Evan Brenner
@evanbrenner.bsky.social
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!
Reposted by Evan Brenner
New @isbscience.org research shows how microbial teamwork behind denitrification can collapse in polluted environments, threatening ecosystem balance and resilience. isbscience.org/news/environ...
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.
isbscience.org
June 18, 2025 at 8:49 PM
New @isbscience.org research shows how microbial teamwork behind denitrification can collapse in polluted environments, threatening ecosystem balance and resilience. isbscience.org/news/environ...
Reposted by Evan Brenner
🚨 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.
"The explanations are bereft of reasoning — virtually in their entirety... unsupported by [facts]."
Each of them are VOID and ILLEGAL, he says.
June 16, 2025 at 6:16 PM
🚨 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.
"The explanations are bereft of reasoning — virtually in their entirety... unsupported by [facts]."
Each of them are VOID and ILLEGAL, he says.
Reposted by Evan Brenner
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...
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...
grants.nih.gov
June 13, 2025 at 5:33 PM
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...
Reposted by Evan Brenner
🦠🧬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.
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.
June 3, 2025 at 12:47 PM
🦠🧬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.
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.
Reposted by Evan Brenner
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.
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.
June 3, 2025 at 12:31 PM
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.
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.
Reposted by Evan Brenner
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
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
May 22, 2025 at 9:56 PM
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
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
Reposted by Evan Brenner
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
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
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.
www.nature.com
May 21, 2025 at 6:41 PM
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
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
Reposted by Evan Brenner
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
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes https://www.biorxiv.org/content/10.1101/2025.05.14.653371v1
May 19, 2025 at 6:37 AM
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
Reposted by Evan Brenner
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...
www.biorxiv.org/content/10.1...
May 19, 2025 at 9:28 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Evan Brenner
an old redraw of one of my fav microbe memes, by @prokaryota.bsky.social
"eAT The DiRT bRöTHer" 🦠
#SciArt #microbes
"eAT The DiRT bRöTHer" 🦠
#SciArt #microbes
May 13, 2025 at 10:18 AM
an old redraw of one of my fav microbe memes, by @prokaryota.bsky.social
"eAT The DiRT bRöTHer" 🦠
#SciArt #microbes
"eAT The DiRT bRöTHer" 🦠
#SciArt #microbes
Reposted by Evan Brenner
Reposted by Evan Brenner
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
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
May 14, 2025 at 2:07 PM
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
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
Reposted by Evan Brenner
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
May 13, 2025 at 11:37 PM
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
Reposted by Evan Brenner
Optometrist: you should really probably spend less time on screens
Me, a computational biologist: I’ll… just take that under advisement, shall I?
Me, a computational biologist: I’ll… just take that under advisement, shall I?
May 13, 2025 at 6:12 PM
Optometrist: you should really probably spend less time on screens
Me, a computational biologist: I’ll… just take that under advisement, shall I?
Me, a computational biologist: I’ll… just take that under advisement, shall I?
Reposted by Evan Brenner
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.
http://spr.ly/63329Nk0yX
http://spr.ly/63329Nk0yX
May 13, 2025 at 5:47 PM
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.
http://spr.ly/63329Nk0yX
http://spr.ly/63329Nk0yX
Reposted by Evan Brenner
The Spencer Foundation is offering rapid response bridge funding for those who lost NSF research grants.
www.spencer.org/grant_types/...
www.spencer.org/grant_types/...
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...
www.spencer.org
May 2, 2025 at 9:07 PM
The Spencer Foundation is offering rapid response bridge funding for those who lost NSF research grants.
www.spencer.org/grant_types/...
www.spencer.org/grant_types/...
Reposted by Evan Brenner
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.
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.
May 2, 2025 at 2:50 PM
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.
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.
Reposted by Evan Brenner
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.
Also, NSF staff expect 341 additional terminations today, bringing the total number of terminations to ~1,380.
May 2, 2025 at 2:20 PM
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.
Also, NSF staff expect 341 additional terminations today, bringing the total number of terminations to ~1,380.
Reposted by Evan Brenner
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...
Exclusive: NSF stops awarding new grants and funding existing ones
US science funder also plans to screen grant applications for compliance with ‘agency priorities’.
www.nature.com
May 1, 2025 at 10:58 PM
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...
Reposted by Evan Brenner
🦟🦠 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/plosntds/art...
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...
journals.plos.org
April 30, 2025 at 5:59 PM
🦟🦠 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/plosntds/art...
Reposted by Evan Brenner
This is a lovely thread of self-introductions from members of the compbio/genomics crowd on BlueSky. It feels a bit more friendly and warm than a starter pack
There are so many people moving over that I'm sure I'm missing folks. Can we make a #compbio / #genomics intro thread to get reacquainted?
I'm at the University of Colorado. I often say that if you pick two of three from #transcriptome, #ML, and #publicdata, my lab is probably interested.
I'm at the University of Colorado. I often say that if you pick two of three from #transcriptome, #ML, and #publicdata, my lab is probably interested.
April 27, 2025 at 2:07 AM
This is a lovely thread of self-introductions from members of the compbio/genomics crowd on BlueSky. It feels a bit more friendly and warm than a starter pack
Reposted by Evan Brenner
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. ⚛️ 🧪👩🔬🎢 🇨🇦
Applications are open for select graduate studies programs at #SFU, including biomedical physiology, chemistry, molecular biology and @sfuphysics.bsky.social. Canadian and US students encouraged to apply by April 25. www.sfu.ca/gradstudies/...
Lead the Way: Graduate Studies at SFU in Canada for Fall 2025 & Spring 2026
Select SFU graduate programs are opening their applications particularly for Canadian students choosing to remain and study in Canada as well as US students looking to study outside the US. Applicatio...
www.sfu.ca
April 18, 2025 at 10:22 PM
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. ⚛️ 🧪👩🔬🎢 🇨🇦
Reposted by Evan Brenner
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 - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 18, 2025 at 7:13 PM
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.
Reposted by Evan Brenner
We're all going to learn about suppy chains the hard way...again.
Right now, I’m paying attention to news from the shipping and trucking industries of leading indicators of how bad things are going to get.
And the trends are alarming.
Beginning to stock up on essentials *now*.
And the trends are alarming.
Beginning to stock up on essentials *now*.
April 18, 2025 at 4:39 PM
We're all going to learn about suppy chains the hard way...again.