🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 25, 2025 at 9:06 AM
🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
🚨 Paper Alert 🚨
Absolutely delighted to share our last paper on "spatial mechano-transcriptomics" @naturemethods👇!!
www.nature.com/articles/s41...
Absolutely delighted to share our last paper on "spatial mechano-transcriptomics" @naturemethods👇!!
www.nature.com/articles/s41...
A computational pipeline for spatial mechano-transcriptomics - Nature Methods
The authors present a computational framework that leverages mechanical force inference and spatial transcriptomics to enable analyses of the interplay between the transcriptomic and mechanical state.
www.nature.com
March 17, 2025 at 12:53 PM
🚨 Paper Alert 🚨
Absolutely delighted to share our last paper on "spatial mechano-transcriptomics" @naturemethods👇!!
www.nature.com/articles/s41...
Absolutely delighted to share our last paper on "spatial mechano-transcriptomics" @naturemethods👇!!
www.nature.com/articles/s41...
#ResultatScientifique🔎| Une nouvelle méthode permet de prédire comment les cellules évoluent et se différencient dans le temps et l’espace. 💻
✍️ @cantinilab.bsky.social et @gabrielpeyre.bsky.social
📕 @naturemethods | buff.ly/XJlsK5P
✍️ @cantinilab.bsky.social et @gabrielpeyre.bsky.social
📕 @naturemethods | buff.ly/XJlsK5P
www.insb.cnrs.fr
December 11, 2025 at 4:30 PM
#ResultatScientifique🔎| Une nouvelle méthode permet de prédire comment les cellules évoluent et se différencient dans le temps et l’espace. 💻
✍️ @cantinilab.bsky.social et @gabrielpeyre.bsky.social
📕 @naturemethods | buff.ly/XJlsK5P
✍️ @cantinilab.bsky.social et @gabrielpeyre.bsky.social
📕 @naturemethods | buff.ly/XJlsK5P
Excited to share our atlas build&use guide, out @naturemethods today. Led by @KHrovatin & @SikkemaLisa w @MDLuecken, our review highlights best practices for building, sharing, and leveraging atlases to unlock new biological discoveries. 🌍@humancellatlas
nature.com/articles/s41592-024-02532-y
nature.com/articles/s41592-024-02532-y
December 13, 2024 at 11:10 AM
Excited to share our atlas build&use guide, out @naturemethods today. Led by @KHrovatin & @SikkemaLisa w @MDLuecken, our review highlights best practices for building, sharing, and leveraging atlases to unlock new biological discoveries. 🌍@humancellatlas
nature.com/articles/s41592-024-02532-y
nature.com/articles/s41592-024-02532-y
🚨 New in @naturemethods.bsky.social
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7
April 22, 2025 at 11:10 AM
🚨 New in @naturemethods.bsky.social
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7
Our heavily updated final version of ROCKET for experiment-guided structure modeling is out in @naturemethods!
New frontiers like high-throughput fragment screening and mid-res tomography are forcing a rethink of how experiments are modeled. ROCKET+OpenFold proposes a solution👇
New frontiers like high-throughput fragment screening and mid-res tomography are forcing a rethink of how experiments are modeled. ROCKET+OpenFold proposes a solution👇
ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH
Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15
Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15
AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network
Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...
rdcu.be
April 1, 2026 at 2:18 PM
Our heavily updated final version of ROCKET for experiment-guided structure modeling is out in @naturemethods!
New frontiers like high-throughput fragment screening and mid-res tomography are forcing a rethink of how experiments are modeled. ROCKET+OpenFold proposes a solution👇
New frontiers like high-throughput fragment screening and mid-res tomography are forcing a rethink of how experiments are modeled. ROCKET+OpenFold proposes a solution👇
🧪🔬💻 Will be posting our best-of videos from the past 10 years at the intersection of microscopy, computer science, and biology. My first @naturemethods paper: "ClearVolume: open-source live 3D visualization for light-sheet microscopy" (2015)
www.nature.com/articles/nme...
www.nature.com/articles/nme...
November 22, 2024 at 2:09 AM
🧪🔬💻 Will be posting our best-of videos from the past 10 years at the intersection of microscopy, computer science, and biology. My first @naturemethods paper: "ClearVolume: open-source live 3D visualization for light-sheet microscopy" (2015)
www.nature.com/articles/nme...
www.nature.com/articles/nme...
Need to design your next Xenium/CosMx/Merfish experiment? Spapros, now out @naturemethods, allows for probe set selection for target spatial tx. Led by @KuemmerleLouis, it optimizes both cell type ID & within-cell type variation. nature.com/articles/s41592-024-02496-z github.com/theislab/spapros
November 20, 2024 at 7:50 AM
Need to design your next Xenium/CosMx/Merfish experiment? Spapros, now out @naturemethods, allows for probe set selection for target spatial tx. Led by @KuemmerleLouis, it optimizes both cell type ID & within-cell type variation. nature.com/articles/s41592-024-02496-z github.com/theislab/spapros
The most sensitive green and red #norepinephrine #sensors engineered to date are out in #naturemethods! Deeply grateful to all our funders and contributors who made this work possible. A true team effort. @erc.europa.eu @snsf.ch doi.org/10.1038/s415...
Next-generation multicolor indicators for in vivo imaging of norepinephrine - Nature Methods
Improved red and green indicators for norepinephrine and their characterization are reported. These indicators allow detection of norepinephrine release in awake behaving mice in dual-color fiber phot...
doi.org
February 26, 2026 at 10:20 AM
The most sensitive green and red #norepinephrine #sensors engineered to date are out in #naturemethods! Deeply grateful to all our funders and contributors who made this work possible. A true team effort. @erc.europa.eu @snsf.ch doi.org/10.1038/s415...
🧵Have you ever tried #SRRF? Yes… then you are gonna 😍 this! No?… What took you so long? 😁 Finally #eSRRF is published @naturemethods! We are taking live-cell 3D #superresolution to the next level🏄♀️ 🔬: www.nature.com/articles/s41...
November 13, 2023 at 4:30 PM
🧵Have you ever tried #SRRF? Yes… then you are gonna 😍 this! No?… What took you so long? 😁 Finally #eSRRF is published @naturemethods! We are taking live-cell 3D #superresolution to the next level🏄♀️ 🔬: www.nature.com/articles/s41...
Check out a Research Highlights on our work at @naturemethods by Lin Tang!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 19, 2025 at 4:36 PM
Check out a Research Highlights on our work at @naturemethods by Lin Tang!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
iFlpMosaics are now published @naturemethods. A compendium of novel genetic tools and related methods for inducing and analysing genetic mosaics in a high-throughput manner.Tweetorial 👇
nature.com/articles/s4159…
nature.com/articles/s4159…
February 11, 2025 at 7:38 AM
iFlpMosaics are now published @naturemethods. A compendium of novel genetic tools and related methods for inducing and analysing genetic mosaics in a high-throughput manner.Tweetorial 👇
nature.com/articles/s4159…
nature.com/articles/s4159…
Interested in neuromodulators, especially #norepinephrine / #noradrenaline? Check out this #Naturemethods paper hot off the press from the Patriarchi lab on next-generation NE sensors. It was a pleasure to contribute to this team effort. A genuinely 💡enlightening 💡 advance for monitoring NE in vivo.
The most sensitive green and red #norepinephrine #sensors engineered to date are out in #naturemethods! Deeply grateful to all our funders and contributors who made this work possible. A true team effort. @erc.europa.eu @snsf.ch doi.org/10.1038/s415...
Next-generation multicolor indicators for in vivo imaging of norepinephrine - Nature Methods
Improved red and green indicators for norepinephrine and their characterization are reported. These indicators allow detection of norepinephrine release in awake behaving mice in dual-color fiber phot...
doi.org
February 26, 2026 at 1:26 PM
Interested in neuromodulators, especially #norepinephrine / #noradrenaline? Check out this #Naturemethods paper hot off the press from the Patriarchi lab on next-generation NE sensors. It was a pleasure to contribute to this team effort. A genuinely 💡enlightening 💡 advance for monitoring NE in vivo.
Against all odds: PdCO, a versatile switchable optogenetic tool for inhibiting synaptic transmission in neuronal terminals in vivo is finally published @naturemethods #neuroskyence #optogenetics
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A bistable inhibitory optoGPCR for multiplexed optogenetic control of neural circuits - Nature Methods
PdCO is a switchable optogenetic tool for inhibiting synaptic transmission in neuronal terminals in vivo, as demonstrated in a variety of contexts mainly in the mouse.
www.nature.com
May 30, 2024 at 6:27 AM
Against all odds: PdCO, a versatile switchable optogenetic tool for inhibiting synaptic transmission in neuronal terminals in vivo is finally published @naturemethods #neuroskyence #optogenetics
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Our paper describing UnitMatch software "tracking neurons across days with high-density probes", appeared in this month's issue of #NatureMethods. Missed it? Read it here: www.nature.com/articles/s41...
April 14, 2025 at 2:45 PM
Our paper describing UnitMatch software "tracking neurons across days with high-density probes", appeared in this month's issue of #NatureMethods. Missed it? Read it here: www.nature.com/articles/s41...
Congratulations to @sergiomarcosalas.bsky.social, @nilssonlab.org, and their team on a new #NatureMethods publication featuring the Xenium platform! Read how Xenium spatial stacked up against 8 other systems & get independently validated best practices & recommendations: go.nature.com/3DZ0PpR
March 27, 2025 at 4:26 PM
Congratulations to @sergiomarcosalas.bsky.social, @nilssonlab.org, and their team on a new #NatureMethods publication featuring the Xenium platform! Read how Xenium spatial stacked up against 8 other systems & get independently validated best practices & recommendations: go.nature.com/3DZ0PpR
👏 Phys.org has featured the work of our colleagues at IOCB Prague.
The team led by @pluskal-lab.org created the world’s largest database of small-molecule #massspec. See more ► doi.org/10.1038/s41592-025-02813-0
#IOCBPrague #massspec #metabolomics #drugdiscovery #NatureMethods
The team led by @pluskal-lab.org created the world’s largest database of small-molecule #massspec. See more ► doi.org/10.1038/s41592-025-02813-0
#IOCBPrague #massspec #metabolomics #drugdiscovery #NatureMethods
September 22, 2025 at 3:07 PM
👏 Phys.org has featured the work of our colleagues at IOCB Prague.
The team led by @pluskal-lab.org created the world’s largest database of small-molecule #massspec. See more ► doi.org/10.1038/s41592-025-02813-0
#IOCBPrague #massspec #metabolomics #drugdiscovery #NatureMethods
The team led by @pluskal-lab.org created the world’s largest database of small-molecule #massspec. See more ► doi.org/10.1038/s41592-025-02813-0
#IOCBPrague #massspec #metabolomics #drugdiscovery #NatureMethods
Build your own online integrated platform for single-cell & spatial transcriptomic data using WebAtlas pipeline
Cell2location
StabMap
Unify image & gene expression files into Zarr format
Compatible with SpatialData
Based on Vitessce framework
#Naturemethods 2024
www.nature.com/articles/s41...
Cell2location
StabMap
Unify image & gene expression files into Zarr format
Compatible with SpatialData
Based on Vitessce framework
#Naturemethods 2024
www.nature.com/articles/s41...
August 21, 2024 at 11:07 AM
Build your own online integrated platform for single-cell & spatial transcriptomic data using WebAtlas pipeline
Cell2location
StabMap
Unify image & gene expression files into Zarr format
Compatible with SpatialData
Based on Vitessce framework
#Naturemethods 2024
www.nature.com/articles/s41...
Cell2location
StabMap
Unify image & gene expression files into Zarr format
Compatible with SpatialData
Based on Vitessce framework
#Naturemethods 2024
www.nature.com/articles/s41...
July 24, 2025 at 9:56 PM
Congratulations to first author Gangadhar Eluru, co-authors Steven De Gieter, Stephan Schenck, Annelore Stroobants, Binesh Shrestha, Paul Erbel and Ruslan Efremov.
#MISO #CryoEM #StructuralBiology #MembraneProteins #VIB-VUB Center for Structural Biology #NatureMethods #DrugDiscovery #BioRender
#MISO #CryoEM #StructuralBiology #MembraneProteins #VIB-VUB Center for Structural Biology #NatureMethods #DrugDiscovery #BioRender
November 14, 2025 at 6:43 PM
Congratulations to first author Gangadhar Eluru, co-authors Steven De Gieter, Stephan Schenck, Annelore Stroobants, Binesh Shrestha, Paul Erbel and Ruslan Efremov.
#MISO #CryoEM #StructuralBiology #MembraneProteins #VIB-VUB Center for Structural Biology #NatureMethods #DrugDiscovery #BioRender
#MISO #CryoEM #StructuralBiology #MembraneProteins #VIB-VUB Center for Structural Biology #NatureMethods #DrugDiscovery #BioRender
Very happy about this months #PointsOfView in #NatureMethods - The Graphical Abstract.
Co-authored with @simonduerr.eu, with whom I share a long-time passion for #Icons #BioIcons and #CC0 figures - and fuelled by our joint workshop for the @sib.swiss at [BC]2!
Here is a 🎁 link lnkd.in/e5ew-E2R
Co-authored with @simonduerr.eu, with whom I share a long-time passion for #Icons #BioIcons and #CC0 figures - and fuelled by our joint workshop for the @sib.swiss at [BC]2!
Here is a 🎁 link lnkd.in/e5ew-E2R
September 10, 2026 at 4:04 PM
Very happy about this months #PointsOfView in #NatureMethods - The Graphical Abstract.
Co-authored with @simonduerr.eu, with whom I share a long-time passion for #Icons #BioIcons and #CC0 figures - and fuelled by our joint workshop for the @sib.swiss at [BC]2!
Here is a 🎁 link lnkd.in/e5ew-E2R
Co-authored with @simonduerr.eu, with whom I share a long-time passion for #Icons #BioIcons and #CC0 figures - and fuelled by our joint workshop for the @sib.swiss at [BC]2!
Here is a 🎁 link lnkd.in/e5ew-E2R
#tidyomics made it to #NatureMethods! "The tidyomics ecosystem: Enhancing omic data analyses", 👏🏽 Will, Timothy, and Team!
32 researchers | 26 institutes | 10 countries | 4 continents
A #crowd/#community-research success
nature.com/articles/s41...
#CZI, Thanks @mikelove.bsky.social !
32 researchers | 26 institutes | 10 countries | 4 continents
A #crowd/#community-research success
nature.com/articles/s41...
#CZI, Thanks @mikelove.bsky.social !
The tidyomics ecosystem: enhancing omic data analyses - Nature Methods
tidyomics offers a software ecosystem for omic data manipulation and analysis that bridges Bioconductor with the tidyverse framework.
https://nature.com/articles/s41592-024-02299-2?utm_source=twitter&utm_medium=social&utm_campaign=nmeth…
June 17, 2024 at 1:20 AM
#tidyomics made it to #NatureMethods! "The tidyomics ecosystem: Enhancing omic data analyses", 👏🏽 Will, Timothy, and Team!
32 researchers | 26 institutes | 10 countries | 4 continents
A #crowd/#community-research success
nature.com/articles/s41...
#CZI, Thanks @mikelove.bsky.social !
32 researchers | 26 institutes | 10 countries | 4 continents
A #crowd/#community-research success
nature.com/articles/s41...
#CZI, Thanks @mikelove.bsky.social !
Surprise, surprise! 😳
This raises an important question…
How will our @naturemethods 2024 Method of the Year, #SpatialProteomics, will tackle this before it becomes a potential pitfall?
Why Bax detection in >1400 publications might be flawed | Cell Death & Disease
www.nature.com/articles/s41...
This raises an important question…
How will our @naturemethods 2024 Method of the Year, #SpatialProteomics, will tackle this before it becomes a potential pitfall?
Why Bax detection in >1400 publications might be flawed | Cell Death & Disease
www.nature.com/articles/s41...
December 27, 2024 at 1:19 AM
Surprise, surprise! 😳
This raises an important question…
How will our @naturemethods 2024 Method of the Year, #SpatialProteomics, will tackle this before it becomes a potential pitfall?
Why Bax detection in >1400 publications might be flawed | Cell Death & Disease
www.nature.com/articles/s41...
This raises an important question…
How will our @naturemethods 2024 Method of the Year, #SpatialProteomics, will tackle this before it becomes a potential pitfall?
Why Bax detection in >1400 publications might be flawed | Cell Death & Disease
www.nature.com/articles/s41...
Andrzej Zieleziński @uam-ibmib.bsky.social with Adam Gudyś & @sdeorowicz.bsky.social dvelopped Vclust: fast and accurate tool for calculating intergenomic similarities (like ANI) and clustering virus/#phage genomes. Just published @naturemethods - congratulations! www.nature.com/articles/s41...
May 16, 2025 at 1:09 PM
Andrzej Zieleziński @uam-ibmib.bsky.social with Adam Gudyś & @sdeorowicz.bsky.social dvelopped Vclust: fast and accurate tool for calculating intergenomic similarities (like ANI) and clustering virus/#phage genomes. Just published @naturemethods - congratulations! www.nature.com/articles/s41...
Check out UDA-seq! 🚀 Combines droplet microfluidics for scalable, multimodal single-cell sequencing. Cost-effective, universal, and ready for 10⁶+ cells! #BiotechBreakthrough PMID:39833568, Nat Methods 2025, @naturemethods @OTSociety https://doi.org/10.1038/s41592-024-02586-y 🧪
March 1, 2025 at 7:30 AM
Check out UDA-seq! 🚀 Combines droplet microfluidics for scalable, multimodal single-cell sequencing. Cost-effective, universal, and ready for 10⁶+ cells! #BiotechBreakthrough PMID:39833568, Nat Methods 2025, @naturemethods @OTSociety https://doi.org/10.1038/s41592-024-02586-y 🧪