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Evan Brenner

@evanbrenner.bsky.social
144 followers 463 following 6 posts

Postdoc in the JRavi Lab at the University of Colorado, applying machine learning methods to figure out how microbes evolve and what risks they pose to human and animal health. Ask me about bacteria!

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Reposted by Evan Brenner
Anna Olina @annaolina.bsky.social · 22/09/2026
Excited to share this part of my research as a part of @multidefence.bsky.social: meet viPAO1 - the very best Pseudomonas strain for phage research😉 Also check out our temperate phage collection featuring PAnicatthedisco, PAthetic and some other new fun names🎉 www.biorxiv.org/content/10.6...
biorxiv.org
Engineering the Pseudomonas aeruginosa virus-isolation host viPAO1 reveals how host genetic barriers shape recoverable phage diversity
Cultured phage collections provide essential access to viral biology, but they capture only a small and biased fraction of natural phage diversity. Key barriers to diverse phage isolation are likely t...
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Casey Dunn @caseywdunn.bsky.social · 25/08/2026
My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.
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I-75 Scientist @flscitriguy.bsky.social · 12/08/2026
Updates to NIH K awards starting with October 2027 deadlines. The individual K awards are being consolidated into 4 awards. 🧪 grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-26-098: Notice of NIH Updates to Career Development (K) Award Programs
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Notice of NIH Updates to Career Development (K) Award Programs NOT-OD-26-098. OD
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IDDjobs @iddjobs.org · 08/08/2026
CLOSING SOON: Postdoc (Singapore, Singapore) AI & Machine Learning for Infectious Disease & Public Health at National University of Singapore More details: iddjobs.org/jobs/2520
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Reposted by Evan Brenner
Nina Friedman @ngfriedman.bsky.social · 04/08/2026
Starting in Spring or Summer 2027 K99/R00 (under its new activity code KT1/R00) will only be available to US citizens, permanent residents, and non-citizen nationals. I am hearing this from many program officers, but NIH has yet to make an official statement to my knowledge.
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STAT @statnews.com · 07/08/2026
The NIH plans to close the door on one of the few pathways available to international students on visas to forge a career in biomedical research in the U.S. www.statnews.com/2026/08/07/n...
statnews.com
NIH plans to block international researchers on visas from accessing key funding avenue
The NIH plans to close the door on one of the few pathways available to international students on visas to forge a career in biomedical research in the U.S.
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Noah Whiteman @nkwhiteman.bsky.social · 06/08/2026
I’m thrilled to share that our search for a tenure-track colleague in my *truly wonderful and collegial* Genetics, Genomics, Evolution and Development Division in the MCB Department at Berkeley @berkeleymcb.bsky.social is live! Please share this broad search widely: aprecruit.berkeley.edu/JPF05481
aprecruit.berkeley.edu
Assistant Professor -Genetics, Genomics, Evolution, and Development - Molecular and Cell Biology
University of California, Berkeley is hiring. Apply now!
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Joanna Masel @joannamasel.bsky.social · 27/07/2026
Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social
academic.oup.com
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models
Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig
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Reposted by Evan Brenner
ISB @isbscience.org · 18/06/2025
New @isbscience.org research shows how microbial teamwork behind denitrification can collapse in polluted environments, threatening ecosystem balance and resilience. isbscience.org/news/environ...
isbscience.org
Microbes That Keep Ecosystems in Balance Can Fall Apart Easily, New Study Finds
Microbial teamwork behind denitrification can collapse in polluted environments, threatening ecosystem balance and resilience.
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Max Kozlov @maxkozlov.bsky.social · 16/06/2025
🚨 BREAKING: Nearly 4 months the NIH cut its first grants, a judge has ruled that the directives and process that led to cuts are arbitrary and capricious. "The explanations are bereft of reasoning — virtually in their entirety... unsupported by [facts]." Each of them are VOID and ILLEGAL, he says.
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MM @phdeez.bsky.social · 13/06/2025
the reissued NOFO for the Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral Fellowship (Parent F31) is finally published! grants.nih.gov/grants/guide...
grants.nih.gov
PA-25-422: Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral Fellowship (Parent F31)
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral Fellowship (Parent F31) PA-25-422. NI...
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InterPro @interprodb.bsky.social · 03/06/2025
🦠🧬Exciting news! BFVD predicted viral protein structures are now available in @InterProDB! For the first time, explore InterPro functional annotations directly on 3D structures of viral proteins not covered by AlphaFold DB. This bridges a critical gap in structural virology research.
CATH-Gene3D annotation visualised on BFVD structure prediction of UniProt A0A075FDU7
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Sebastian Schmidt @tsbschm.bsky.social · 03/06/2025
The Koonin Law of Computatoinal Biology: Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.
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Kristian G. Andersen @kgandersen.bsky.social · 22/05/2025
The spread of Mpox in Sierra Leone is unlike anything we have ever seen - and we have been keeping an eye on this bug in the region for >15 years. Given geographical spread, 50/50 men vs women, this is no "sexual network". This could be the next one. clt.npha.gov.sl/outbreak.aspx
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Max Kozlov @maxkozlov.bsky.social · 21/05/2025
Who's calling the shots at NIH? Sworn testimonies and internal e-mails reveal for the first time the breadth of DOGE's control over the world's largest public biomedical funder. DOGE has provided lists of hundreds of grants to cut, and DOGE is now reviewing ALL NIH awards before they're released
nature.com
NIH killed grants on orders from Elon Musk’s DOGE
Court documents and internal correspondence show the cost-cutting force has broad control over the world’s largest public biomedical funder.
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Gemma C. Atkinson @gemmaatkinson.bsky.social · 19/05/2025
Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social
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Zamin Iqbal @zaminiqbal.bsky.social · 19/05/2025
Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...
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Petra Korlević @petrathepostdoc.bsky.social · 13/05/2025
an old redraw of one of my fav microbe memes, by @prokaryota.bsky.social "eAT The DiRT bRöTHer" 🦠 #SciArt #microbes
screenshot of a twitter post, the poster is Elisa Granato @Prokaryota
the picture is the swole and weak shiba meme, the swole shiba on the left says
BACTERIA IN NATURE
eating literal dirt
defying the physical limits of life
this is my third eukaryotic extinction event in a row (raised hands emoji)

the right weak shibe text is
BACTERIA IN THE LAB
not my favourite sugar (three sad smiley emojis)
the pH is off by 0.001
is this tap water? I'm allergicmy redraw of Elisa Granato's bacteria meme
left has a buff orange bacteria with massive flagellas and a 10 pack, text says
BACTERIA IN NATURE
eating literal dirt
defying the physical limits of life
this is my third eukaryotic extinction event in a row (raised hands emoji)

the right has a weakly pink brown blobby bacteria with tiny hairs, text says
BACTERIA IN THE LAB
not my favourite sugar (three sad smiley emojis)
the pH is off by 0.001
is this tap water? I'm allergic
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Reposted by Evan Brenner
Chiara Masnovo @chiaramasnovophd.bsky.social · 16/05/2025
Having a hard time processing this. HHMI is pausing all competitions. Very demoralizing for early career scientists like me @hhmi.org
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Daniel Tamarit @danieltamarit.bsky.social · 14/05/2025
New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky
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Michael Baym @baym.lol · 14/05/2025
Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab
A screenshot of the termination notice showing "Outstanding Investigator Grants"A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted
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Dr. Stephanie @punkrockscience.bsky.social · 13/05/2025
Optometrist: you should really probably spend less time on screens Me, a computational biologist: I’ll… just take that under advisement, shall I?
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BEACON @beaconbio.bsky.social · 13/05/2025
Nine cases of Middle East Respiratory Syndrome (MERS) have been reported in Saudi Arabia including two fatalities and a cluster of seven cases linked to healthcare associated transmission. spr.ly/63329Nk0yX
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Jeremy Berg @jeremymberg.bsky.social · 07/05/2025
New Notice on No Cost Extensions (or lack thereof) grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-25-110: Updated NIH Processes for No-Cost Extensions
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Updated NIH Processes for No-Cost Extensions NOT-OD-25-110. NIH
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Dr. Suzanne Le Menestrel @drsl.bsky.social · 02/05/2025
The Spencer Foundation is offering rapid response bridge funding for those who lost NSF research grants. www.spencer.org/grant_types/...
spencer.org
Rapid Response Bridge Funding Program
In the face of recent abrupt shifts in federal funding for education research, including large-scale terminations of National Science Foundation (NSF) research grant awards, we have developed a rap...
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Max Kozlov @maxkozlov.bsky.social · 02/05/2025
BREAKING: Reports that Trump would try to cut NIH's budget by 40% have come true. The request released moments ago would: - Cut $18 BILLION to NIH's $47b budget - Eliminate NIMHD, NCCIH, FIC - Collapse ICs into five 'focus areas' There's also a long screed about NIH's deficiencies.
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Dan Garisto @dangaristo.bsky.social · 02/05/2025
NEW: Starting May 5, NSF will implement an across-the-board 15% indirect cost rate (mirroring policies at DOE, NIH) Also, NSF staff expect 341 additional terminations today, bringing the total number of terminations to ~1,380.
Effective May 5, 2025, NSF will apply a standard indirect cost rate not to exceed 15% to all
grants and cooperative agreements awarded to IHEs for which indirect costs are allowable.1 The
awardee is authorized to determine the appropriate rate up to this limit.
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Dan Garisto @dangaristo.bsky.social · 01/05/2025
BREAKING: NSF has frozen all grant funding, as of yesterday. It's unclear when they will resume funding awards, or why the pause has been put in place. www.nature.com/articles/d41...
nature.com
Exclusive: NSF stops awarding new grants and funding existing ones
US science funder also plans to screen grant applications for compliance with ‘agency priorities’.
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Colin Carlson @colincarlson.bsky.social · 30/04/2025
🦟🦠 NEW! We looked at every experiment going back to the 1960s, and found that mosquitoes are almost certainly not primary or secondary vectors of Oropouche virus - a common claim in both the scientific literature and public health communication. #EpiSky #IDSky 😷🧪 journals.plos.org/plosntds/art...
journals.plos.org
Vector competence for Oropouche virus: A systematic review of pre-2024 experiments
Oropouche virus has recently become an urgent threat to public health in Central and South America. OROV is mainly transmitted by biting midges; however, some public health agencies and scientific sou...
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Physgal ⚛️ @physgal.bsky.social · 18/04/2025
Calling all US and Canadian students thinking about graduate studies! Come study science at #SFU in beautiful British Columbia, Canada. Graduate admissions have been reopened. Apply by April 25th. ⚛️ 🧪👩‍🔬🎢 🇨🇦
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ace-gtdb.bsky.social @ace-gtdb.bsky.social · 18/04/2025
GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.
gtdb.ecogenomic.org
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
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Neil Lewis, Jr. @neillewisjr.bsky.social · 18/04/2025
We're all going to learn about suppy chains the hard way...again.
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Max Kozlov @maxkozlov.bsky.social · 18/04/2025
Per source, NIH has been instructed to hold off from issuing ALL awards to Harvard, Cornell, Columbia, Brown, and Northwestern (including med schools) Agency staff have also been instructed to not speak about this funding freeze to grantees and applicants
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Ryan H Glaubke @ocnogrphr.bsky.social · 16/04/2025
This is ridiculous. NSF is pausing *all* outgoing grants awarded this cycle and subjecting them to a “secondary review” by DOGE. Gumming up the funding pipeline like this threatens the job security of nearly a million graduate students and post docs, to say nothing of the science…
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Lena Sun @lenasun.bsky.social · 16/04/2025
SCOOP: Internal budget doc reveals extent of Trump’s proposed health cuts. About 1/3 of HHS discretionary budget. Our story w @carolynyjohnson.bsky.social @rachelroubein.bsky.social @joelachenbach.bsky.social @laurenweberhp.bsky.social www.washingtonpost.com/health/2025/...
washingtonpost.com
Internal budget document reveals extent of Trump’s proposed health cuts
HHS would be asked to absorb a $40 billion cut, about one third of its discretionary budget.
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Krista Freeman @kfreeman.bsky.social · 16/04/2025
Hurray, it is finally out! Meet bacteriophage Bxb1 - the subject of my first full-phage cryo-EM study. My structures are beautifully complemented by the Park Lab’s cryo-ET analysis, shedding light on mycobacteriophage structural changes during infection. www.sciencedirect.com/science/arti...
sciencedirect.com
Structure and infection dynamics of mycobacteriophage Bxb1
Mycobacteriophage Bxb1 is a well-characterized virus of Mycobacterium smegmatis with double-stranded DNA and a long, flexible tail. Mycobacteriophages…
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Hensley Lab @scottehensley.bsky.social · 16/04/2025
After 8 months of peer review, our manuscript was published today @nature.com showing that bovine H5N1 viruses bind poorly to human-type sialic acid receptors. We now know that the virus is only 1 HA substitution away from efficiently binding human receptors. www.nature.com/articles/s41...
nature.com
Bovine H5N1 binds poorly to human-type sialic acid receptors - Nature
Nature - Bovine H5N1 binds poorly to human-type sialic acid receptors
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Eduardo Rocha @epcrocha.bsky.social · 16/04/2025
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!
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David Gilbert @davidgilbert.bsky.social · 15/04/2025
SCOOP: HHS has been gutted leaving critical health systems in danger of collapsing overnight. And no one's in charge: “Those in charge are AWOL. I’m doing nothing productive. This ship has no captain whatsoever, and I’m playing in the band while the Titanic sinks.” www.wired.com/story/depart...
wired.com
HHS Systems Are in Danger of Collapsing, Workers Say
The purging of IT and cybersecurity staff at the Department of Health and Human Services could threaten the systems used by the agency’s staff and the safety of critical health data.
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Jacob T. Levy @jacobtlevy.bsky.social · 14/04/2025
I had been doubtful that we were going to have a "this is the crisis moment" with Trump, as opposed to "everything about this is a destructive catastrophe." But the Abrego Garcia case is the crisis moment. 1/
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Lothar Kalmbach @lkalmbach.bsky.social · 11/04/2025
🌱 🔬 🚨 There is a 2-year postdoc position available in my group in Neuchâtel 🚨 Please share! Details here: www.unine.ch/biologie/wp-...
unine.ch
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Jeremy Berg @jeremymberg.bsky.social · 05/04/2025
A permanent injection in indirect cost case. The “NIH” rule change violated administrative procedures act. Appeal to come.
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Sciences @sciences.skyfleet.blue · 03/04/2025
Archaea go multicellular under pressure | Science
science.org
Archaea go multicellular under pressure | Science
A microbe from the Dead Sea switches to a tissue-like form when compressed
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Max Kozlov @maxkozlov.bsky.social · 02/04/2025
NEW: Researchers have sued the NIH and HHS, alleging that they have engaged in a "reckless and illegal purge to stamp out NIH-funded research that addresses topics and populations that they disfavor" by terminating hundreds of grants, violating the APA, Fifth Amendment and the Separation of Powers.
storage.courtlistener.com
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Mathieu Gautier @mgda76.bsky.social · 02/04/2025
🚨 Postdoc Opportunity in Quantitative & Population Genetics! We’re hiring a 2-year postdoc at CBGP (INRAE, Montpellier, France) to work on quantitative and population genetics applied to Drosophila biarmipes. 📍 More details: umr-cbgp.fr/rejoindre-le... #Postdoc #Genetics #Drosophila
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ASM @asm.org · 01/04/2025
Removing the top leadership at NIAID, NIH and other health agencies, including the CDC and FDA, will damage America’s position as a leader in groundbreaking research in disease prevention and treatment. That puts us all at risk. Read our statement: asm.org/Press-Releas...
asm.org
ASM Statement on Removal of NIH & NIAID Leadership
Removing the top leadership at NIAID, NIH and other health agencies including CDC and FDA will damage America’s position as a leader in groundbreaking research in disease prevention and treatment.
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Marisa Kabas @marisakabas.bsky.social · 01/04/2025
New — Here is a running list of Dept. of Health and Human Services (HHS) offices that have either been fully eliminated or gutted into non-functionality as a result of today's mass firings (provided to me directly by a CDC staffer):
NCCDPHP
Division of Reproductive Health
Division of Population Health 
   BCSB 
   EPI branch
   Prevention Research Translation Branch
Office of Smoking and Health  

NCHHSTP
Division of TB elimination
-Communication, Education, and Behavioral Studies Branch 
PBEMB
 
GLOBAL 
Division of HIV and TB 
Communications Branch
SPIN
SPICE
PBEMB
MCHB
HIDMSB
EHSRB
Scientific Integrity Branch

NCEH 
Division of Environmental Science/Practice Asthma and Air Quality branch 
















NCIRD 
ISD/Partnerships 

NIOSH 
Miner safety 
Health effects lab division 
Respiratory health division 

NCBDDD
Office of the Director 
Disability Health 

NCIPC 
Division of Violence Prevention
Division of Injury Prevention 
OD
Office of Health Equity

OCOO
Office of Human Resources
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 28/03/2025
Job offers: 1 funded PhD position and 1 postdoc in computational genomics between Univ Lille and Helsinki Uni, details: kamimrcht.github.io/webpage/jobs.html we're looking for candidates, please share 🙏🏻
kamimrcht.github.io
PhD and Postdoc in computational genomics
CRIStAL, CNRS, Université de Lille
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Scott Delaney @scott-delaney.bsky.social · 31/03/2025
The latest NIH grant chaos: NIH apparently sent stop-work orders to all *97* MARC and U-RISE programs in the country. These programs support underrepresented undergrads interested in health research careers. MARC dates to 1977. Over 48 years, the programs have supported thousands of students.
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