Sign in

Richard Neher

@neher.io
699 followers 272 following 37 posts
PostsRepliesMedia
Richard Neher @neher.io · 18/09/2026
The preprint is here: www.biorxiv.org/content/10.6...
biorxiv.org
Epistasis and the changing fitness landscapes of SARS-CoV-2
Since its emergence in late 2019, millions of SARS-CoV-2 genomes have been generated as part of global efforts to monitor the evolution and spread of the virus. This unprecedented volume of data provi...
061
Reposted by Richard Neher
Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
110545
Richard Neher @neher.io · 17/06/2026
Sorry to hear that. Preprint screening is a thankless task that unfortunately can misfire, but this sounds ridiculous. Not sure where you submitted, but you could try the q-bio.PE section on arxiv.org
arxiv.org
arXiv.org e-Print archive
271
Reposted by Richard Neher
Ian Dunt @iandunt.bsky.social · 04/06/2026
This was a groundbreaking piece of work. A work so good it means a life well spent. Millions of people understand Iran, the diaspora and the weird bittersweet details of the immigrant experience through the work she did.
17781156
Reposted by Richard Neher
Nick Loman @pathogenomenick.bsky.social · 18/05/2026
Rapid genomic data release and analysis from DRC and Uganda public health teams on Bundibugyo Ebola outbreak confirms new spillover: virological.org/t/initial-ge... - sequences shared via @pathoplexus.org
virological.org
Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda
Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda, reveal a new spillover event Context On 15 May 2026, the Ministry of Public Health, ...
1199
Reposted by Richard Neher
Federico Gueli @siamosolocani.bsky.social · 16/05/2026
Not enough space to this great SC2 Variant report by @corneliusroemer.bsky.social for @neher.io lab: github.com/neherlab/SAR... I agree very much with everything and i suggest to read the section on the next best Vaccine candidate :
github.com
0116
Richard Neher @neher.io · 01/05/2026
Congratulations!!!
020
Reposted by Richard Neher
Helen Branswell 🇨🇦 @helenbranswell.bsky.social · 25/04/2026
The world of influenza science has lost one of its giants. Nancy Cox, who led #CDC's flu division for years & worked assiduously to improve global flu surveillance, died Thursday. I learned a ton from Nancy Cox. RIP. www.statnews.com/2026/04/25/n...
statnews.com
Nancy Cox, a CDC veteran and a stalwart in global flu research, dies at 77
Nancy Cox, a CDC veteran who for decades was a global leader in influenza research, has died at 77.
012732
Richard Neher @neher.io · 12/04/2026
Thank you, Hungary!
041
Reposted by Richard Neher
Jon Cooper @joncooper-us.bsky.social · 11/04/2026
Tonight in Budapest’s Heroes’ Square, a sea of young Hungarians—who’ve only ever known Orbán’s corrupt, suffocating regime—are packed together, singing, chanting, and daring to dream of freedom again. Their hope is raw, their courage is real. The heart of Europe is beating in Budapest tonight. 🇭🇺❤️🇪🇺
538188165086
Reposted by Richard Neher
Benjamin Towbin @betowbin.bsky.social · 08/04/2026
Join us at the LS2 #Theory #across #Biology chalk talk symposium! 12 June 2026 in Bern, CH. @lifesciswitzerland.bsky.social No movies that fail, no Mac to PC issues. Only the best ideas and exchange across biology from evolution and ecology to physics of life. meetings.ls2.ch/theory-acros...
14317
Reposted by Richard Neher
Reza H. Akbari @rezahakbari.bsky.social · 06/04/2026
American and Israeli missiles hit Sharif University in Tehran tonight. Often called #Iran’s MIT, the institution has been home to some of the country’s best and brightest minds in science, technology, engineering, and mathematics since 1966. 1/2
12431252
Richard Neher @neher.io · 19/03/2026
It'll hopefully be a while before we get there. But then I imagine we do the same as pango did for SC2 and use double letters.
120
Reposted by Richard Neher
Nathan Grubaugh @nathangrubaugh.bsky.social · 16/02/2026
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/...
24816
Richard Neher @neher.io · 27/01/2026
#NieWieder #WehretDenAnfängen #GegenDasVergessen #WeRemember
020
Reposted by Richard Neher
EMBO @embo.org · 17/01/2026
We mourn the passing of Peer Bork, EMBO Member since 2000: www.embl.org/news/embl-announcement…
embl.org
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General. 
58636
Reposted by Richard Neher
Kai Kupferschmidt @kakape.bsky.social · 07/01/2026
“[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 🧪
science.org
Fresh conflicts erupt around giant database for flu and COVID-19 sequences
Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic
45421
Reposted by Richard Neher
Kavli Institute for Theoretical Physics @kitp-ucsb.bsky.social · 25/11/2025
Boris Shraiman points a physicist’s eye on biological quandaries news.ucsb.edu/2025/022264/... 🧪
news.ucsb.edu
Boris Shraiman points a physicist’s eye on biological quandaries
Boris Shraiman is awarded the American Physical Society’s Max Delbrück Prize in Biological Physics.
02718
Reposted by Richard Neher
Alexander Harms @aharms485.bsky.social · 20/11/2025
🚨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
1121290
Richard Neher @neher.io · 14/11/2025
Congratulations! Can't think of a better choice! 🎉
110
Reposted by Richard Neher
Nextstrain @nextstrain.org · 06/11/2025
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
413079
Reposted by Richard Neher
Christophe Dessimoz @dessimoz.bsky.social · 23/10/2025
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.refline.ch
Director, Center for Pathogen Bioinformatics
The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...
0716
Reposted by Richard Neher
Biozentrum, University of Basel @biozentrum.unibas.ch · 17/10/2025
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
0109
Reposted by Richard Neher
Meredith Whittaker @meredithmeredith.bsky.social · 06/10/2025
📣 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.
3022381606
Reposted by Richard Neher
Biozentrum, University of Basel @biozentrum.unibas.ch · 29/09/2025
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
04852
Reposted by Richard Neher
Richard Sever @richardsever.bsky.social · 24/09/2025
HHMI adopts Plan U journals.plos.org/plosbiology/...
914969
Reposted by Richard Neher
Erik van Nimwegen @erikvannimwegen.bsky.social · 17/09/2025
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...
biorxiv.org
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 ...
1104
Reposted by Richard Neher
Pathoplexus @pathoplexus.org · 10/09/2025
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
virological.org
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...
1279
Reposted by Richard Neher
Zamin Iqbal @zaminiqbal.bsky.social · 10/09/2025
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...
nature.com
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.
519099
Reposted by Richard Neher
Biozentrum, University of Basel @biozentrum.unibas.ch · 08/09/2025
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.
1206
Reposted by Richard Neher
Kai Kupferschmidt @kakape.bsky.social · 05/09/2025
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...
virological.org
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...
3251103
Richard Neher @neher.io · 05/09/2025
Congratulations!!
010
Reposted by Richard Neher
David Brückner @davidbrueckner.bsky.social · 04/09/2025
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!
2514615
Reposted by Richard Neher
Pathoplexus @pathoplexus.org · 27/08/2025
🗓 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
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'
13820
Reposted by Richard Neher
David Brückner @davidbrueckner.bsky.social · 25/08/2025
🤔 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...
nature.com
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...
34410
Richard Neher @neher.io · 23/08/2025
"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.
110
Richard Neher @neher.io · 23/08/2025
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
docs.pangraph.org
Introduction to Pangraph | Pangraph docs
Pangraph is currently under heavy development. Bugs and crashes are to be expected.
030
Richard Neher @neher.io · 23/08/2025
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]
110
Richard Neher @neher.io · 23/08/2025
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]
Linkage decay in phage core genomes.Population structure increases background levels of SNP linkage.
220
Richard Neher @neher.io · 23/08/2025
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]
120
Richard Neher @neher.io · 23/08/2025
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]
construction of pangenomes graphs of phage genomes
162
Richard Neher @neher.io · 23/08/2025
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...
phagesdb.org
The Actinobacteriophage Database | Home
13817
Reposted by Richard Neher
Erik van Nimwegen @erikvannimwegen.bsky.social · 09/05/2025
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...
biorxiv.org
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...
9335108
Reposted by Richard Neher
Ryan Hisner @ryanhisner.bsky.social · 10/04/2025
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? 1/18
37921
Richard Neher @neher.io · 05/04/2025
The Guardian with a clear take: www.theguardian.com/commentisfre...
theguardian.com
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
020
Reposted by Richard Neher
Mor Naaman @informor.bsky.social · 05/04/2025
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.
9804531811525
Reposted by Richard Neher
Anderson F. Brito @andersonfbrito.bsky.social · 04/04/2025
🧬 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
1113
Reposted by Richard Neher
Carl T. Bergstrom @carlbergstrom.com · 01/04/2025
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.
161349225
Reposted by Richard Neher
Ian Boudreau @ianboudreau.com · 31/03/2025
France raises a fascinating hypothetical point: what if the law still exists even if people might get mad at you
114186163589
Richard Neher @neher.io · 28/03/2025
From my colleague @cellarchlab.com and his lab at the @biozentrum.unibas.ch I continue to be amazed by what cyro-electron tomography can do...
0234