Geof Hannigan, PhD
@living-bio.bsky.social
Biology. Computers. Research. Startups. Opinions my own.
Reposted by Geof Hannigan, PhD
🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...
Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st
academic.oup.com
December 3, 2025 at 2:34 AM
🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...
🚨 New blog post is live!
🦃 What better way is there to end a weekend (and for many of us, end the Thanksgiving holiday) than with a deep dive into circular RNA therapeutics?
livingbio.substack.com/p/circular-r...
🦃 What better way is there to end a weekend (and for many of us, end the Thanksgiving holiday) than with a deep dive into circular RNA therapeutics?
livingbio.substack.com/p/circular-r...
Circular RNA Therapeutics: Current Investment Landscape & Recent Developments
An overview of how circular RNA is being used to treat diseases, and what ventures are gaining traction
livingbio.substack.com
December 1, 2025 at 2:51 AM
🚨 New blog post is live!
🦃 What better way is there to end a weekend (and for many of us, end the Thanksgiving holiday) than with a deep dive into circular RNA therapeutics?
livingbio.substack.com/p/circular-r...
🦃 What better way is there to end a weekend (and for many of us, end the Thanksgiving holiday) than with a deep dive into circular RNA therapeutics?
livingbio.substack.com/p/circular-r...
🚨 Another new blog post is live!
🦠 Can the COVID-19 vaccine support cancer treatment? And what role could the microbiome be playing?
👀 Check it out, including a lot of good resources for additional, detailed reading!
livingbio.substack.com/p/can-the-co...
🦠 Can the COVID-19 vaccine support cancer treatment? And what role could the microbiome be playing?
👀 Check it out, including a lot of good resources for additional, detailed reading!
livingbio.substack.com/p/can-the-co...
Can the COVID-19 Vaccine Support Cancer Treatment?
And what role could the microbiome be playing?
livingbio.substack.com
October 29, 2025 at 1:44 AM
🚨 Another new blog post is live!
🦠 Can the COVID-19 vaccine support cancer treatment? And what role could the microbiome be playing?
👀 Check it out, including a lot of good resources for additional, detailed reading!
livingbio.substack.com/p/can-the-co...
🦠 Can the COVID-19 vaccine support cancer treatment? And what role could the microbiome be playing?
👀 Check it out, including a lot of good resources for additional, detailed reading!
livingbio.substack.com/p/can-the-co...
Reposted by Geof Hannigan, PhD
Big news: The Vicković Lab’s study on colon aging has been accepted by @natbiotech.nature.com! The team built a detailed atlas of aging colon tissue, using spatial transcriptomics + a new tool (cSplotch) to profile ~1,500 samples & 400k nuclei.
🔗 Read more: bit.ly/4hj3ry7
#SpatialTranscriptomics
🔗 Read more: bit.ly/4hj3ry7
#SpatialTranscriptomics
October 22, 2025 at 12:53 PM
Big news: The Vicković Lab’s study on colon aging has been accepted by @natbiotech.nature.com! The team built a detailed atlas of aging colon tissue, using spatial transcriptomics + a new tool (cSplotch) to profile ~1,500 samples & 400k nuclei.
🔗 Read more: bit.ly/4hj3ry7
#SpatialTranscriptomics
🔗 Read more: bit.ly/4hj3ry7
#SpatialTranscriptomics
November biotech networking is happening!
Be sure to mark your calendar to join the Twin Cities Biotech meetup group for another great evening.
October recap and November details/registration are available on our SubStack!
twincitiesbiotech.substack.com/p/new-month-...
Be sure to mark your calendar to join the Twin Cities Biotech meetup group for another great evening.
October recap and November details/registration are available on our SubStack!
twincitiesbiotech.substack.com/p/new-month-...
New Month, New Biotech Networking Event!
It's Happening In November!
twincitiesbiotech.substack.com
October 20, 2025 at 1:54 AM
November biotech networking is happening!
Be sure to mark your calendar to join the Twin Cities Biotech meetup group for another great evening.
October recap and November details/registration are available on our SubStack!
twincitiesbiotech.substack.com/p/new-month-...
Be sure to mark your calendar to join the Twin Cities Biotech meetup group for another great evening.
October recap and November details/registration are available on our SubStack!
twincitiesbiotech.substack.com/p/new-month-...
Reposted by Geof Hannigan, PhD
🔬 Microbiology job seekers 🧫 go to BMA Job Board to view open positions! Have a vacancy to fill? Posting instructions also available (scroll to bottom). blackinmicrobiology....
October 15, 2025 at 9:33 PM
🔬 Microbiology job seekers 🧫 go to BMA Job Board to view open positions! Have a vacancy to fill? Posting instructions also available (scroll to bottom). blackinmicrobiology....
October biotech is happening today in Minneapolis!
The autumn biotech season is in full swing, and now that Twin Cities Startup Week is behind us, it’s time for the Twin Cities Biotech meetup!
Checkout the link for details and registration!
twincitiesbiotech.substack.com/p/october-bi...
The autumn biotech season is in full swing, and now that Twin Cities Startup Week is behind us, it’s time for the Twin Cities Biotech meetup!
Checkout the link for details and registration!
twincitiesbiotech.substack.com/p/october-bi...
October Biotech is Happening Today!
The autumn biotech season is in full swing!
twincitiesbiotech.substack.com
October 14, 2025 at 1:00 PM
October biotech is happening today in Minneapolis!
The autumn biotech season is in full swing, and now that Twin Cities Startup Week is behind us, it’s time for the Twin Cities Biotech meetup!
Checkout the link for details and registration!
twincitiesbiotech.substack.com/p/october-bi...
The autumn biotech season is in full swing, and now that Twin Cities Startup Week is behind us, it’s time for the Twin Cities Biotech meetup!
Checkout the link for details and registration!
twincitiesbiotech.substack.com/p/october-bi...
Hi everyone! Please share/repost for reach!
I’m building a really cool startup bootcamp program, and I’m figuring out who might be interested!
Topics will include fundraising, pilots, regulatory, etc. All medical.
Let me know if I should add you to my "first to know" list for when it goes live.
I’m building a really cool startup bootcamp program, and I’m figuring out who might be interested!
Topics will include fundraising, pilots, regulatory, etc. All medical.
Let me know if I should add you to my "first to know" list for when it goes live.
October 4, 2025 at 9:02 PM
Hi everyone! Please share/repost for reach!
I’m building a really cool startup bootcamp program, and I’m figuring out who might be interested!
Topics will include fundraising, pilots, regulatory, etc. All medical.
Let me know if I should add you to my "first to know" list for when it goes live.
I’m building a really cool startup bootcamp program, and I’m figuring out who might be interested!
Topics will include fundraising, pilots, regulatory, etc. All medical.
Let me know if I should add you to my "first to know" list for when it goes live.
Reposted by Geof Hannigan, PhD
Stem-cell models provide evidence that viral DNA sequences that entered the human genome in the past were repurposed to aid early stages of embryonic development
go.nature.com/4nRJyA4
go.nature.com/4nRJyA4
Ancient viral DNA in the human genome shapes early development
Stem-cell models provide evidence that viral DNA sequences that entered the human genome in the past were repurposed to aid early stages of embryonic development.
go.nature.com
October 4, 2025 at 10:15 AM
Stem-cell models provide evidence that viral DNA sequences that entered the human genome in the past were repurposed to aid early stages of embryonic development
go.nature.com/4nRJyA4
go.nature.com/4nRJyA4
🚨 New blog post is live!
🤔 For this post, I reflected on recent publications asking the question: "What does it mean to write in the age of Large Language Models?"
👀 Check it out!
livingbio.substack.com/p/is-scienti...
🤔 For this post, I reflected on recent publications asking the question: "What does it mean to write in the age of Large Language Models?"
👀 Check it out!
livingbio.substack.com/p/is-scienti...
Is Scientific Writing a Journey or a Destination?
What does it mean to write in the age of Large Language Models?
livingbio.substack.com
October 3, 2025 at 12:41 PM
🚨 New blog post is live!
🤔 For this post, I reflected on recent publications asking the question: "What does it mean to write in the age of Large Language Models?"
👀 Check it out!
livingbio.substack.com/p/is-scienti...
🤔 For this post, I reflected on recent publications asking the question: "What does it mean to write in the age of Large Language Models?"
👀 Check it out!
livingbio.substack.com/p/is-scienti...
Reposted by Geof Hannigan, PhD
Nature research paper: Robot-assisted mapping of chemical reaction hyperspaces and networks
go.nature.com/3Iy42Pw
go.nature.com/3Iy42Pw
Robot-assisted mapping of chemical reaction hyperspaces and networks - Nature
A low-cost robotic platform using mainly optical detection to quantify yields of products and by-products allows the analysis of multidimensional chemical reaction hyperspaces and networks much faster than is possible by human chemists.
go.nature.com
October 1, 2025 at 10:22 AM
Nature research paper: Robot-assisted mapping of chemical reaction hyperspaces and networks
go.nature.com/3Iy42Pw
go.nature.com/3Iy42Pw
Reposted by Geof Hannigan, PhD
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/...
🚨 Great fellowship opportunity for grad students!
🎓 A lot of folks are aware of the NSF GRFP but a lot less are aware of the similar DoD NDSEG.
💡 This competitive fellowship covers stipend and travel. It's a seriously great resource that not enough students know about.
ndseg.sysplus.com
🎓 A lot of folks are aware of the NSF GRFP but a lot less are aware of the similar DoD NDSEG.
💡 This competitive fellowship covers stipend and travel. It's a seriously great resource that not enough students know about.
ndseg.sysplus.com
DoD NDSEG Fellowship Program - Home Page
ndseg.sysplus.com
September 16, 2025 at 12:46 AM
🚨 Great fellowship opportunity for grad students!
🎓 A lot of folks are aware of the NSF GRFP but a lot less are aware of the similar DoD NDSEG.
💡 This competitive fellowship covers stipend and travel. It's a seriously great resource that not enough students know about.
ndseg.sysplus.com
🎓 A lot of folks are aware of the NSF GRFP but a lot less are aware of the similar DoD NDSEG.
💡 This competitive fellowship covers stipend and travel. It's a seriously great resource that not enough students know about.
ndseg.sysplus.com
Host-specific microbiome and genomic signatures in Bifidobacteriumreveal co-evolutionary and functional adaptations across diverse animal hosts
www.cell.com/cell-host-mi...
www.cell.com/cell-host-mi...
Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts
Bifidobacterium are beneficial members of the microbiota across animal hosts. Kujawska
et al. demonstrate that bifidobacteria have likely co-evolved more closely with mammals,
particularly primates, a...
www.cell.com
September 12, 2025 at 1:13 PM
Host-specific microbiome and genomic signatures in Bifidobacteriumreveal co-evolutionary and functional adaptations across diverse animal hosts
www.cell.com/cell-host-mi...
www.cell.com/cell-host-mi...
We had a super fun September biotech meetup, and October is officially scheduled.
Here’s a link to the September recap and details for October:
twincitiesbiotech.substack.com/p/september-...
Here’s a link to the September recap and details for October:
twincitiesbiotech.substack.com/p/september-...
September Biotech Was Great! Now Get Ready For October!
We had the September biotech networking event this week at Pryes Brewing Company.
twincitiesbiotech.substack.com
September 12, 2025 at 1:05 PM
We had a super fun September biotech meetup, and October is officially scheduled.
Here’s a link to the September recap and details for October:
twincitiesbiotech.substack.com/p/september-...
Here’s a link to the September recap and details for October:
twincitiesbiotech.substack.com/p/september-...
🚨 New blog post is live!
🤔 In this one I reflect on using science and adaptability to build successful startups and innovation programs (including those in large companies)!
✨ I had a lot of fun writing this one!
👀 Be sure to check it out!
livingbio.substack.com/p/building-s...
🤔 In this one I reflect on using science and adaptability to build successful startups and innovation programs (including those in large companies)!
✨ I had a lot of fun writing this one!
👀 Be sure to check it out!
livingbio.substack.com/p/building-s...
Building Successful Startups With Science & Adaptability
A wide-ranging review of the Lean Startup framework
livingbio.substack.com
August 29, 2025 at 12:49 PM
🚨 New blog post is live!
🤔 In this one I reflect on using science and adaptability to build successful startups and innovation programs (including those in large companies)!
✨ I had a lot of fun writing this one!
👀 Be sure to check it out!
livingbio.substack.com/p/building-s...
🤔 In this one I reflect on using science and adaptability to build successful startups and innovation programs (including those in large companies)!
✨ I had a lot of fun writing this one!
👀 Be sure to check it out!
livingbio.substack.com/p/building-s...
To anyone in the Minneapolis Startup community, or anyone who wants to learn more about startups (especially students), there is a great meetup happening in September!
Details on the event page:
lu.ma/n40cxaem?tk=...
Details on the event page:
lu.ma/n40cxaem?tk=...
The Medical Alley Startup Meetup · Luma
Meet the Medical Alley Startup community at the next monthly meetup!
This is a casual event to meet cool people and talk about startups, research, medtech,…
lu.ma
August 19, 2025 at 12:28 PM
To anyone in the Minneapolis Startup community, or anyone who wants to learn more about startups (especially students), there is a great meetup happening in September!
Details on the event page:
lu.ma/n40cxaem?tk=...
Details on the event page:
lu.ma/n40cxaem?tk=...
We had an awesome time at the Twin Cities Biotech meetup yesterday evening, this time at Pryes Brewing!
Be sure to signup for our meetup SubStack, which is the best way to keep updated on upcoming meetups!
twincitiesbiotech.substack.com
Be sure to signup for our meetup SubStack, which is the best way to keep updated on upcoming meetups!
twincitiesbiotech.substack.com
August 13, 2025 at 7:50 PM
We had an awesome time at the Twin Cities Biotech meetup yesterday evening, this time at Pryes Brewing!
Be sure to signup for our meetup SubStack, which is the best way to keep updated on upcoming meetups!
twincitiesbiotech.substack.com
Be sure to signup for our meetup SubStack, which is the best way to keep updated on upcoming meetups!
twincitiesbiotech.substack.com
If anyone is looking for an awesome biotech networking event in Minnesota, be sure to checkout the Twin Cities biotech meetup!
We have our next event tomorrow! They are always a lot of fun!
twincitiesbiotech.substack.com/p/its-time-f...
We have our next event tomorrow! They are always a lot of fun!
twincitiesbiotech.substack.com/p/its-time-f...
It's Time For August Biotech!
It’s time for another great evening of summer biotech networking, this time at a great new location!
twincitiesbiotech.substack.com
August 12, 2025 at 1:22 AM
If anyone is looking for an awesome biotech networking event in Minnesota, be sure to checkout the Twin Cities biotech meetup!
We have our next event tomorrow! They are always a lot of fun!
twincitiesbiotech.substack.com/p/its-time-f...
We have our next event tomorrow! They are always a lot of fun!
twincitiesbiotech.substack.com/p/its-time-f...
A note to any founders who are eager to tell their story to a room full of investors, corporates, founders, an more!
Applications are open to present at our upcoming Medical Alley Innovation Showcase on September 22!
Applications close on August 14th!
forms.office.com/r/g5d4NAC3kT
Applications are open to present at our upcoming Medical Alley Innovation Showcase on September 22!
Applications close on August 14th!
forms.office.com/r/g5d4NAC3kT
Microsoft Forms
forms.office.com
August 11, 2025 at 7:36 PM
A note to any founders who are eager to tell their story to a room full of investors, corporates, founders, an more!
Applications are open to present at our upcoming Medical Alley Innovation Showcase on September 22!
Applications close on August 14th!
forms.office.com/r/g5d4NAC3kT
Applications are open to present at our upcoming Medical Alley Innovation Showcase on September 22!
Applications close on August 14th!
forms.office.com/r/g5d4NAC3kT
Reposted by Geof Hannigan, PhD
What happens to the colossal stash of C- and N-rich (but chemically inaccessible) chitin generated by the global insect population? Love this @plosbiology.org paper from Justin Nodwell & co which shows that #Streptomyces have the equipment to exploit it...
More than a billion tons of #chitin are produced on Earth each year. This study shows that the soil #bacterium #Streptomyces venezuelae thrives on chitin from #insect #exoskeletons, using a potent mix of chitinases and a dedicated chitobiose importer @plosbiology.org 🧪 plos.io/45sg4S5
August 7, 2025 at 8:28 AM
What happens to the colossal stash of C- and N-rich (but chemically inaccessible) chitin generated by the global insect population? Love this @plosbiology.org paper from Justin Nodwell & co which shows that #Streptomyces have the equipment to exploit it...
Reposted by Geof Hannigan, PhD
Jennifer Readshaw
nuclease now shown
BREX and beyond block phages
mystery cracking
#sciku 🧪🧬🔬🧫🦠 #Phages2025
doi.org/10.1093/nar/...
nuclease now shown
BREX and beyond block phages
mystery cracking
#sciku 🧪🧬🔬🧫🦠 #Phages2025
doi.org/10.1093/nar/...
PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB
Abstract. BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly d
doi.org
August 6, 2025 at 3:22 PM
Jennifer Readshaw
nuclease now shown
BREX and beyond block phages
mystery cracking
#sciku 🧪🧬🔬🧫🦠 #Phages2025
doi.org/10.1093/nar/...
nuclease now shown
BREX and beyond block phages
mystery cracking
#sciku 🧪🧬🔬🧫🦠 #Phages2025
doi.org/10.1093/nar/...
🚨 New blog post alert!
👀 Checkout my deep dive into AI for human-pathogen interaction modeling at the protein level! Based on a cool recent pub in @plos.org Comp Bio!
🧫 This was a lot of fun to write, as I continue along this theme of protein analytics!
livingbio.substack.com/p/fighting-p...
👀 Checkout my deep dive into AI for human-pathogen interaction modeling at the protein level! Based on a cool recent pub in @plos.org Comp Bio!
🧫 This was a lot of fun to write, as I continue along this theme of protein analytics!
livingbio.substack.com/p/fighting-p...
Fighting Pathogens With AI-Predicted Protein Structures
A Deep Dive Into Recently Published Research in PLOS Computational Biology
livingbio.substack.com
August 6, 2025 at 1:13 PM
🚨 New blog post alert!
👀 Checkout my deep dive into AI for human-pathogen interaction modeling at the protein level! Based on a cool recent pub in @plos.org Comp Bio!
🧫 This was a lot of fun to write, as I continue along this theme of protein analytics!
livingbio.substack.com/p/fighting-p...
👀 Checkout my deep dive into AI for human-pathogen interaction modeling at the protein level! Based on a cool recent pub in @plos.org Comp Bio!
🧫 This was a lot of fun to write, as I continue along this theme of protein analytics!
livingbio.substack.com/p/fighting-p...
Reposted by Geof Hannigan, PhD
Elucidating #plant #Biosynthetic pathways: @jjjvanderhooft.bsky.social @marnixmedema.bsky.social &co develop #MEANtools, an unsupervised computational workflow that integrates #MultiOmics data to predict #metabolic pathways by linking transcripts to metabolites @plosbiology.org 🧪 plos.io/4odL94g
July 31, 2025 at 8:49 AM
Elucidating #plant #Biosynthetic pathways: @jjjvanderhooft.bsky.social @marnixmedema.bsky.social &co develop #MEANtools, an unsupervised computational workflow that integrates #MultiOmics data to predict #metabolic pathways by linking transcripts to metabolites @plosbiology.org 🧪 plos.io/4odL94g
Reposted by Geof Hannigan, PhD
It was great fun writing this review with @gemccallum.bsky.social , even if our conclusions are rather scary. Lots of important pathogen evolution must be occurring outside of the infection context...
Delighted to have this review out with @jpjhall.bsky.social!
We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠
doi.org/10.1038/s442...
We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠
doi.org/10.1038/s442...
The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens
doi.org
July 31, 2025 at 3:22 PM
It was great fun writing this review with @gemccallum.bsky.social , even if our conclusions are rather scary. Lots of important pathogen evolution must be occurring outside of the infection context...