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@JohnGrossSF

@johngrosssf.bsky.social
483 followers 191 following 40 posts

Biochemist, aspiring cyclist, husband, empty nester with a dog. grosslab.ucsf.edu

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@JohnGrossSF @johngrosssf.bsky.social · 19/09/2026
Congratulations to Gabriel Braun and collaborators Rakesh Kumar and Alan Hinnebusch for uncovering how deadenylase and decapping enzyme cofactors activate the DEAD-Box ATPase Dhh1. We wonder if this enzyme coordinates the 3' and 5' ends during mRNA turnover. academic.oup.com/nar/article/...
academic.oup.com
Validate User
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Alex Holehouse @alexholehouse.bsky.social · 14/09/2026
Doing the lords work over here
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Hauke Hillen @haukehillen.bsky.social · 11/09/2026
Happy to share our new preprint on the structure of the human mitochondrial RNA degradosome, a central player in organellar RNA metabolism! Work led by graduate student @paulafprado.bsky.social in our group. www.biorxiv.org/content/10.6... 🧵 1/9
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Virginia Busetto @virginiabusetto.bsky.social · 08/09/2026
Very excited to share our new preprint: “A pseudohelicase-centered complex couples assembly-dependent RNA cleavage to poly(UG)ylation”! 🎉 Want to know more? 🧵👇 www.biorxiv.org/content/10.6...
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Seychelle Vos @voslab.org · 08/09/2026
⚡Preprint alert⚡ So proud of @amohamed98.bsky.social! Abdallah determined the cryo-EM structure of BRD4 bound to the kinase P-TEFb, defining the molecular basis of this key transcription interaction — and revealing that BRD4 and AFF4 binding are mutually exclusive to P-TEFb. Lots more inside 👇
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Jean-Paul Armache @valendraica.bsky.social · 08/07/2026
If you or someone you know is interested in joining a fun and productive lab (JP Armache laboratory at Penn State University) to work on exciting projects, please follow or share the link below. psu.wd1.myworkdayjobs.com/PSU_Academic...
psu.wd1.myworkdayjobs.com
Postdoctoral Position
APPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a...
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Stella Hurtley @smhsci.bsky.social · 21/08/2026
Out now in @science.org Virome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasion | Science www.science.org/doi/10.1126/...
science.org
Virome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasion
Viruses are intracellular parasites that reprogram the host proteome to promote replication and evade immune recognition. We applied a virome-wide library of ~10,000 open reading frames to discover vi...
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Francis O'Reilly @fjoreilly.bsky.social · 14/08/2026
PhIX-MS is out in Molecular Cell! Rapid in situ photo-crosslinking traps transient proteasome interactions before purification; crosslinking MS, cryo-EM and AlphaFold tell us where they bind. Paper: doi.org/10.1016/j.mo... Preview: doi.org/10.1016/j.mo...
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@JohnGrossSF @johngrosssf.bsky.social · 10/08/2026
Congratulations to Yange Niu et al for showing how SIVsmm Vif was pre-equipped to antagonize human A3H-haplotype II through cryoEM and virological studies of the HIV-2 Vif-A3H complex. Another satisfying collaboration with Nicholas Chesarino and @memerman.bsky.social www.nature.com/articles/s41...
nature.com
The structural mechanism of HIV-2 Vif antagonism of human APOBEC3H - Nature Communications
HIV-2 Vif counteracts a broad range of APOBEC3 restriction factors to promote viral infectivity. Here, the authors determine the structure of HIV-2 Vif bound to human APOBEC3H and the host cofactor CB...
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Castañeda Lab at SU @castanedalab.bsky.social · 30/07/2026
We are actively looking for a NMR facility manager for our growing NMR needs in Syracuse! This facility hosts an 800 with TCI cryoprobe (perfect for disordered protein research) and 600 with Prodigy cryoprobe. Please share with your communities!
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@JohnGrossSF @johngrosssf.bsky.social · 24/07/2026
Strain-specific epistasis shapes fitness landscapes of APOBEC3G antagonism by HIV-1 Vif proteins | Science Advances www.science.org/doi/10.1126/... Congratulations on this beautiful work!
science.org
Strain-specific epistasis shapes fitness landscapes of APOBEC3G antagonism by HIV-1 Vif proteins
Unexpected flexibility and evolutionary constraints shape how HIV-1 overcomes a key human antiviral protein.
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@JohnGrossSF @johngrosssf.bsky.social · 15/07/2026
Virome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasion | Science www.science.org/doi/full/10.... Viruses don't play by the same rules as host proteins: a CRISPR screen shows rotavirus NSP1 hijacks CUL3 using ELOBC as a surrogate for BTB protein, backed up by cryoEM!
science.org
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Jeff Mugridge @jeffmugridge.bsky.social · 29/06/2026
💥 Final version of our Elp3 paper is now live @natcomms.nature.com! We show how the radical SAM enzyme Elp3 uses a molecular tunnel to transport acetate molecules and modify tRNA! We think our proposed mechanism answers long-standing questions about how this important enzyme works! rdcu.be/fq2bw
rdcu.be
Elp3 uses a conserved molecular tunnel to transport acetate between distant active sites and catalyze tRNA wobble base modification
Nature Communications - tRNA modifications are essential for accurate translation, but how Elp3 catalyses them across distant active sites was unclear. Here, the authors show that Elp3 uses a...
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Chembu🌺🧶♿ - Ko-Fi shop Updated. Checkout please! @chembarathi.northsky.social · 09/06/2026
In the midst of hate, I found there was, within me, an invincible love. In the midst of tears, I found there was, within me, an invincible smile. In the midst of chaos, I found there was, within me, an invincible calm. - Albert Camus #Poetry 💙📚👀
Within Me

Albert Camus (1913-1960)

In the midst of hate, I found there was, within me, an invincible love.

In the midst of tears, I found there was, within me, an invincible smile.

In the midst of chaos, I found there was, within me, an invincible calm.

I realized, through it all, that...

In the midst of winter, I found there was, within me, an invincible summer.

And that makes me happy. For it says that no matter how hard the world pushes against me,

within me, there's something stronger something better, pushing right back. -
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Cynthia Wolberger @cwolberger.bsky.social · 22/05/2026
I was told that I needed to request permission to collaborate with physicians from European countries before testing the effects of patient mutations they identified on an enzyme we study. For each collaborator, NIH is asking for email, institution, street address, phone number (!!). Insane.
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Vijay Ramani @vram142.bsky.social · 06/05/2026
Delighted to share our lab's latest (w/ inimitable @genophoria.bsky.social) in final form at @nature.com. Enormous lift by Sean Wang, @palindromephd.bsky.social & @martyyang.bsky.social to address extensive & constructive reviewer comments & see this through. (1/n) www.nature.com/articles/s41...
nature.com
Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature
An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 24/04/2026
Conformational Ensembles of the Disordered 4E-BP2:eIF4E Complex Restrained by smFRET Experiments www.biorxiv.org/content/10.64898/20…
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 12/02/2026
Interested in transcriptional regulation, enhancers and 3D genome folding? In this new study we wondered about the role of cohesin loading at enhancers for long-range transcriptional control www.biorxiv.org/content/10.6... detailed 🧵👇
biorxiv.org
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Harmit Singh Malik @harmitmalik.bsky.social · 21/04/2026
A herculean effort by many, but esp. the first three authors: Ujjwal Rathore, Eli Dugan, and Hunter Thornton working in the Krogan and Marson labs, with a veritable army of collaborators from HARC (harc.ucsf.edu) and beyond. Press release: gladstone.org/news/scienti... (inc. paper link)
gladstone.org
Scientists Map How HIV Hijacks Human Cells—and How Cells Can Fight Back
A new genetic roadmap reveals hundreds of hidden players in HIV infection, including two proteins that stop HIV in its tracks.
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Ian Kelsall @iankelsall.bsky.social · 05/02/2026
What would you think to be thus used? This is the strangers case; And this your mountainish inhumanity.
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Martin Kampmann @kampmann.bsky.social · 28/01/2026
Our paper is (finally) out in Cell today! CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis www.cell.com/cell/fulltex... Great collaborative effort - read more from first author @asamelson.bsky.social 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...
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Princess Vimentin PhD | Cancer Biologist @princess-vimentin.bsky.social · 21/01/2026
🧪 Russel Vought wants to kill the #NIH, in a slow, sneaky way. The NIH appropriations include language that allows multi-year funding of grants. No 40% cut. Yay. No. Allowing multi-year funding allows fewer grants will be funded. This toxic compromise will kill science. We deserve better.
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@JohnGrossSF @johngrosssf.bsky.social · 19/01/2026
"One has not only a legal but a moral responsibility to obey just laws. Conversely, one has a moral responsibility to disobey unjust laws.” Dr. MLK Jr, Letter from a Birmingham Jail
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@JohnGrossSF @johngrosssf.bsky.social · 17/01/2026
"The arc of the moral universe is long, but it bends toward justice.” Dr. Martin Luther King Jr.
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David Bartel's Lab @bartellab.bsky.social · 06/01/2026
We are thrilled to share our latest work uncovering the mechanistic basis of target-directed microRNA degradation (TDMD). This work was driven by @jakobfarnung.bsky.social and @elenaslo.bsky.social in a fantastic collaboration with Brenda Schulman's lab. tinyurl.com/E3TDMD (1/5)
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 03/01/2026
Nice description of ipTM problems & how actifPTM, LIS, & ipSAE fix those for scoring protein-protein interactions. New script on ipSAE github: af2rechain.py takes an input AF2 model of one protein & breaks it into chains given domain boundaries for input to ipSAE to calculate intraprotein ipSAE.
af2rechain.py

Takes input legacy-PDB format file and splits single chain AF2 model into separate chains given starting residue numbers for domains/regions.

Output pdb file can then be input into ipsae.py to calculate intraprotein ipSAE values between domains.

Example:
   python3 af2rechain.py AGC_AKT1_model.pdb 123 141 409

will create output PDB file named "AGC_AKT1_model_rechain.pdb" with
     chain A: residues 1-122
     chain B: residues 123-140
     chain C: residues 141-408
     chain D: residues 409-480 (end of original chain A)

Note: by default, first chain begins on residue 1 and last chain ends on last residue of input chain A

Then run ipsae.py on json file and PDB file to get intraprotein ipSAE values:
       python3 ipsae.py AGC_AKT1_model.json AGC_AKT1_model_rechain.pdb 10 15
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Lucas Farnung @lucas.farnunglab.com · 24/10/2025
I love AlphaFold—but please include PAE (Predicted Aligned Error) plots for every “interaction.” Pretty PDBs ≠ proof. If the PAE doesn’t show an interface, it ain’t one. Show the plots. Structural biology's reputation is on the line.
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@JohnGrossSF @johngrosssf.bsky.social · 12/09/2025
Order from Chaos in protein LCDs acknowledged by the Lasker Foundation, laskerfoundation.org/winners/stru...
laskerfoundation.org
Structures and functions of low-complexity domains - Lasker Foundation
For their discovery of the two distinct classes of lymphocytes, B and T cells – a monumental achievement that provided the organizing principle of the adaptive immune system and launched the course of...
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Steven Corsello @corsello.bsky.social · 02/09/2025
Excited to share our discovery of potent TRIM21 molecular glues with anticancer activity, online today @CD_AACR: "Defining the antitumor mechanism of action of a clinical-stage compound as a selective degrader of the nuclear pore complex". 1/18
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Harmit Singh Malik @harmitmalik.bsky.social · 03/08/2025
apnews.com/article/texa... researcher faces deportation after being held for week at San Francisco airport
apnews.com
Texas researcher faces deportation after being held for week at San Francisco airport
A legal permanent resident with a green card who flew back to the U.S. after visiting family in South Korea was detained by immigration authorities and held for more than a week at the San Francisco I...
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Jeremy Berg @jeremymberg.bsky.social · 01/08/2025
Another email to Bhattacharya about his interview and his continued statements that NIH's gain of function research caused the COVID pandemic and killed millions of people. 1/8
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Jen Heemstra @jenheemstra.bsky.social · 26/07/2025
First copies of my book are here!! As a new faculty member, I realized that in addition to my research job, I also had a leadership job…and I wasn’t prepared for that. This book is the guide I wish I’d had then, with the goal of helping others now.   jenheemstra.com/book
Picture of a smiling person holding up a copy of a book.
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Kelly Nguyen @kellythd-nguyen.bsky.social · 10/07/2025
Proud to share our work where we resolved a longstanding question regarding the existence of a human telomerase dimer and provided insights into its function. Led by 3 amazing lab members in collaboration with @yiliangding.bsky.social and @rdaslab.bsky.social. www.science.org/doi/10.1126/...
science.org
Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization
Telomerase ribonucleoprotein (RNP) synthesizes telomeric repeats at chromosome ends using a telomerase reverse transcriptase (TERT) and a telomerase RNA (hTR in humans). Previous structural work showe...
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Jeremy Berg @jeremymberg.bsky.social · 10/07/2025
Powerful story from Kate Zernike from the NYT Covers the diversity of young scientists targeted by the anti-DEI BS. Definitely worth a read and a share. [Gift link] www.nytimes.com/2025/07/10/u...
nytimes.com
The Surprising Scientists Hit by Trump’s D.E.I. Cuts
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Microsoft Research @msftresearch.bsky.social · 10/07/2025
Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale. www.science.org/doi/10.1126/...
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Brendan Harley @profharley.bsky.social · 08/06/2025
A reminder. The budget that just passed the House slashes US scientific research by half. Please call or email your senators and tell them you do not want the NIH and NSF cut. You can find your senators contact info here: www.senate.gov/senators/sen...
Us cancer survival statistics
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Harmit Singh Malik @harmitmalik.bsky.social · 08/06/2025
(Longish thread. Apologies) I have met many inspiring colleagues over the past few months, many of whom are in academic institutions targeted by the current administration, and many others who are about to be (the analogy to the ‘eye of Sauron’ has been invoked many times; gallows humor). 1/
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@JohnGrossSF @johngrosssf.bsky.social · 04/06/2025
Congratulations to Fei Li, Bob Stroud , Rob Edwards and coworkers for VGLUT2 structure , substrate recognition and allosteric regulation. www.nature.com/articles/s41...
nature.com
Substrate recognition and allosteric regulation of synaptic vesicle glutamate transporter VGLUT2 - Nature Structural & Molecular Biology
Guided by a structure of VGLUT2 with substrate, Li et al. identify the mechanisms for selective substrate recognition, a role for lipid modification in limiting axonal dispersion and for the cytoplasm...
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 03/06/2025
Nice summary of our ipSAE score for rescoring protein-protein and protein/nucleic-acid interactions in AF2, AF3, and Boltz-1. It works better than ipTM for full-length Uniprot sequences.
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Jeff Mugridge @jeffmugridge.bsky.social · 08/05/2025
💥Latest preprint from our lab is now live! We propose a crazy(!?) new mechanism for how the radical SAM enzyme Elp3 (a subunit of the Elongator complex) modifies tRNA! #RNAsky #enzymes 🧵...
Graphical abstract shows molecules of acetate traveling through a molecular tunnel in Elp3 that connects its distant active sites
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Dolphin Pilot @theamitie.bsky.social · 12/05/2025
DARTH VADER: I just want to say to all of the alderaanians.. I see you. I hear you
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Lori Passmore @lapassmore.bsky.social · 02/05/2025
New work from Matti Turtola showing that mRNA poly(A) tail length is controlled by a kinetic ruler. A real pleasure to work with him! www.biorxiv.org/content/10.1...
biorxiv.org
A kinetic ruler controls mRNA poly(A) tail length
Poly(A) tails of newly synthesized mRNAs have uniform lengths, arising through cooperation between the cleavage and polyadenylation complex (CPAC) and poly(A) binding proteins (PABPs). In the budding ...
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@JohnGrossSF @johngrosssf.bsky.social · 23/04/2025
The unstructured biology of mRNA decay in budding yeast revealed by motif discovery engine developed by Joe Lobel and @nickingolia.bsky.social . Kudos! www.nature.com/articles/s41...
nature.com
Deciphering disordered regions controlling mRNA decay in high-throughput - Nature
Using high-throughput functional profiling, how disordered regions control mRNA stability and translation is explored.
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Briggs Group @briggsgroup.bsky.social · 04/04/2025
Our work on HIV-1 matrix, led by James Stacey and @dhrebik.bsky.social, is in this week's @nature.com. Extended explanatory video from @margotriggi.bsky.social. www.nature.com/articles/s41...
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George Burslem @gburslem.bsky.social · 26/03/2025
Non-canonical acylation of lysine residues catalyzed by HDACs! Congratulations to @dremilygoldberg.bsky.social for such beautiful work and thanks for bringing us along for the ride!
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Ardem Patapoutian @ardemp.bskyverified.social · 10/02/2025
Petition to Reverse the NIH Indirect Cost Cap initiated by Tom Maniatis. Please amplify Sign the Petition: chng.it/kK2HMP5pGk "Share with Leadership & Faculty. Reach out to professional societies, biotech and pharma leaders, and philanthropic organizations to raise awareness and mobilize support."
chng.it
Sign the Petition
Petition to Reverse the NIH Indirect Cost Cap (NOT-OD-25-068)
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 21/02/2025
Ok scientists & those who love science 🧪: here is another exhortation. Call Congress TODAY about the freeze on NIH Council Meetings and Study Sections. Emphasize that this means NO new grants are being funded & labs will soon start to shut down and fire employees. Phone numbers are at: 5calls.org
5calls.org
5 Calls
Spend 5 minutes. Make 5 calls. Make your voice heard.
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James Fraser @fraserlab.com · 18/02/2025
🚨 New preprint alert! 🚨 How does SARS-CoV-2 use as much of its genome as possible to evade our immune response? Our latest study dissects how Orf9b, which is encoded in an alternate reading frame from the N(ucleocapsid) protein, can regulate interferon signaling. www.biorxiv.org/content/10.1... 🧵👇
biorxiv.org
Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response
Open Reading Frame 9b (Orf9b), an accessory protein of SARS-CoV and -2, is involved in innate immune suppression through its binding to the mitochondrial receptor Translocase of Outer Membrane 70 (Tom...
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Jeremy Berg @jeremymberg.bsky.social · 12/02/2025
Finally read popular.info/p/trump-main... "Between February 3, 2024, and February 10, 2024, the NIH issued 513 grant awards totaling $218,273,053. Between February 3 and February 10 this year, the NIH issued just 11 grant awards totaling $4,981,089." No wonder I didn't many responses about NoAs...
popular.info
Trump maintains funding freeze at NIH, defying court order
The Trump administration is still prohibiting National Institutes of Health (NIH) staff from issuing virtually all grant funding, an NIH official tells Popular Information.
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Megan, PhD @drmeganphd.bsky.social · 28/01/2025
Read my review!
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