Alex Hübner
@alexhbnr.bsky.social
computational biologist working on reconstructing the past microbial diversity from ancient DNA samples; postdoc in the lab of Tina Warinner at MPI EVA, Leipzig.
Reposted by Alex Hübner
🚨 New release of #AncientMetagenomeDir! (v25.09.0, Site of Palmyra)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/4)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/4)
Release v25.09: Site of Palmyra · SPAAM-community/AncientMetagenomeDir
Release v25.09.0 includes 5 new publications, representing 33 new ancient host-associated metagenome samples, 40 new ancient microbial genomes, and 90 new ancient environmental samples. This brings...
github.com
October 17, 2025 at 12:20 PM
🚨 New release of #AncientMetagenomeDir! (v25.09.0, Site of Palmyra)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/4)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/4)
I'm very proud of being part of this team, @matejahajdi.bsky.social! Hopefully many more @eshesociety.bsky.social conferences will come!
Second time attending @eshesociety.bsky.social conference together ❤️💀 last year baby Ollie helped his mama to organise #ESHE2024 in Zageb 🇭🇷, this year celebrating being 5 months old at #ESHE2025 in Paris. 🇨🇵
Could not have made it without the support of @alexhbnr.bsky.social ❤️
Could not have made it without the support of @alexhbnr.bsky.social ❤️
September 26, 2025 at 7:40 PM
I'm very proud of being part of this team, @matejahajdi.bsky.social! Hopefully many more @eshesociety.bsky.social conferences will come!
Reposted by Alex Hübner
The @nytimes.com has rarely felt as hopelessly out of its depth as in the past two days or so. There is still much I admire, many journalists I respect and trust, but on the Charlie Kirk assassination it simply hasn’t been very informative - not to mention some atrocious opinion “journalism”.
September 13, 2025 at 9:35 AM
The @nytimes.com has rarely felt as hopelessly out of its depth as in the past two days or so. There is still much I admire, many journalists I respect and trust, but on the Charlie Kirk assassination it simply hasn’t been very informative - not to mention some atrocious opinion “journalism”.
Reposted by Alex Hübner
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Reposted by Alex Hübner
A study led by @zhofmanova.bsky.social @mpi-eva-leipzig.bsky.social used ancient DNA to investigate the spread of Slavic language and culture 1,500 years ago. “This wasn’t a migration of elites, or a few male warriors,” 1 co-author says. “This was the migration of an entire population.” @science.org
Ancient skeletons’ genes reveal origin of the Slavic people
DNA connects modern Slavs to a wave of migration following the fall of the Roman Empire
www.science.org
September 3, 2025 at 3:30 PM
A study led by @zhofmanova.bsky.social @mpi-eva-leipzig.bsky.social used ancient DNA to investigate the spread of Slavic language and culture 1,500 years ago. “This wasn’t a migration of elites, or a few male warriors,” 1 co-author says. “This was the migration of an entire population.” @science.org
Reposted by Alex Hübner
A huge thanks to all the amazing speakers and participants at #SPAAM7 yesterday 🧬🙌
The sessions were full of inspiring talks and great discussions!✨
The sessions were full of inspiring talks and great discussions!✨
August 27, 2025 at 3:45 PM
A huge thanks to all the amazing speakers and participants at #SPAAM7 yesterday 🧬🙌
The sessions were full of inspiring talks and great discussions!✨
The sessions were full of inspiring talks and great discussions!✨
Reposted by Alex Hübner
I am so thrilled for this opportunity and to talk about #ancient #pathogenomics!! There is still time to register for #SPAAM7, happening this 26th of August in Turin!! (also online!): join us for a day of #ancient #metagenomics with the welcoming community of @spaam-community.bsky.social
We are thrilled to announce our keynote speaker for #SPAAM7 – Aida Andrades Valtueña!🎉
@aidanva.bsky.social
@aidanva.bsky.social
July 30, 2025 at 9:09 AM
I am so thrilled for this opportunity and to talk about #ancient #pathogenomics!! There is still time to register for #SPAAM7, happening this 26th of August in Turin!! (also online!): join us for a day of #ancient #metagenomics with the welcoming community of @spaam-community.bsky.social
Reposted by Alex Hübner
find me this weekend at the #LymeRegisFossilFestival Hub point for some chill #SciArt dinosaur coloring/doodling!
June 11, 2025 at 9:19 AM
find me this weekend at the #LymeRegisFossilFestival Hub point for some chill #SciArt dinosaur coloring/doodling!
Reposted by Alex Hübner
We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2
Researchers have been trying for a long time to nail down where in nature mpox lurks.
Now they appear to have caught the virus that causes mpox in the act of spilling over from squirrels to monkeys.
“It is the best clue so far for what the reservoir might be”, says @kgandersen.bsky.social
#IDsky 🧪
Now they appear to have caught the virus that causes mpox in the act of spilling over from squirrels to monkeys.
“It is the best clue so far for what the reservoir might be”, says @kgandersen.bsky.social
#IDsky 🧪
How do mpox outbreaks start? Dead baby monkey provides important clue
“Landmark” study fingers fire-footed rope squirrel as a reservoir of fatal disease
www.science.org
April 9, 2025 at 6:24 AM
We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2
The next release is out!
🚨 New release of #AncientMetagenomeDir! (v25.03.0, Historic Centre of Cordoba)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/5)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/5)
Release v25.03: Historic Centre of Cordoba · SPAAM-community/AncientMetagenomeDir
Release v25.03.0 includes 8 new publications, representing 132 new ancient host-associated metagenome samples, 33 new ancient microbial genomes, and 0 new ancient environmental samples. This brings...
github.com
April 9, 2025 at 6:33 AM
The next release is out!
Reposted by Alex Hübner
I'm beyond excited to share our new paper in Nature! We sequenced the first ancient human autosomal genomes from the Central Sahara, two ~7,000-year-old individuals from Takarkori in Libya, revealing a long-isolated North African lineage: www.nature.com/articles/s41...
Here's a short thread: (1/n)
Here's a short thread: (1/n)
Ancient DNA from the Green Sahara reveals ancestral North African lineage - Nature
Pastoralism spread through cultural diffusion into the Green Sahara, where an isolated, distinct North African ancestry persisted.
www.nature.com
April 2, 2025 at 4:37 PM
I'm beyond excited to share our new paper in Nature! We sequenced the first ancient human autosomal genomes from the Central Sahara, two ~7,000-year-old individuals from Takarkori in Libya, revealing a long-isolated North African lineage: www.nature.com/articles/s41...
Here's a short thread: (1/n)
Here's a short thread: (1/n)
Reposted by Alex Hübner
Just over 2 weeks left to apply for this 3-y position. It qualifies for the full UK visa sponsorship. Come work with us on a truly exciting project, with visits to different #museums #aDNA #popgen
3-y postdoc position in (meta)Genomics of Population Declines elxw.fa.em3.oraclecloud.com/hcmUI/Candid.... If you have experience with low-coverage genomic data, care about biodiversity loss, want to understand host-microbiomes interactions, this post is for you! #museomics #ancientDNA #mammals
March 10, 2025 at 6:24 PM
Reposted by Alex Hübner
Reposted by Alex Hübner
Last week’s AncientMetagenomeDir hackathon was a great success 🚀. More than 20 participants added new studies, updated the documentation, fixed bugfixes, and added the first 14C dates to the study 💪!
February 14, 2025 at 3:41 PM
Last week’s AncientMetagenomeDir hackathon was a great success 🚀. More than 20 participants added new studies, updated the documentation, fixed bugfixes, and added the first 14C dates to the study 💪!
Reposted by Alex Hübner
The Tai Chimpanzee Project is making available microCT scans from their collections on human-fossil-record.org. All proceeds are used to support their mission of conservation and non-invasive research in Tai National Park (taichimpproject.org).
The Human Fossil Record: A Digital Resource for Research and Education
The Human Fossil Record: A Digital Resource for Research and Education
human-fossil-record.org
February 13, 2025 at 7:50 AM
The Tai Chimpanzee Project is making available microCT scans from their collections on human-fossil-record.org. All proceeds are used to support their mission of conservation and non-invasive research in Tai National Park (taichimpproject.org).
Reposted by Alex Hübner
New paper out! 📄
My first adventures in (ancient) metagenomics. 🦠
“Exploring DNA degradation in situ and in museum storage through genomics and metagenomics” www.nature.com/articles/s42...
Curious about the water color painting (see ALT text)? 🦌
Thread (Bluetorial?) with findings!
🧶👇 (1/n)
My first adventures in (ancient) metagenomics. 🦠
“Exploring DNA degradation in situ and in museum storage through genomics and metagenomics” www.nature.com/articles/s42...
Curious about the water color painting (see ALT text)? 🦌
Thread (Bluetorial?) with findings!
🧶👇 (1/n)
February 12, 2025 at 1:05 PM
New paper out! 📄
My first adventures in (ancient) metagenomics. 🦠
“Exploring DNA degradation in situ and in museum storage through genomics and metagenomics” www.nature.com/articles/s42...
Curious about the water color painting (see ALT text)? 🦌
Thread (Bluetorial?) with findings!
🧶👇 (1/n)
My first adventures in (ancient) metagenomics. 🦠
“Exploring DNA degradation in situ and in museum storage through genomics and metagenomics” www.nature.com/articles/s42...
Curious about the water color painting (see ALT text)? 🦌
Thread (Bluetorial?) with findings!
🧶👇 (1/n)
Reposted by Alex Hübner
Many zoonotic diseases are believed to have emerged during prehistory, but can we actually identify their past host range using ancient DNA? In the first publication of the Key Lab we present a 4000y old Yersinia pestis genome reconstructed from domesticated sheep. 🧵 www.biorxiv.org/content/10.1...
Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage
Most human pathogens are of zoonotic origin. Many emerged during prehistory, coinciding with domestication providing more opportunities for spillover from original host species. However, we lack direc...
www.biorxiv.org
February 10, 2025 at 5:10 PM
Many zoonotic diseases are believed to have emerged during prehistory, but can we actually identify their past host range using ancient DNA? In the first publication of the Key Lab we present a 4000y old Yersinia pestis genome reconstructed from domesticated sheep. 🧵 www.biorxiv.org/content/10.1...
Reposted by Alex Hübner
Edmond Albius was just a 12-year-old boy, enslaved and without formal education, in 1841. He managed to develop an innovative technique to pollinate vanilla orchids quickly and profitably, solving an enigma that intrigued prominent botanists of the time. (The rest in comments)
February 2, 2025 at 9:59 PM
Edmond Albius was just a 12-year-old boy, enslaved and without formal education, in 1841. He managed to develop an innovative technique to pollinate vanilla orchids quickly and profitably, solving an enigma that intrigued prominent botanists of the time. (The rest in comments)
Reposted by Alex Hübner
If you like hearing about #aDNA of animals by Early Career Researchers - join us at AaRC for our seminar series, on the last Friday of every month!
January 29, 2025 at 5:52 PM
If you like hearing about #aDNA of animals by Early Career Researchers - join us at AaRC for our seminar series, on the last Friday of every month!
Please join us for our AncientMetagenomeDir hackathon!
Only a few days are left to register to this year's AncientMetagenomeDir hackathon: docs.google.com/forms/d/e/1F... If you would like to contribute to a brilliant ancient DNA project and work together with like-minded people, don't hesitate to sign up. Everyone is welcome, from novice to veteran.
January 24, 2025 at 4:22 PM
Please join us for our AncientMetagenomeDir hackathon!
Reposted by Alex Hübner
We're searching for a database and lab manager to work at U Notre Dame on the Amboseli Baboons! Please circulate and apply! 🐵 🖥️ 🐵 🖥️ docs.google.com/document/d/1...
@jennytung.bsky.social @jbsilk.bsky.social @amboselibaboonrp.bsky.social @matthewzipple.bsky.social @awfuldodger.bsky.social
@jennytung.bsky.social @jbsilk.bsky.social @amboselibaboonrp.bsky.social @matthewzipple.bsky.social @awfuldodger.bsky.social
January 20, 2025 at 8:30 AM
We're searching for a database and lab manager to work at U Notre Dame on the Amboseli Baboons! Please circulate and apply! 🐵 🖥️ 🐵 🖥️ docs.google.com/document/d/1...
@jennytung.bsky.social @jbsilk.bsky.social @amboselibaboonrp.bsky.social @matthewzipple.bsky.social @awfuldodger.bsky.social
@jennytung.bsky.social @jbsilk.bsky.social @amboselibaboonrp.bsky.social @matthewzipple.bsky.social @awfuldodger.bsky.social
Reposted by Alex Hübner
We are back! 🧬 Do you want to help to make easier to find the data of #AncientMetagenomics samples? On the 7th of February 2025 we will have our next AncientMetagenomeDir hackathon (www.spaam-community.org/events/news/...) 🧵 [1/4]
AncientMetagenomeDir - hackathon (Feb 2025) · SPAAM Community
www.spaam-community.org
January 15, 2025 at 11:41 AM
We are back! 🧬 Do you want to help to make easier to find the data of #AncientMetagenomics samples? On the 7th of February 2025 we will have our next AncientMetagenomeDir hackathon (www.spaam-community.org/events/news/...) 🧵 [1/4]
Reposted by Alex Hübner
In Top10 @ScienceMagazine 2024 breakthroughs of the year: Reconstructing ancient pedigrees + IBD segment sharing in aDNA. 😮😊 🎉
Great write-up by @spoke32.bsky.social ! 👏👏
Great write-up by @spoke32.bsky.social ! 👏👏
December 30, 2024 at 3:59 PM
In Top10 @ScienceMagazine 2024 breakthroughs of the year: Reconstructing ancient pedigrees + IBD segment sharing in aDNA. 😮😊 🎉
Great write-up by @spoke32.bsky.social ! 👏👏
Great write-up by @spoke32.bsky.social ! 👏👏
Reposted by Alex Hübner
Publishing software is often easier than maintaining it - but we’re committed to keeping ours up to date! 🛠️ We've enhanced the documentation for our mtDNA variant calling pipeline, with detailed guides for both graphical and command-line use with Nextflow:
mitoverse.readthedocs.io/mtdna-server...
mitoverse.readthedocs.io/mtdna-server...
mtDNA-Server 2 - Mitoverse
mitoverse.readthedocs.io
December 28, 2024 at 4:59 PM
Publishing software is often easier than maintaining it - but we’re committed to keeping ours up to date! 🛠️ We've enhanced the documentation for our mtDNA variant calling pipeline, with detailed guides for both graphical and command-line use with Nextflow:
mitoverse.readthedocs.io/mtdna-server...
mitoverse.readthedocs.io/mtdna-server...
Reposted by Alex Hübner
📢 Interested in micro and nanoplastic research? New exciting post doc opportunity at NHM Denmark working with me and Elvis Genbo Xu reconstructing past plastic levels using historical samples. Deadline for applications 17th Jan!
jobportal.ku.dk/videnskabeli...
jobportal.ku.dk/videnskabeli...
Postdoctoral researcher on ‘Unveiling the Ocean’s plastic time capsule"
jobportal.ku.dk
December 23, 2024 at 10:33 PM
📢 Interested in micro and nanoplastic research? New exciting post doc opportunity at NHM Denmark working with me and Elvis Genbo Xu reconstructing past plastic levels using historical samples. Deadline for applications 17th Jan!
jobportal.ku.dk/videnskabeli...
jobportal.ku.dk/videnskabeli...