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Reposted by Richard Neher

Meredith Whittaker @meredithmeredith.bsky.social · 4d

📣 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.

Signal @signal.org · 6d

We are alarmed by reports that Germany is on the verge of a catastrophic about-face, reversing its longstanding and principled opposition to the EU’s Chat Control proposal which, if passed, could spell the end of the right to privacy in Europe. signal.org/blog/pdfs/ge...

signal.org

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Reposted by Richard Neher

Biozentrum, University of Basel @biozentrum.unibas.ch · 10d

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

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Reposted by Richard Neher

Richard Sever @richardsever.bsky.social · 15d

HHMI adopts Plan U journals.plos.org/plosbiology/...

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Reposted by Richard Neher

Erik van Nimwegen @erikvannimwegen.bsky.social · 22d

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...

RealTrace: Uncovering biological dynamics hidden under measurement noise in time-lapse microscopy data

One of the most powerful approaches for identifying the mechanisms underlying complex biological phenomena is not just to measure bulk populations, or even take single-cell snapshots, but to directly ...

www.biorxiv.org

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Reposted by Richard Neher

Pathoplexus @pathoplexus.org · Sep 10

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...

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The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host

Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

virological.org

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Reposted by Richard Neher

Zamin Iqbal @zaminiqbal.bsky.social · Sep 10

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...

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

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Reposted by Richard Neher

Biozentrum, University of Basel @biozentrum.unibas.ch · Sep 8

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.

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Reposted by Richard Neher

Kai Kupferschmidt @kakape.bsky.social · Sep 5

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...

The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host

Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

virological.org

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Richard Neher @neher.io · Sep 5

Congratulations!!

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Reposted by Richard Neher

David Brückner @davidbrueckner.bsky.social · Sep 4

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!

Biozentrum, University of Basel @biozentrum.unibas.ch · Sep 4

Why do some cells become neurons and others muscle?
Physicist Prof. David Brückner @davidbrueckner.bsky.social @biozentrum.unibas.ch @unibas.ch receives a prestigious #ERCStartingGrant to uncover how cells make life-shaping decisions. @erc.europa.eu
www.biozentrum.unibas.ch/news/detail/...

ERC Starting Grant for Physicist David Brückner

How do cells decide which role to take on in the body? Prof. David Brückner from the Biozentrum of the University of Basel is investigating this and similar questions. Over the next five years, a Star...

www.biozentrum.unibas.ch

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Reposted by Richard Neher

Pathoplexus @pathoplexus.org · Aug 27

🗓 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...

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David Brückner @davidbrueckner.bsky.social · Aug 25

🤔 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...

The actin cortex acts as a mechanical memory of morphology in confined migrating cells - Nature Physics

Cells often navigate through confined spaces. Now it is shown that cells retain a mechanical memory of previous confinement events, which makes them more efficient at migrating through narrow microenv...

www.nature.com

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Richard Neher @neher.io · Aug 23

"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.

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Richard Neher @neher.io · Aug 23

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.

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docs.pangraph.org

Introduction to Pangraph | Pangraph docs

Pangraph is currently under heavy development. Bugs and crashes are to be expected.

docs.pangraph.org

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Richard Neher @neher.io · Aug 23

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.

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Richard Neher @neher.io · Aug 23

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.

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Population structure increases background levels of SNP linkage.

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Richard Neher @neher.io · Aug 23

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.

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Richard Neher @neher.io · Aug 23

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).

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construction of pangenomes graphs of phage genomes

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Richard Neher @neher.io · Aug 23

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.

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www.biorxiv.org/content/10.1...

The Actinobacteriophage Database | Home

phagesdb.org

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Reposted by Richard Neher

Erik van Nimwegen @erikvannimwegen.bsky.social · May 9

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...

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data

Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

www.biorxiv.org

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Reposted by Richard Neher

Ryan Hisner @ryanhisner.bsky.social · Apr 10

A fascinating SARS-CoV-2 sequence was recently uploaded—collected from a dog in Kazakhstan in July 2022.

Usher puts the sequence one nuc mutation from the Wuhan reference (C21846T, S:T95I)—i.e. pre-D614G. Could this sequence somehow have a close connection to the first days of the pandemic?
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Richard Neher @neher.io · Apr 5

The Guardian with a clear take:

www.theguardian.com/commentisfre...

The Guardian view on Donald Trump’s tariff ultimatum: tribute for access to America’s empire | Editorial

Editorial: As the White House retools US imperialism with import duties, others must resist dependency – deepening regional ties and reducing exposure to chokepoints

www.theguardian.com

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Reposted by Richard Neher

Mor Naaman @informor.bsky.social · Apr 5

I have never seen anything like this in NYC. 5th Ave covered from 42nd St well to the 20s. Nobody prepared for this volume. Volunteers are holding the traffic on all the side streets. No police in sight. #handsoff

Full of people down 5th avenue, view from 39th Street.

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Anderson F. Brito @andersonfbrito.bsky.social · Apr 4

🧬 Pathoplexus at GA4GH April Connect

At the @broadinstitute.org, experts gathered to discuss the future of genomic data sharing. Alongside Anna Parker (ETH Zurich) & @theo.io (LSHTM), we introduced Pathoplexus.org and Loculus to members of @ga4gh.org. 1/4

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Reposted by Richard Neher

Carl T. Bergstrom @carlbergstrom.com · Apr 1

Mr. Trump, this statute at the National Museum of African American History and Culture does not "undermine the remarkable achievements of the United States".

It does not "fosters a sense of national shame."

It does not "advance a corrosive ideology."

It is literally what might redeem the USA.

Statue of Tommie Smith and Juan Carlos on the podium at the 1968 Olympic Games, gloved fists raise in silent protest.

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