🚨 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)

I'm very proud of being part of this team, @matejahajdi.bsky.social! Hopefully many more @eshesociety.bsky.social conferences will come!

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”.

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...

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

A huge thanks to all the amazing speakers and participants at #SPAAM7 yesterday 🧬🙌 The sessions were full of inspiring talks and great discussions!✨

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

find me this weekend at the #LymeRegisFossilFestival Hub point for some chill #SciArt dinosaur coloring/doodling!

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!

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)

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

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 💪!

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).

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)

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...

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)

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!

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

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]

In Top10 @ScienceMagazine 2024 breakthroughs of the year: Reconstructing ancient pedigrees + IBD segment sharing in aDNA. 😮😊 🎉 Great write-up by @spoke32.bsky.social ! 👏👏

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...

📢 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...

Many people talk about the "Golden Age of Antibiotics", but I hadn't seen it visualized properly. Just how many types of antibiotics were discovered during that time? So, I visualized it myself!

🧪🎅 12 Days of Tools for Science Management 🦠🎄 Day five: Pomodoro tracking Writing doesn't come naturally to me so I need every trick I can find. Pizza slicing* (i.e. breaking down tasks into small chunks) is one way I can convince myself to get words to paper.

I am very happy to share our new paper on the genetics of some of the first modern humans who ever lived in Europe! We sequenced nuclear DNA from 13 specimens from Ranis in Germany, and found that they belonged to at least 6 individuals. www.nature.com/articles/s41... (1/n)

Out today in @sciencemagazine, we've journeyed into our shared history with Neandertals by analyzing over 300 present-day and ancient modern humans, including 59 individuals who lived between 2,000 and 45,000 years ago. www.science.org/doi/10.1126/...

Are you working on natural products? We’ve just released version 4.0 of the MIBiG data standard and repository! It now includes 3059 biosynthetic gene clusters, thanks to the combined efforts of 288 expert contributors. A thread: (1/8) academic.oup.com/nar/advance-...

Let’s celebrate the Bluesky exodus with an exciting software update. 📢 slendr popgen simulation #rstats package has reached version 1.0! This magic number signifies that slendr can now do most of what I had hoped it would do. TL;DR for those familiar with slendr: you can now simulate selection! 💣

Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla. doi.org/10.1101/2024... @wwood @rhysnewell @CMR_QUT 🧵1/6

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience

I'm excited to announce that {legendry} has hit the shelves over at CRAN! Get yours while they're still fresh! Good reasons to roll out my second blog post: teunbrand.github.io/teunbrand_bl... #rstats #ggplot2

The wonderful @spaam-community.bsky.social is now on Bluesky! 🦠💀🦷🧬 #aDNA #metagenomics

🦠🧬💻 Bakta v1.10 - largest update so far: Highlights: - user-provided HMMs: --hmms - output file recovery from JSON files: bakta_io - export of inference metrics: inference.tsv - bypass overlap filters: --skip-filter - improved genome plots github.com/oschwengers/... 👇 (1/11)

So happy to announce that we're now accepting abstracts for the 11th international symposium on biomolecular archaeology! www.isba11.com

Camille Marchet comparing genome collections with Wikipedia, YouTube and the Internet #GenomeInformatics24

Two new chapters from my free online book in human genetics out this weekend! These complete Part 3 of the book, on human population structure and history: 3.3: Human prehistory [separate thread] 3.4: Ancient DNA: a genetic time capsule [this thread] web.stanford.edu/group/pritch...

Wusstet ihr, dass kroatische Extremisten und jugoslawischer Geheimdienst ihre Konflikte in den 70er Jahren auch in Deutschland ausgetragen haben - mit mehreren Dutzend Toten und regelmäßigen Terroranschlägen? Nein? Dann solltet ihr diesen Podcast hören: www.hr-inforadio.de/podcast/krie...

Always wondered how the immune system knows whom to fight? #PhD position in our lab to study evolutionary genetics of adaptive immunity in humans and/or fish. We use comput. and mol. approaches. Topic open, to be matched with student's interest/skills. #MHC #TCR www.uni-hamburg.de/en/stellenan...

From @ksamuk.bsky.social 's thread: You can restore the old explicit missingness using bcftools: bcftools +setGT your.vcf.gz -- -t q -n . -e 'FMT/DP>=1'

What a nice occasion for my augural post here: I have been recently selected as one of the recipients of the Microverse Early Career Scientist Award: www.microverse-cluster.de/en/news/earl... This nicely honours our work done at the groups of @christinawarinner.bsky.social and Pierre Stallforth!

Last week I gave a talk at the Microbiome Virtual International Forum (@microbiomevif.bsky.social): 'Understanding the Biodiversity of an Ecosystem Under Stress: Tales from Inflammatory Bowel Diseases'. It's now on YouTube if you'd like to hear my annoying voice.