Geoff Zahn
@geoffzahn.bsky.social
mycology, microbial ecology, symbiosis, conservation, data science, ecopoet
Translational Insights into microbial Diversity Assembly & Linkages
https://gzahn.github.io/
Recruiting PhD students in Applied Science at William & Mary
Translational Insights into microbial Diversity Assembly & Linkages
https://gzahn.github.io/
Recruiting PhD students in Applied Science at William & Mary
Pinned
Geoff Zahn
@geoffzahn.bsky.social
· Sep 4
TIDAL Lab
Translational Insights into microbial Diversity, Assembly, & Linkages
gzahn.github.io
Hey, I'm recruiting for up to two funded PhD positions in #mycology or community #ecology. Please share!
Good stipend, lovely location in the woods near the beach. Field, lab, and computational projects. Seeking wide interests and bold ideas!
Lab: gzahn.github.io
Apply:
forms.gle/jK7bJkyrTAUH...
Good stipend, lovely location in the woods near the beach. Field, lab, and computational projects. Seeking wide interests and bold ideas!
Lab: gzahn.github.io
Apply:
forms.gle/jK7bJkyrTAUH...
Reposted by Geoff Zahn
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
A Grammar of Graphics for Comparative Genomics
An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…
thackl.github.io
November 18, 2025 at 7:02 PM
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
Reposted by Geoff Zahn
Funded PhD Opportunity: Seagrass Disease Ecology
Explore how the pseudofungus Phytophthora gemini impacts Zostera marina and restoration success. Lab + fieldwork @thembauk.bsky.social @plymuni.bsky.social & OCT. Combine microbiology, ecology & restoration science 🌱
👉 www.jobs.ac.uk/job/DPK439/p...
Explore how the pseudofungus Phytophthora gemini impacts Zostera marina and restoration success. Lab + fieldwork @thembauk.bsky.social @plymuni.bsky.social & OCT. Combine microbiology, ecology & restoration science 🌱
👉 www.jobs.ac.uk/job/DPK439/p...
November 17, 2025 at 8:30 AM
Funded PhD Opportunity: Seagrass Disease Ecology
Explore how the pseudofungus Phytophthora gemini impacts Zostera marina and restoration success. Lab + fieldwork @thembauk.bsky.social @plymuni.bsky.social & OCT. Combine microbiology, ecology & restoration science 🌱
👉 www.jobs.ac.uk/job/DPK439/p...
Explore how the pseudofungus Phytophthora gemini impacts Zostera marina and restoration success. Lab + fieldwork @thembauk.bsky.social @plymuni.bsky.social & OCT. Combine microbiology, ecology & restoration science 🌱
👉 www.jobs.ac.uk/job/DPK439/p...
Check out our latest dispatch where we make a (very convincing ☺️) case that marine #mycology is the next big thing and highlight a recent paper by Breyer et al.
Marine fungi have biomass = 22 MILLION blue whales!
Free link:
authors.elsevier.com/a/1lzT-3QW8S...
#aquaticfungi #microbiome #fungi
Marine fungi have biomass = 22 MILLION blue whales!
Free link:
authors.elsevier.com/a/1lzT-3QW8S...
#aquaticfungi #microbiome #fungi
authors.elsevier.com
October 21, 2025 at 10:19 PM
Check out our latest dispatch where we make a (very convincing ☺️) case that marine #mycology is the next big thing and highlight a recent paper by Breyer et al.
Marine fungi have biomass = 22 MILLION blue whales!
Free link:
authors.elsevier.com/a/1lzT-3QW8S...
#aquaticfungi #microbiome #fungi
Marine fungi have biomass = 22 MILLION blue whales!
Free link:
authors.elsevier.com/a/1lzT-3QW8S...
#aquaticfungi #microbiome #fungi
Yes, we all knew this of course. It's the entire brand.
October 14, 2025 at 6:51 PM
Yes, we all knew this of course. It's the entire brand.
New "Fidelity" #rstats package release with Abbey Neat can
quantify and compare the specificity of #microbiome communities associated with certain hosts or groups!
It intelligently handles rare taxa removal.
And check that handcrafted hex sticker! 😍
quantify and compare the specificity of #microbiome communities associated with certain hosts or groups!
It intelligently handles rare taxa removal.
And check that handcrafted hex sticker! 😍
October 14, 2025 at 4:18 PM
New "Fidelity" #rstats package release with Abbey Neat can
quantify and compare the specificity of #microbiome communities associated with certain hosts or groups!
It intelligently handles rare taxa removal.
And check that handcrafted hex sticker! 😍
quantify and compare the specificity of #microbiome communities associated with certain hosts or groups!
It intelligently handles rare taxa removal.
And check that handcrafted hex sticker! 😍
Lovely visit to U of Maine. Great folks and fun conversations about microbes!
October 12, 2025 at 2:11 PM
Lovely visit to U of Maine. Great folks and fun conversations about microbes!
Reposted by Geoff Zahn
Check out what we have been achieving through @iucnaquafungi.bsky.social towards the conservation of #AquaticFungi 🌟
📢 NEW REPORT 📢
The @iucnaquafungi.bsky.social report for 2024-2025 is now published. 👇
iucn.org/sites/defaul...
Get in touch if you want to collaborate with us to advance the #conservation of #aquaticfungi. 💧 🍄
@iucnfungi.bsky.social @protectspecies.bsky.social
The @iucnaquafungi.bsky.social report for 2024-2025 is now published. 👇
iucn.org/sites/defaul...
Get in touch if you want to collaborate with us to advance the #conservation of #aquaticfungi. 💧 🍄
@iucnfungi.bsky.social @protectspecies.bsky.social
iucn.org
October 3, 2025 at 8:21 PM
Check out what we have been achieving through @iucnaquafungi.bsky.social towards the conservation of #AquaticFungi 🌟
Reposted by Geoff Zahn
This moment from our latest episode with science writer @edyong209.bsky.social is 🔥
We asked Ed — how do we talk up the benefits of science in the face of government cuts? He told us that's the wrong approach. 🧪
Listen wherever, or watch on Spotify 👇
open.spotify.com/episode/7Evh...
We asked Ed — how do we talk up the benefits of science in the face of government cuts? He told us that's the wrong approach. 🧪
Listen wherever, or watch on Spotify 👇
open.spotify.com/episode/7Evh...
October 1, 2025 at 2:56 PM
This moment from our latest episode with science writer @edyong209.bsky.social is 🔥
We asked Ed — how do we talk up the benefits of science in the face of government cuts? He told us that's the wrong approach. 🧪
Listen wherever, or watch on Spotify 👇
open.spotify.com/episode/7Evh...
We asked Ed — how do we talk up the benefits of science in the face of government cuts? He told us that's the wrong approach. 🧪
Listen wherever, or watch on Spotify 👇
open.spotify.com/episode/7Evh...
youtu.be/8AeCo3AD1cM?...
"How could you even begin to pay me enough to do such a feat of Sisyphian futility?!"
Beautiful
"How could you even begin to pay me enough to do such a feat of Sisyphian futility?!"
Beautiful
Confused Teacher Crashes Out Over His Job | Mitchell and Webb Are Not Helping | Channel 4 Comedy
YouTube video by Channel 4 Comedy
youtu.be
September 23, 2025 at 3:47 PM
youtu.be/8AeCo3AD1cM?...
"How could you even begin to pay me enough to do such a feat of Sisyphian futility?!"
Beautiful
"How could you even begin to pay me enough to do such a feat of Sisyphian futility?!"
Beautiful
Reposted by Geoff Zahn
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
COVID vaccine gun show!
(Yeah I have asthma, diabetes, a weak heart, smoke 3 packs a day, or whatever lies you have to tell to get preventative medicine)
(Yeah I have asthma, diabetes, a weak heart, smoke 3 packs a day, or whatever lies you have to tell to get preventative medicine)
September 7, 2025 at 8:38 PM
COVID vaccine gun show!
(Yeah I have asthma, diabetes, a weak heart, smoke 3 packs a day, or whatever lies you have to tell to get preventative medicine)
(Yeah I have asthma, diabetes, a weak heart, smoke 3 packs a day, or whatever lies you have to tell to get preventative medicine)
RIP to my add_blast_header.sh script
The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....
September 7, 2025 at 11:42 AM
RIP to my add_blast_header.sh script
Reposted by Geoff Zahn
We are hiring! The #PlantBio department at UIUC is looking to recruit an Assistant Professor in Plant-Fungal interactions. Application deadline is October 31st @dallingjim.bsky.social see the link below for more details:
illinois.csod.com/ux/ats/caree...
illinois.csod.com/ux/ats/caree...
Assistant Professor- Department of Plant Biology
Duties & Responsibilities
illinois.csod.com
September 4, 2025 at 1:48 PM
We are hiring! The #PlantBio department at UIUC is looking to recruit an Assistant Professor in Plant-Fungal interactions. Application deadline is October 31st @dallingjim.bsky.social see the link below for more details:
illinois.csod.com/ux/ats/caree...
illinois.csod.com/ux/ats/caree...
10 years using Ubuntu and other linux distros and I JUST NOW learned that you can mount any server address in the file browser so easily!?
September 4, 2025 at 8:42 PM
10 years using Ubuntu and other linux distros and I JUST NOW learned that you can mount any server address in the file browser so easily!?
Hey, I'm recruiting for up to two funded PhD positions in #mycology or community #ecology. Please share!
Good stipend, lovely location in the woods near the beach. Field, lab, and computational projects. Seeking wide interests and bold ideas!
Lab: gzahn.github.io
Apply:
forms.gle/jK7bJkyrTAUH...
Good stipend, lovely location in the woods near the beach. Field, lab, and computational projects. Seeking wide interests and bold ideas!
Lab: gzahn.github.io
Apply:
forms.gle/jK7bJkyrTAUH...
TIDAL Lab
Translational Insights into microbial Diversity, Assembly, & Linkages
gzahn.github.io
September 4, 2025 at 12:43 AM
Hey, I'm recruiting for up to two funded PhD positions in #mycology or community #ecology. Please share!
Good stipend, lovely location in the woods near the beach. Field, lab, and computational projects. Seeking wide interests and bold ideas!
Lab: gzahn.github.io
Apply:
forms.gle/jK7bJkyrTAUH...
Good stipend, lovely location in the woods near the beach. Field, lab, and computational projects. Seeking wide interests and bold ideas!
Lab: gzahn.github.io
Apply:
forms.gle/jK7bJkyrTAUH...
Wow, that editor really used the desk-rejection of my paper to channel some of their disappointment and anger. I hope they feel better soon. We're all on the Titanic together.
August 31, 2025 at 11:29 AM
Wow, that editor really used the desk-rejection of my paper to channel some of their disappointment and anger. I hope they feel better soon. We're all on the Titanic together.
This. Yes. It's worse than you think
The fact that folks in genZ broadly don't understand filesystems, I get, & it is indeed not their fault. However, the fact that I regularly encounter upper-level, genZ, CS majors who don't understand filesystems; that's not OK, & there is plenty of blame there to go around, some of which is theirs.
Gen Z doesn't Understand Filesystems. It's not their fault.
Apple's early abstraction of mobile data storage has caused...confusion to say the least.
But what does the *real* iOS filesystem look like?
As a researcher myself; it's kind of insanely complicated:
Apple's early abstraction of mobile data storage has caused...confusion to say the least.
But what does the *real* iOS filesystem look like?
As a researcher myself; it's kind of insanely complicated:
August 27, 2025 at 1:56 AM
This. Yes. It's worse than you think
Reposted by Geoff Zahn
In Fall '26 the Himmel Lab will open at NJIT Biological Sciences. I'm beyond stoked!
Interested in a PhD/postdoc in the function/evolution/origins of the senses (computation or experimentation)? Message me and come join a great department in the NY metro! Sharing is appreciated. Info: himmellab.org
Interested in a PhD/postdoc in the function/evolution/origins of the senses (computation or experimentation)? Message me and come join a great department in the NY metro! Sharing is appreciated. Info: himmellab.org
July 4, 2025 at 11:55 AM
In Fall '26 the Himmel Lab will open at NJIT Biological Sciences. I'm beyond stoked!
Interested in a PhD/postdoc in the function/evolution/origins of the senses (computation or experimentation)? Message me and come join a great department in the NY metro! Sharing is appreciated. Info: himmellab.org
Interested in a PhD/postdoc in the function/evolution/origins of the senses (computation or experimentation)? Message me and come join a great department in the NY metro! Sharing is appreciated. Info: himmellab.org
Reposted by Geoff Zahn
If you are a postdoc working on any topic related to environmental microbiology and are looking for exposure, the Thermal Biology Institute (tbi.montana.edu) has slots open for virtual talks via zoom this fall. Email me if you are interested! Seminars are most Mondays, 3-4 pm Mountain Time.
Thermal Biology Institute - Default | Montana State University
Index to the Thermal Biology Institute's website.
tbi.montana.edu
August 6, 2025 at 5:08 PM
If you are a postdoc working on any topic related to environmental microbiology and are looking for exposure, the Thermal Biology Institute (tbi.montana.edu) has slots open for virtual talks via zoom this fall. Email me if you are interested! Seminars are most Mondays, 3-4 pm Mountain Time.
Reposted by Geoff Zahn
my lil reproducibility talk from today / I really wanted to instill the PhD students some simple first practices and ways to step up your game from there github.com/tjmahr/2025-...
August 20, 2025 at 11:52 PM
my lil reproducibility talk from today / I really wanted to instill the PhD students some simple first practices and ways to step up your game from there github.com/tjmahr/2025-...
Reposted by Geoff Zahn
FYI finally tidied this up into something usable github.com/feargalr/bac...
GitHub - feargalr/bacdive_harvester: R tools for scraping and extracting bacterial data from the BacDive database (Bacterial Diversity Metadatabase)
R tools for scraping and extracting bacterial data from the BacDive database (Bacterial Diversity Metadatabase) - feargalr/bacdive_harvester
github.com
August 19, 2025 at 2:33 AM
FYI finally tidied this up into something usable github.com/feargalr/bac...
Reposted by Geoff Zahn
Have you heard about MycoEd yet? A model educational program offering training for students on fungal genome sequencing and analysis. how powerful!! #mycofam #thefutureisfungal
journals.plos.org/plospathogen...
journals.plos.org/plospathogen...
Myco-Ed: Mycological curriculum for education and discovery
Fungi are important and hyperdiverse organisms, yet chronically understudied. Most fungal clades have no reference genomes, impeding our understanding of their ecosystem functions and use as solutions...
journals.plos.org
July 22, 2025 at 3:48 PM
Have you heard about MycoEd yet? A model educational program offering training for students on fungal genome sequencing and analysis. how powerful!! #mycofam #thefutureisfungal
journals.plos.org/plospathogen...
journals.plos.org/plospathogen...
Reposted by Geoff Zahn
The U.S. government has fueled decades of world-leading scientific and technical innovation by funding research efforts through grants programs & universities where researchers controlled decisions.
In the USSR, no decisions were made by scientists alone. Every decision required political approval.
In the USSR, no decisions were made by scientists alone. Every decision required political approval.
One more effort to politicize federal grantmaking.
*Grants must by approved by a political appointee, working with OMB.
*"Discretionary awards must, where applicable, demonstrably advance the President’s policy priorities."
*Cannot "promote anti-American values"
www.whitehouse.gov/presidential...
*Grants must by approved by a political appointee, working with OMB.
*"Discretionary awards must, where applicable, demonstrably advance the President’s policy priorities."
*Cannot "promote anti-American values"
www.whitehouse.gov/presidential...
Improving Oversight of Federal Grantmaking
By the authority vested in me as President by the Constitution and the laws of the United States of America, and to improve the process of Federal
www.whitehouse.gov
August 8, 2025 at 2:32 AM
The U.S. government has fueled decades of world-leading scientific and technical innovation by funding research efforts through grants programs & universities where researchers controlled decisions.
In the USSR, no decisions were made by scientists alone. Every decision required political approval.
In the USSR, no decisions were made by scientists alone. Every decision required political approval.
Reposted by Geoff Zahn
Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota
August 7, 2025 at 2:50 AM
Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota
Reposted by Geoff Zahn
A database of AM fungi of Australia. Incredible resource and publication. Congrats to all the authors.
onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
August 7, 2025 at 9:42 AM
A database of AM fungi of Australia. Incredible resource and publication. Congrats to all the authors.
onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com/doi/10.1111/...