Richard Neher
@neher.io
Reposted by Richard Neher
🚨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
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
November 20, 2025 at 8:40 PM
🚨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
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
Reposted by Richard Neher
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
November 6, 2025 at 9:46 PM
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
Reposted by Richard Neher
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 or spread the word!
apply.refline.ch/499599/0346/...
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...
apply.refline.ch
October 23, 2025 at 5:34 AM
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 or spread the word!
apply.refline.ch/499599/0346/...
Reposted by Richard Neher
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
@biozentrum.unibas.ch @unibas.ch
October 17, 2025 at 9:22 AM
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
@biozentrum.unibas.ch @unibas.ch
Reposted by Richard Neher
📣 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.
Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.
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
October 6, 2025 at 6:46 AM
📣 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.
Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.
Reposted by Richard Neher
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
www.biozentrum.unibas.ch/open-positio...
#biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging
September 29, 2025 at 2:58 PM
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
www.biozentrum.unibas.ch/open-positio...
#biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging
Reposted by Richard Neher
HHMI adopts Plan U journals.plos.org/plosbiology/...
September 24, 2025 at 6:08 PM
HHMI adopts Plan U journals.plos.org/plosbiology/...
Reposted by Richard Neher
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...
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
September 17, 2025 at 2:19 PM
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...
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...
Reposted by Richard Neher
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
Read more: virological.org/t/the-16th-e...
1/7
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
September 10, 2025 at 10:00 AM
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
Read more: virological.org/t/the-16th-e...
1/7
Reposted by Richard Neher
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 Richard Neher
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.
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.
September 8, 2025 at 9:13 AM
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.
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.
Reposted by Richard Neher
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...
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
September 5, 2025 at 8:02 AM
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...
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...
Reposted by Richard Neher
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!
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!
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/...
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
September 4, 2025 at 11:27 AM
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!
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!
Reposted by Richard Neher
🗓 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
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
August 27, 2025 at 3:57 PM
🗓 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
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
Reposted by Richard Neher
🤔 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...
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
August 25, 2025 at 9:49 AM
🤔 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...
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...
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...
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
The Actinobacteriophage Database | Home
phagesdb.org
August 23, 2025 at 4:21 PM
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...
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
Reposted by Richard Neher
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...
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
May 9, 2025 at 10:49 AM
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...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Reposted by Richard Neher
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
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
April 10, 2025 at 12:48 AM
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
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
Reposted by Richard Neher
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
April 5, 2025 at 6:33 PM
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
Reposted by Richard Neher
🧬 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
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
April 4, 2025 at 8:20 PM
🧬 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
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
Reposted by Richard Neher
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.
It does not "fosters a sense of national shame."
It does not "advance a corrosive ideology."
It is literally what might redeem the USA.
April 1, 2025 at 6:54 AM
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.
It does not "fosters a sense of national shame."
It does not "advance a corrosive ideology."
It is literally what might redeem the USA.
Reposted by Richard Neher
France raises a fascinating hypothetical point: what if the law still exists even if people might get mad at you
March 31, 2025 at 12:55 PM
France raises a fascinating hypothetical point: what if the law still exists even if people might get mad at you
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...
I continue to be amazed by what cyro-electron tomography can do...
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.
Learn more: scim.ag/41PWgYc
Learn more: scim.ag/41PWgYc
In-cell architecture of the mitochondrial respiratory chain
Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, workin...
scim.ag
March 28, 2025 at 5:27 PM
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...
I continue to be amazed by what cyro-electron tomography can do...
Reposted by Richard Neher
March 25, 2025 at 3:40 AM