains, rivers, towns, farms
you could most readily do without.

State briefly the ideas, ideals, or hopes,
the energy sources, the kinds of security;
for which vou would kill a child
Name, please, the children whom
you would be willing to kill.

516090

Reposted by Shawn Costello

Sam Lewis, Ph.D. @samlewis.bsky.social · 18/12/2025

⚡️Mitochondria make ATP, the energy that powers life. But in neurons, with axons up to a meter long, how do these tiny power plants stay functional in the right places? We went looking. 1/n www.biorxiv.org/content/10.6...

biorxiv.org

Self-renewal of neuronal mitochondria through asymmetric division

Mitochondrial ATP production is essential for life. Mitochondrial function depends on the spatio-temporal coordination of nuclear and mitochondrial genome expression, yet how this coordination occurs ...

29343

Reposted by Shawn Costello

Ariel Edwards-Levy @aedwardslevy.bsky.social · 10/12/2025

"there's a new serif in town"

1004146822489

Reposted by Shawn Costello

Will Ratcliff @wcratcliff.bsky.social · 09/12/2025

1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size! www.biorxiv.org/content/10.6...

biorxiv.org

The fitness costs of reproductive specialization scale inversely with organismal size

The evolution of reproductive specialization represents a fundamental innovation in multicellular life, yet the conditions favoring its evolution remain poorly understood. Here, we develop a populatio...

615467

Reposted by Shawn Costello

Gabriel Rocklin @grocklin.bsky.social · 19/11/2025

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

412241

Reposted by Shawn Costello

Alex Crits-Christoph @acritschristoph.bsky.social · 14/11/2025

Defunding scientists for the nationality of who they co-author with or who they train. One of the most radical attack on freedom of speech in US history. A far right nationalist destruction of US science. Such a shameful time to be an American that this racist stupidity has become mainstream.

314678

Reposted by Shawn Costello

Alex Crits-Christoph @acritschristoph.bsky.social · 12/11/2025

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

Figure 2. PET screen results and RB-TnSeq gene fitness results

57938

Reposted by Shawn Costello

Jase Gehring @skyjase.bsky.social · 10/11/2025

not to dunk on this conclusion, but it's an insidious mindset that has become pervasive. how you spend your time, how you make your money, is one of the most important ethical and political choices you can make. convincing ourselves otherwise is arguably The Whole Problem in American society today

241

Reposted by Shawn Costello

Josh Riback @superscijew.bsky.social · 04/11/2025

(1/10) How do diverse leukemia mutations converge on the same molecular program? In #RibackLab first manuscript @cp-cell.bsky.social, collaboration with @goodell-lab.bsky.social shows that disparate mutations rewire shared protein networks to form nuclear condensates called C-bodies.

75423

Reposted by Shawn Costello

Emily C. Hughes @emilyhughes.bsky.social · 09/11/2025

pre-writing a devastating obituary for your enemy is god-tier hating of a kind you don’t often see anymore. renaissance haterism. beautiful stuff.

13143594270

Reposted by Shawn Costello

Lior Pachter @lpachter.bsky.social · 08/11/2025

Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted. liorpachter.wordpress.com/2018/05/18/j...

liorpachter.wordpress.com

James Watson in his own words

“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…

18335118

Reposted by Shawn Costello

Zohran Kwame Mamdani @zohrankmamdani.bsky.social · 03/11/2025

A few days after the presidential election one year ago, we went to Fordham Road in the Bronx. It was a little different last week.

303141972787

Reposted by Shawn Costello

John Hollingsworth @fiatjusticia.bsky.social · 25/10/2025

As a child I ate government cheese and free school lunches. I then went on to uni thanks largely to Pell grants. I now (HAPPILY) pay taxes on an income that would not have been possible without that support. Taking care of your citizens is good actually.

8634141

Reposted by Shawn Costello

Anna Bower @annabower.bsky.social · 20/10/2025

EXCLUSIVE: One Saturday afternoon in October, my phone lit up with a notification. I glanced down at the message. “Anna, Lindsey Halligan here,” it began. So began my text exchange with the woman who is prosecuting the president's perceived political enemies. www.lawfaremedia.org/article/anna...

"Anna, Lindsey Halligan Here."
Anna Bower
Monday, October 20, 2025, 5:40 PM
Share On: f X inK My Signal exchange with the interim U.S. attorney about
the Letitia James grand jury.

1502220676844

Reposted by Shawn Costello

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 18/10/2025

A university that signs the “compact” is one that acknowledges its own inability to compete and succeed based talent and merit. It would signal insecurity and mediocrity to current and future students and faculty. Say no. Recruit the best people, protect their freedom and support their hard work.

025284

Reposted by Shawn Costello

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 15/10/2025

Second, I’m slowly getting to be in the camp that proteins don’t have functions but instead have properties. What biology does with those properties is a somewhat different matter. So maybe we need to predict properties (kcat, Kd, etc) as well

3152

Reposted by Shawn Costello

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 15/10/2025

This is great. A few additions. I suspect that what we really need is a model of macromolecular thermodynamics. Prediction potential alternative conformations is nice but unless we can assign weights it’s difficult to link to biology. Same for stability etc.

171

Reposted by Shawn Costello

Emery Usher, Ph.D. 🏳️‍🌈🏳️‍⚧️🧪 @idpemery.bsky.social · 19/09/2025

If y'all don't see me at some conferences this year... it's because this has been YEARS in the making. Trans people aren't safe here. PLEASE stand up--personally and professionally (lookin' at you, academics)--for the trans people in your life.

23514

Reposted by Shawn Costello

Polly Fordyce @pollyfordyce.bsky.social · 17/09/2025

Please apply to our tenure-track faculty position at @stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely! chemh.stanford.edu/opportunitie...

chemh.stanford.edu

Faculty Recruitment

02825

Reposted by Shawn Costello

Roxana Hadadi @roxana-hadadi.bsky.social · 15/09/2025

happy for THE PITT but heartbroken for ANDOR, a TV show the likes of which we will never, ever see again

417924

Reposted by Shawn Costello

Sarah Shammas @sarahshammas.bsky.social · 08/09/2025

Over 10% of human transcription factors are oligomeric. Stoichiometry might be dialled to modulate transcription. We show CREB searches in DNA mixtures as a dimer, and suggest this might be common amongst other members of the bZIP family which fold on binding DNA. www.biorxiv.org/content/10.1...

All but one bZIP monomer, Jun, has significantly higher affinity for other monomers than its own DNA target, favouring the dimer pathway for target search at equilibrium.

1233

Reposted by Shawn Costello

The Author, Séamas O'Reilly @seamas.bsky.social · 10/09/2025

- you clean up that banksy? - sure did, your honour, leaving a perfect, permanent outline, imbuing the work with real fuckin gravitas while making its point better than the artist did himself just like you asked

124199265778

Reposted by Shawn Costello

Bria Castellano @queerentist.bsky.social · 05/09/2025

🗓️Join us for the 4th Stanford.Berkeley.UCSF Next Generation Faculty Symposium on 9/10/25! We highlight the work of 18 exceptional early-career scientists across biomedical sciences. Register and more information below: www.berkeleystanfordnextgensymposium.com/speakersalumni

0104

Reposted by Shawn Costello

Polly Fordyce @pollyfordyce.bsky.social · 08/09/2025

Only 2 days to go! Register and join us to hear these amazing talks!

013

Reposted by Shawn Costello

Polly Fordyce @pollyfordyce.bsky.social · 05/09/2025

Incredibly excited for this year's iteration of the Next Generation Faculty Symposium on 9/10/25! This is a fantastic opportunity to hear 10 minute talks describing fantastic cutting-edge science from researchers preparing to launch a faculty search. Please register (link below) & forward widely :)

073

Reposted by Shawn Costello

Kevin Mitchell @wiringthebrain.bsky.social · 07/09/2025

When reporting on these kinds of claims, the media should ask:

1. Is this a one-off study or a replicated finding?
2. Is it cherry-picked or consistent?
3. Was the study big enough to be reliable?
4. Did it employ robust statistical methods?
5. How big is the effect size? (If there’s a statistical association, does it amount to a big risk or a small one?)
6. Is there any evidence for a causal link or is it just a correlation?
7. Could the correlation reflect some confounding factor?
8. How does this supposed factor sit in the context of other factors (especially genetic risk for autism, which is very highly heritable)?

1221665

Reposted by Shawn Costello

Dr. Lucky Tran @luckytran.com · 04/09/2025

The “problem” with vaccines? They so effective at preventing deaths that they create generations of people that question whether disease was a problem in the first place because they have never experienced the horrors of a world without vaccines.

570265487762