Philmus Lab @ OSU
@philmuslab.bsky.social
This is the lab account for the research lab of Dr. Benjamin (BJ) Philmus (he/him). College of Pharmacy at Oregon State and focusing on natural products.
Pinned
Philmus Lab @ OSU
@philmuslab.bsky.social
· Jul 16
Here's a fun perspective piece on Cyanobacteria as prolific natural product producers with great potential for drug discovery. Thanks especially to @philmuslab.bsky.social for ringleading and letting us contribute!
pubs.rsc.org/en/content/a...
pubs.rsc.org/en/content/a...
Green genes from blue greens: challenges and solutions to unlocking the potential of cyanobacteria in drug discovery
Cyanobacteria are prolific producers of biologically active compounds that are important in influencing ecology, behavior of interacting organisms, and as leads in drug discovery efforts. Here we disc...
pubs.rsc.org
Come read about our thoughts on why cyanobacteria are underrepresented in drug discovery and how both synthetic biology and native hosts can help.
This was fun to work on with a great group of people who include @dtdoering.bsky.social @danudwary.secondarymetabolism.com @eustaquiolab.bsky.social
This was fun to work on with a great group of people who include @dtdoering.bsky.social @danudwary.secondarymetabolism.com @eustaquiolab.bsky.social
Reposted by Philmus Lab @ OSU
Little gist for getting coauthor list from PubMed for NSF COA list. Thanks to coauthors gpt5 and claude. gist.github.com/davidaknowle...
Get COA coauthor list for NSF including affiliations from PUBMED
Get COA coauthor list for NSF including affiliations from PUBMED - coa.py
gist.github.com
November 5, 2025 at 2:50 PM
Little gist for getting coauthor list from PubMed for NSF COA list. Thanks to coauthors gpt5 and claude. gist.github.com/davidaknowle...
I am excited to host Dr. @lizahaart.bsky.social in our Pharmaceutical Sciences Seminar Series this coming Thursday. I am really looking forward to learning more about science communication!!
November 5, 2025 at 12:09 AM
I am excited to host Dr. @lizahaart.bsky.social in our Pharmaceutical Sciences Seminar Series this coming Thursday. I am really looking forward to learning more about science communication!!
Reposted by Philmus Lab @ OSU
A new AI model is opening the black box of the leading artificial intelligence tool for predicting how proteins will interact with small molecules, such as drugs. www.sciencenews.org/article/ai-m... #biotech #AI #science
The AI model OpenFold3 takes a crucial step in making protein predictions
The open-source AI model improves transparency in predicting how proteins interact with other molecules, which could speed up drug discovery.
www.sciencenews.org
October 29, 2025 at 2:40 PM
A new AI model is opening the black box of the leading artificial intelligence tool for predicting how proteins will interact with small molecules, such as drugs. www.sciencenews.org/article/ai-m... #biotech #AI #science
Reposted by Philmus Lab @ OSU
reminder that my (wonderful, diverse, interdisciplinary) department at the University of Oregon is seeking applications for an Associate/Full Professor of Data Science -- deadline 10/31 and only cover letter/CV needed to apply
academicjobsonline.org/ajo/jobs/30328
academicjobsonline.org/ajo/jobs/30328
University of Oregon, Department of Data Science
Job #AJO30328, 535565 Associate or Full Professor of Data Science, Department of Data Science, University of Oregon, Eugene, Oregon, US
academicjobsonline.org
October 22, 2025 at 6:55 PM
reminder that my (wonderful, diverse, interdisciplinary) department at the University of Oregon is seeking applications for an Associate/Full Professor of Data Science -- deadline 10/31 and only cover letter/CV needed to apply
academicjobsonline.org/ajo/jobs/30328
academicjobsonline.org/ajo/jobs/30328
Reposted by Philmus Lab @ OSU
October 21, 2025 at 9:07 PM
Reposted by Philmus Lab @ OSU
New biology: stink bugs inoculate their eggs with a fungus that protects them from parasitoids
www.sciencemagazinedigital.org/sciencemagaz...
www.sciencemagazinedigital.org/sciencemagaz...
Science Magazine - Defensive fungal symbiosis on insect hindlegs
Tympanal organs have repeatedly evolved in diverse insects and were thought to be required for auditory perception (1).
www.sciencemagazinedigital.org
October 17, 2025 at 11:35 AM
New biology: stink bugs inoculate their eggs with a fungus that protects them from parasitoids
www.sciencemagazinedigital.org/sciencemagaz...
www.sciencemagazinedigital.org/sciencemagaz...
Reposted by Philmus Lab @ OSU
Thrilled to share with you a recent work from our group: Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome | Journal of Natural Products pubs.acs.org/doi/10.1021/... Please have a look to the associated MassQL compendium.
Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome
An advanced metabolomic workflow featuring expert knowledge-tailored mass spectral queries and multi-informative molecular networking was applied to French DNA-barcoded collections of Amanita species ...
pubs.acs.org
October 13, 2025 at 6:00 AM
Thrilled to share with you a recent work from our group: Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome | Journal of Natural Products pubs.acs.org/doi/10.1021/... Please have a look to the associated MassQL compendium.
I am a little late in putting this out there, but I had the opportunity to work with some amazing hashtag#ComputerScience Capstone students from College of Engineering – Oregon State University this past year. We worked on designing and implementing a game-based learning app called PharmacyGO!
October 7, 2025 at 10:34 PM
I am a little late in putting this out there, but I had the opportunity to work with some amazing hashtag#ComputerScience Capstone students from College of Engineering – Oregon State University this past year. We worked on designing and implementing a game-based learning app called PharmacyGO!
Reposted by Philmus Lab @ OSU
BindCraft: an AlphaFold2-powered de novo protein binder design tool 🧬✨
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.
www.nature.com
October 5, 2025 at 12:07 PM
BindCraft: an AlphaFold2-powered de novo protein binder design tool 🧬✨
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
Excited to have just finished the first day of the #UIDP workshop. So many exciting ideas and enthusiasm for supporting graduate students. Thank you @oregonstate.edu for the opportunity to be part of the team and discussions.
September 30, 2025 at 12:44 AM
Excited to have just finished the first day of the #UIDP workshop. So many exciting ideas and enthusiasm for supporting graduate students. Thank you @oregonstate.edu for the opportunity to be part of the team and discussions.
Reposted by Philmus Lab @ OSU
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
September 29, 2025 at 3:01 PM
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
Reposted by Philmus Lab @ OSU
Engineering microbiomes for natural product discovery and production
-in Nat Prod Rep by Francesco Del Carratore and Rainer Breitling
pubs.rsc.org/en/content/a...
-in Nat Prod Rep by Francesco Del Carratore and Rainer Breitling
pubs.rsc.org/en/content/a...
September 28, 2025 at 11:20 AM
Engineering microbiomes for natural product discovery and production
-in Nat Prod Rep by Francesco Del Carratore and Rainer Breitling
pubs.rsc.org/en/content/a...
-in Nat Prod Rep by Francesco Del Carratore and Rainer Breitling
pubs.rsc.org/en/content/a...
Reposted by Philmus Lab @ OSU
Okay so I definitely need a CRISPR system and the only real path forward is the OpenCrispr protein. A friend donated a human optimized plasmid, so first is retooling for plants. If anyone wants access to it early, help me pay for the synthesis. DM's open. 💚
a computer generated image of a cell with the word cas9 on the bottom
ALT: a computer generated image of a cell with the word cas9 on the bottom
media.tenor.com
September 27, 2025 at 6:29 PM
Okay so I definitely need a CRISPR system and the only real path forward is the OpenCrispr protein. A friend donated a human optimized plasmid, so first is retooling for plants. If anyone wants access to it early, help me pay for the synthesis. DM's open. 💚
Reposted by Philmus Lab @ OSU
Aaand it's out! Meet MITE - the natural product tailoring enzyme database, just published in @narjournal.bsky.social! MITE DB captures the substrate- and reaction-specificity of tailoring enzymes, allowing to capture this information in a human- and machine-readable way! doi.org/10.1093/nar/...
September 27, 2025 at 9:11 AM
Aaand it's out! Meet MITE - the natural product tailoring enzyme database, just published in @narjournal.bsky.social! MITE DB captures the substrate- and reaction-specificity of tailoring enzymes, allowing to capture this information in a human- and machine-readable way! doi.org/10.1093/nar/...
Reposted by Philmus Lab @ OSU
Reposted by Philmus Lab @ OSU
Assistant Professor of Plant Pathology & Fungal Biology, UC Davis. 🍄🌱 recruit.ucdavis.edu/JPF07339 Deadline Dec 1, 2025. 👀 "Primary teaching responsibilities will be teaching Introductory Mycology, an upper-division lab class, and SAS 30, Mushroom, Molds & Society"
Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
recruit.ucdavis.edu
September 23, 2025 at 3:15 AM
Assistant Professor of Plant Pathology & Fungal Biology, UC Davis. 🍄🌱 recruit.ucdavis.edu/JPF07339 Deadline Dec 1, 2025. 👀 "Primary teaching responsibilities will be teaching Introductory Mycology, an upper-division lab class, and SAS 30, Mushroom, Molds & Society"
Reposted by Philmus Lab @ OSU
Dean Sidelinger of the Oregon Health Authority: “Effective Wednesday, September 17, pharmacists in Oregon will have the authority to continue to administer COVID vaccines without a prescription.”
FINALLY Oregon makes accessing COVID vaccines easier!
FINALLY Oregon makes accessing COVID vaccines easier!
Oregon Moves to Make It Easier to Get the COVID-19 Vaccine
The state has authorized pharmacists in Oregon to administer Covid-19 vaccines without a prescription.
www.wweek.com
September 18, 2025 at 1:44 AM
Dean Sidelinger of the Oregon Health Authority: “Effective Wednesday, September 17, pharmacists in Oregon will have the authority to continue to administer COVID vaccines without a prescription.”
FINALLY Oregon makes accessing COVID vaccines easier!
FINALLY Oregon makes accessing COVID vaccines easier!
We are proud to be able to offer this as an OpenAccess article!
pmc.ncbi.nlm.nih.gov/articles/PMC.... Thank you to #NaturalProductReports for helping us.
#SecMet
pmc.ncbi.nlm.nih.gov/articles/PMC.... Thank you to #NaturalProductReports for helping us.
#SecMet
September 16, 2025 at 5:13 PM
We are proud to be able to offer this as an OpenAccess article!
pmc.ncbi.nlm.nih.gov/articles/PMC.... Thank you to #NaturalProductReports for helping us.
#SecMet
pmc.ncbi.nlm.nih.gov/articles/PMC.... Thank you to #NaturalProductReports for helping us.
#SecMet
Reposted by Philmus Lab @ OSU
Want to know what natural products are in clinical trials? Read this review! Great job from Mark Butler, Rob Capon, Mark Blaskovich! pubs.rsc.org/en/content/a...
#naturalproducts #antibiotic #amr #drugdiscovery #drug
#naturalproducts #antibiotic #amr #drugdiscovery #drug
Natural product-derived compounds in clinical trials and drug approvals
Covering: January 2014–June 2025. Previous review: Natural Product Reports, 2014, 31, 1612Natural products (NPs) have long been foundational in medicine, from ancient herbal remedies to the discovery ...
pubs.rsc.org
September 10, 2025 at 3:01 PM
Want to know what natural products are in clinical trials? Read this review! Great job from Mark Butler, Rob Capon, Mark Blaskovich! pubs.rsc.org/en/content/a...
#naturalproducts #antibiotic #amr #drugdiscovery #drug
#naturalproducts #antibiotic #amr #drugdiscovery #drug
Reposted by Philmus Lab @ OSU
Reposted by Philmus Lab @ OSU
There’s a route that our drug molecules can take after dosing that we haven’t been paying enough attention to. Many might not even realize it exists;
An Underappreciated Fate of Drugs in Vivo
www.science.org
September 8, 2025 at 8:22 PM
There’s a route that our drug molecules can take after dosing that we haven’t been paying enough attention to. Many might not even realize it exists;
Reposted by Philmus Lab @ OSU
Reposted by Philmus Lab @ OSU
OK, this seems to be working well! New feed is full of good stuff, and the posts stick around. 🧪🦠🖥️🧬 #secmet
One wrinkle, though: I switched things up so that the words "natural product(s)" require approval. Otherwise, we're getting far too many non-scientific kinds of posts clogging the feed. 1/n
One wrinkle, though: I switched things up so that the words "natural product(s)" require approval. Otherwise, we're getting far too many non-scientific kinds of posts clogging the feed. 1/n
I've updated the "Secondary Metabolism" feed to run from @blueskyfeedcreator.com. The previous feed only held posts for 7 days. This should retain the last 100 posts, and even more if I decide to start paying (or get donations). It should be much more useful!
Feed is here!
bsky.app/profile/danu...
Feed is here!
bsky.app/profile/danu...
September 6, 2025 at 3:53 PM
OK, this seems to be working well! New feed is full of good stuff, and the posts stick around. 🧪🦠🖥️🧬 #secmet
One wrinkle, though: I switched things up so that the words "natural product(s)" require approval. Otherwise, we're getting far too many non-scientific kinds of posts clogging the feed. 1/n
One wrinkle, though: I switched things up so that the words "natural product(s)" require approval. Otherwise, we're getting far too many non-scientific kinds of posts clogging the feed. 1/n
Reposted by Philmus Lab @ OSU
By investigating the role compounds produced by cyanobacteria gene clusters play in freshwater ecosystems, research by @philmuslab.bsky.social of @oregonstate.edu will support the development of predictive models of microbial behavior in terrestrial-aquatic interfaces.
jointgeno.me/FY25FG
jointgeno.me/FY25FG
September 4, 2025 at 5:34 PM
By investigating the role compounds produced by cyanobacteria gene clusters play in freshwater ecosystems, research by @philmuslab.bsky.social of @oregonstate.edu will support the development of predictive models of microbial behavior in terrestrial-aquatic interfaces.
jointgeno.me/FY25FG
jointgeno.me/FY25FG
Reposted by Philmus Lab @ OSU
Please share! I'm looking for a postdoc. The position is to lead one of the following projects: 1) regulation of plant specialized metabolism by cell fate, or 2) foliar embryogenesis in the succulent plant Kalanchoe.
Learn more abt projects: cxli233.github.io/cxLi_lab/res...
Learn more abt projects: cxli233.github.io/cxLi_lab/res...
Plant cells are totipotent, meaning individual cells have the potential to develop into a full organism, a property unique to the zygote for animals. However, in most species for most cells, plant cells are not spontaneously totipotent, since they must be treated with specific hormone combinations to unlock their totipotency. Species within the Kalanchoe genus is unique as they spontaneously develop foliar embryos that are fully realized plantlets with shoot and root from notches along the edges of leaves. We speculate that the progenitor cells that give rise to these foliar embryos are totipotent, and we are using single cell techniques to identify & characterize them. In addition to being a fundamental process for plant biology, we foresee unlocking totipotency has many biotechnological applications, such as faciliating genetic transformation and the development of synthetic organs of biomanufacturing.
cxli233.github.io
September 4, 2025 at 2:00 PM
Please share! I'm looking for a postdoc. The position is to lead one of the following projects: 1) regulation of plant specialized metabolism by cell fate, or 2) foliar embryogenesis in the succulent plant Kalanchoe.
Learn more abt projects: cxli233.github.io/cxLi_lab/res...
Learn more abt projects: cxli233.github.io/cxLi_lab/res...