Avi Flamholz
@flamholz.bsky.social
NYC; Lab of Environmental Microbiology @rockefelleruniv.bsky.social
Was great to host @deepakkrish.bsky.social at @rockefeller.edu this week. Thanks for the conversation and phenomenal talk.
January 8, 2026 at 11:43 PM
Was great to host @deepakkrish.bsky.social at @rockefeller.edu this week. Thanks for the conversation and phenomenal talk.
These stats are super important AND also obscure the fact that a great way to reduce traffic deaths is by reducing vehicle miles driven. Should explicitly report miles driven per resident.
December 31, 2025 at 1:40 AM
These stats are super important AND also obscure the fact that a great way to reduce traffic deaths is by reducing vehicle miles driven. Should explicitly report miles driven per resident.
Reposted by Avi Flamholz
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)
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)
December 24, 2025 at 3:03 PM
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)
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)
Thanks to @yairmau.com for the pics
December 18, 2025 at 4:04 PM
Thanks to @yairmau.com for the pics
Heading to #AGU25 tomorrow to talk about continuum models of SOC in session B32B Weds morning. Hope to see some friends there.
agu.confex.com/agu/agu25/me...
agu.confex.com/agu/agu25/me...
Statistical approaches to soil carbon dynamics
Terrestrial ecosystems absorb ≈30% of anthropogenic CO2 emissions in a process ...
agu.confex.com
December 15, 2025 at 1:03 PM
Heading to #AGU25 tomorrow to talk about continuum models of SOC in session B32B Weds morning. Hope to see some friends there.
agu.confex.com/agu/agu25/me...
agu.confex.com/agu/agu25/me...
very disappointing. at least they finally put that traffic light at michigan and del mar
December 4, 2025 at 6:00 PM
very disappointing. at least they finally put that traffic light at michigan and del mar
This is pretty great.
What does E. coli do when food runs out? We spent years looking at it with our quantitative glasses, and now put the final preprint online: www.biorxiv.org/content/10.1...
Congrats to Théo Gervais for the 'tour de force'!
Congrats to Théo Gervais for the 'tour de force'!
www.biorxiv.org
December 4, 2025 at 5:00 PM
This is pretty great.
The Anthropocene
![Comic: Typical Geologic core sample. [Cylindrical core sample with labels for difference sections from top to bottom] Topsoil, till, granite bedrock, bottomsoil, roof of subway car, floor of subway car, more granite, municipal water main [gouge in core sample], slightly different granite, piece of screaming spelunker’s forearm, cool crystals with no resale value, mangled fragments of drillbit from previous attempt, some boring intrusive rock that’s basically granite but has a name like “diorite” or “Andalite” that you always have to look up, netherrack, Balrog wing. [break between next chunk of core sample] Granite, topsoil, cement, floorboards, carpet, possessions of a confused and angry homeowner in the other hemisphere.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreicffnydtpbb2x24cfbblv2qtcwbr37zyw44vtqx47ocj2a26b2j2u@jpeg)
November 26, 2025 at 3:22 AM
The Anthropocene
Glad to see this beautful work from Daniel Amador-Noguez’s group is out now. journals.asm.org/doi/10.1128/...
Thermodynamics shapes the in vivo enzyme burden of glycolytic pathways | mBio
Cells regulate metabolic fluxes to balance energy production, biosynthesis, and the
efficient use of limited resources, including the finite capacity for synthesizing
and maintaining metabolic enzymes...
journals.asm.org
November 25, 2025 at 2:14 AM
Glad to see this beautful work from Daniel Amador-Noguez’s group is out now. journals.asm.org/doi/10.1128/...
Reposted by Avi Flamholz
On Thu, Nov 20 @ 11am ET, join us for a virtual science seminar with @rockefeller.edu's @flamholz.bsky.social: Statistical Approaches to Soil Carbon Dynamics. Free + open to all. #ecology Register: www.eventbrite.com/e/statistica...
November 17, 2025 at 1:29 PM
On Thu, Nov 20 @ 11am ET, join us for a virtual science seminar with @rockefeller.edu's @flamholz.bsky.social: Statistical Approaches to Soil Carbon Dynamics. Free + open to all. #ecology Register: www.eventbrite.com/e/statistica...
Rockefeller / MSK theory lunch #3 — Chromatin as a memory machine with Dr Jeremy Owen
November 14, 2025 at 5:16 PM
Rockefeller / MSK theory lunch #3 — Chromatin as a memory machine with Dr Jeremy Owen
Reposted by Avi Flamholz
Every cubic meter of air contains anywhere from 10 to 10 million microbes, depending on the altitude, location, season and time of day. At an observatory Watop Puy de Dôme, a 4,800-foot inactive volcano in France, microbiologists sample the aeromicrobiome.
Microbes Also Change the Climate. Could That Help Us? | Quanta Magazine
A collection of short dispatches from the field of climate microbiology conveys the contributions that single-celled life forms make to our climate system, and how we can work with them to address…
www.quantamagazine.org
November 7, 2025 at 4:46 PM
Every cubic meter of air contains anywhere from 10 to 10 million microbes, depending on the altitude, location, season and time of day. At an observatory Watop Puy de Dôme, a 4,800-foot inactive volcano in France, microbiologists sample the aeromicrobiome.
Glad you take a conservative approach. Certainly in favor of doing these sorts of assessments when the questions/data take you there (e.g., fig 6 of ref below). Still, seems to me there are many conceptual and statistical issues that are often ignored...
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
October 9, 2025 at 4:19 PM
Glad you take a conservative approach. Certainly in favor of doing these sorts of assessments when the questions/data take you there (e.g., fig 6 of ref below). Still, seems to me there are many conceptual and statistical issues that are often ignored...
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
I see. I think this is a good strategy. I agree that KEGG is super useful, but I still don't really understand how we know which genes go in which pathways.
October 8, 2025 at 8:36 PM
I see. I think this is a good strategy. I agree that KEGG is super useful, but I still don't really understand how we know which genes go in which pathways.
Seems like it would be really hard to control these analyses for multiple hypothesis testing, no?
October 6, 2025 at 7:28 PM
Seems like it would be really hard to control these analyses for multiple hypothesis testing, no?
Reposted by Avi Flamholz
The vast majority of permafrost exists in the subsurface. What happens when this deep, ancient permafrost thaws? How fast does it take microbial communities to "wake up"?
This project now published in JGR, with @isotopes.bsky.social , @kopflab.bsky.social , et al., aims to address that question!
This project now published in JGR, with @isotopes.bsky.social , @kopflab.bsky.social , et al., aims to address that question!
Microbial Resuscitation and Growth Rates in Deep Permafrost: Lipid Stable Isotope Probing Results From the Permafrost Research Tunnel in Fox, Alaska
Microbial growth is extremely slow within the first 30 days of thaw. Temperature may drive which taxa are active, but not growth rates Subsurface microbes preferentially produce glycolipids over ...
agupubs.onlinelibrary.wiley.com
September 26, 2025 at 6:35 PM
The vast majority of permafrost exists in the subsurface. What happens when this deep, ancient permafrost thaws? How fast does it take microbial communities to "wake up"?
This project now published in JGR, with @isotopes.bsky.social , @kopflab.bsky.social , et al., aims to address that question!
This project now published in JGR, with @isotopes.bsky.social , @kopflab.bsky.social , et al., aims to address that question!
Congrats to Jan, Sean and the whole Brady lab crew.
Now out in @natbiotech.nature.com: Newly identified compounds from the #BradyLab appear effective against drug-resistant bacteria. The technique used to reveal them could uncover many more antibiotics, as well as help illuminate a previously hidden microbial world. #RockefellerScience
Hundreds of new bacteria, and two potential antibiotics, found in soil - News
Most bacteria cannot be cultured in the lab—and that’s been bad news for medicine. Many of our frontline antibiotics originated from microbes, yet as antibiotic resistance spreads and drug pipelines r...
www.rockefeller.edu
September 15, 2025 at 11:59 AM
Congrats to Jan, Sean and the whole Brady lab crew.
Reposted by Avi Flamholz
Applications are now open for September 2026 enrollment in The David Rockefeller Graduate Program in Bioscience.
Join a vibrant community of scientists pushing the boundaries of discovery.
Learn more here: https://www.rockefeller.edu/education-and-training/graduate-program-in-bioscience/
Join a vibrant community of scientists pushing the boundaries of discovery.
Learn more here: https://www.rockefeller.edu/education-and-training/graduate-program-in-bioscience/
September 8, 2025 at 6:44 PM
Applications are now open for September 2026 enrollment in The David Rockefeller Graduate Program in Bioscience.
Join a vibrant community of scientists pushing the boundaries of discovery.
Learn more here: https://www.rockefeller.edu/education-and-training/graduate-program-in-bioscience/
Join a vibrant community of scientists pushing the boundaries of discovery.
Learn more here: https://www.rockefeller.edu/education-and-training/graduate-program-in-bioscience/
Pretty strong case for open review processes.
This wpuld seem like a no-brainer.
Yet the same people having horrible experiences in such journals are the first to suggest it for the next submission. 🤷♂️
Yet the same people having horrible experiences in such journals are the first to suggest it for the next submission. 🤷♂️
August 29, 2025 at 9:45 PM
Pretty strong case for open review processes.
Reposted by Avi Flamholz
OIST is hiring Open-Rank Faculty!!
This call is open to several fields, including Ecology, Environmental Science, and Earth Science🌏🌳🐦🐟🐝🦠
Come be part of a truly diverse and inspiring community!!
This call is open to several fields, including Ecology, Environmental Science, and Earth Science🌏🌳🐦🐟🐝🦠
Come be part of a truly diverse and inspiring community!!
📢 #FacultyHiring: OIST is hiring! We invite exceptional scientists to apply for faculty positions in:
- Ecology, Environmental Science, Earth Science, and Oceanography
- Physics and Quantum Science (including related fields)
🔗: www.oist.jp/careers/facu...
- Ecology, Environmental Science, Earth Science, and Oceanography
- Physics and Quantum Science (including related fields)
🔗: www.oist.jp/careers/facu...
August 20, 2025 at 1:50 PM
OIST is hiring Open-Rank Faculty!!
This call is open to several fields, including Ecology, Environmental Science, and Earth Science🌏🌳🐦🐟🐝🦠
Come be part of a truly diverse and inspiring community!!
This call is open to several fields, including Ecology, Environmental Science, and Earth Science🌏🌳🐦🐟🐝🦠
Come be part of a truly diverse and inspiring community!!
Reposted by Avi Flamholz
EMBL is back on hiring faculty! Check out the multiple open positions:
3 PIs- 2 in Heidelberg incl. our Molecular Systems Biology Unit, 1 in Grenoble
1 Head of Unit (Cell Biology & Biophysics, Heidelberg).
Closing deadlines in Sep!
+3 more positions to come out then, stay tuned...
@embl.org
3 PIs- 2 in Heidelberg incl. our Molecular Systems Biology Unit, 1 in Grenoble
1 Head of Unit (Cell Biology & Biophysics, Heidelberg).
Closing deadlines in Sep!
+3 more positions to come out then, stay tuned...
@embl.org
August 12, 2025 at 5:25 AM
EMBL is back on hiring faculty! Check out the multiple open positions:
3 PIs- 2 in Heidelberg incl. our Molecular Systems Biology Unit, 1 in Grenoble
1 Head of Unit (Cell Biology & Biophysics, Heidelberg).
Closing deadlines in Sep!
+3 more positions to come out then, stay tuned...
@embl.org
3 PIs- 2 in Heidelberg incl. our Molecular Systems Biology Unit, 1 in Grenoble
1 Head of Unit (Cell Biology & Biophysics, Heidelberg).
Closing deadlines in Sep!
+3 more positions to come out then, stay tuned...
@embl.org
Reposted by Avi Flamholz
Please repost and amplify !
We are hiring a faculty position in Evolutionary Genetics in the Biology Department at U of South Carolina!
Check us out and come be our colleague!
sc.edu/study/colleg...
Deadline for applications is Oct 1
#AcademicJobs #EvoBio
We are hiring a faculty position in Evolutionary Genetics in the Biology Department at U of South Carolina!
Check us out and come be our colleague!
sc.edu/study/colleg...
Deadline for applications is Oct 1
#AcademicJobs #EvoBio
Assistant Professor position in Evolutionary Genetics - Department of Biological Sciences | University of South Carolina
sc.edu
August 12, 2025 at 5:29 PM
Please repost and amplify !
We are hiring a faculty position in Evolutionary Genetics in the Biology Department at U of South Carolina!
Check us out and come be our colleague!
sc.edu/study/colleg...
Deadline for applications is Oct 1
#AcademicJobs #EvoBio
We are hiring a faculty position in Evolutionary Genetics in the Biology Department at U of South Carolina!
Check us out and come be our colleague!
sc.edu/study/colleg...
Deadline for applications is Oct 1
#AcademicJobs #EvoBio
Reposted by Avi Flamholz
🍄 UGA Plant Pathology is hiring TT faculty in Mycology/Fungal Biology/Fungal Ecology at the Asst/Assc level! Please pass along this opportunity to anyone you know who may be interested. I'm on the search committee and happy to answer questions. 🍄 www.ugajobsearch.com/postings/445...
Assistant or Associate Professor - Fungal Biology/Mycology
The Department of Plant Pathology in the College of Agricultural and Environmental Sciences (CAES) at the University of Georgia is recruiting for the position of Assistant or Associate Professor in Fu...
www.ugajobsearch.com
August 21, 2025 at 5:14 PM
🍄 UGA Plant Pathology is hiring TT faculty in Mycology/Fungal Biology/Fungal Ecology at the Asst/Assc level! Please pass along this opportunity to anyone you know who may be interested. I'm on the search committee and happy to answer questions. 🍄 www.ugajobsearch.com/postings/445...
Reposted by Avi Flamholz
⁉️ Are you our next faculty member?
The Department of Earth, Environmental and Planetary Sciences at Rice University, seeks applications for a tenure-track assistant professor position.
Learn more or apply by October 15th: eeps.rice.edu/eeps-job-opp...
The Department of Earth, Environmental and Planetary Sciences at Rice University, seeks applications for a tenure-track assistant professor position.
Learn more or apply by October 15th: eeps.rice.edu/eeps-job-opp...
August 28, 2025 at 5:02 PM
⁉️ Are you our next faculty member?
The Department of Earth, Environmental and Planetary Sciences at Rice University, seeks applications for a tenure-track assistant professor position.
Learn more or apply by October 15th: eeps.rice.edu/eeps-job-opp...
The Department of Earth, Environmental and Planetary Sciences at Rice University, seeks applications for a tenure-track assistant professor position.
Learn more or apply by October 15th: eeps.rice.edu/eeps-job-opp...
Reposted by Avi Flamholz
Full-time, 9-month, Tenure-track Assistant Professor in Paleoclimatology position at the University of Hawaii.
www.indeed.com/viewjob?jk=4...
www.indeed.com/viewjob?jk=4...
Assistant Professor in Paleoclimatology - Honolulu, HI - Indeed.com
University of Hawaii
www.indeed.com
August 29, 2025 at 11:59 AM
Full-time, 9-month, Tenure-track Assistant Professor in Paleoclimatology position at the University of Hawaii.
www.indeed.com/viewjob?jk=4...
www.indeed.com/viewjob?jk=4...