Something very different and cool for my lab. Sequencing a 4.4mb TB genome using the Artic-style PCR amplicon method with >5128 primers in two reactions 🤯
Enables culture-free WGS for TB!
journals.asm.org/doi/10.1128/...
#NieWieder
#WehretDenAnfängen
#GegenDasVergessen
#WeRemember
We mourn the passing of Peer Bork, EMBO Member since 2000: https://www.embl.org/news/embl-announcements/in-remembrance-of-peer-bork/
“[P]utting data into GISAID is like dropping it in a mail slot in an unmarked building,” says @colincarlson.bsky.social. “It’s wonderful that there’s so much cool stuff in that building. It would be great if we knew who owned it, or who paid for it, or what they plan to do with it.”
#IDsky 🧪
Boris Shraiman points a physicist’s eye on biological quandaries news.ucsb.edu/2025/022264/... 🧪
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.
Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.
A thread 1/8
Congratulations! Can't think of a better choice! 🎉
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
Job alert🚨📢! Join us as Director of the SIB Centre for Pathogen Bioinformatics, on a topic where global collaboration is particularly important, in a highly stimulating environment. This is a research infrastructure leadership position.
Apply or spread the word!
apply.refline.ch/499599/0346/...
Apply for our Master of Science in Physics of Life – training in cutting-edge research at the interface of physics, mathematics, engineering and life sciences. Scholarships available. Application deadline: 30 November. More: www.biozentrum.unibas.ch/education/de...
@biozentrum.unibas.ch @unibas.ch
📣 Germany's close to reversing its opposition to mass surveillance & private message scanning, & backing the Chat Control bill. This could end private comms-& Signal-in the EU.
Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.
Assistant/Associate Professor in Structural Biology, Biophysics or Biological Imaging
www.biozentrum.unibas.ch/open-positio...
#biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging
HHMI adopts Plan U journals.plos.org/plosbiology/...
What novel biological dynamics might be hiding under the measurement noise of your time-lapse fluorescence microscopy data?
Try our new RealTrace tool to find out!
Fantastic work by Bjoern Kscheschinski and others.
Tweetorial follows. 1/n
www.biorxiv.org/content/10.1...
Amid the concerning news of a new Ebola Zaire outbreak in DRC, teams on the ground have already managed to sample, sequence, and share data. This rapid turnaround is a testament to their commitment and capacity to respond.
Read more: virological.org/t/the-16th-e...
1/7
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...
Join us for an exciting #BiozentrumDiscovery lecture!
Prof. Tami Lieberman from @mit.edu will speak about the dynamic selective landscape of human microbiomes. Her lab studies microbial evolution in real time, with a focus on mutations occurring within individual human microbiomes.
Sequence data from the new Ebola outbreak in DRC suggests it is indeed a new spillover.
And just incredible to see the virus sequenced and the data publicly shared less than 24 hours after confirmation of the outbreak.
#IDsky 🧪
virological.org/t/the-16th-e...
Congratulations!!
Super excited that our group will be supported by an ERC Starting Grant!
In project "InfoFate" we will study how cells use information in dynamical, neighborhood & mechanical signals to make decisions.
We'll have PhD and Postdoc positions available, please get in touch if interested!
An image of a birthday cake with scientific doodles around it, 9 colourful candles, and the Pathoplexus logo in the middle, with the words 'Happy 1 year'
🗓 Pathoplexus turns ONE! 🎂🎉
In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...
1/10
🤔 Can migrating cells 'remember' their past trajectories?
In collab w/ @sgabriele.bsky.social & @kyohalie.bsky.social, we address this question:
Confined cells undergo geometry-sensitive morphology switches, and these switches depend on the past migration history!
www.nature.com/articles/s41...
"little linkage within subgroups" means that mutations occur pretty independently of each other on different genetic backgrounds within the group. But mutations differentiating the larger subgroups tend to co-occur irrespective of their separation along the chromosome.
Analyzing these data as pangenome graphs was very helpful to disentangle contributions of homologous recombination and accessory genome evolution at different scales. I hope this will continue to help us to shed light on the dynamic world of bacteria and phages.
[6/6]
docs.pangraph.org
This wide-spread homologous recombination seems to happen despite often substantial divergence >5% between genomes. But sometimes populations seem to fragment into groups with much less exchange – whether this is driven by geographic separation, ecological factors, or divergence is unclear.
[5/6]
Linkage decay in phage core genomes.
Population structure increases background levels of SNP linkage.
Within the syntenic core genome, linkage between SNPs decays rapidly with distance. LD approaches background levels after about 1000 bases. The background level itself is often set by population structure with little linkage within subgroups but genome wide coupling across subgroups.
[4/6]
Using these cluster-wide pangenome graphs, we find a strongly conserved synteny of core phams. Accessory genome diversity is typically concentrated in well defined hotspots.
[3/6]
construction of pangenomes graphs of phage genomes
Phages are known to recombine with each other and have flexible and fluid genomes. We analyzed diversity within the clusters of the Acinetobacteriophage Database by organizing their genomes into pangenome graphs based on homologous phams (protein families).
[2/6]
It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
