Noah Bruderer
@noahbruderer.bsky.social
PhD candidate @MSarsCentre / Computational biology / Development biology / Image analysis / Data diver
Reposted by Noah Bruderer
Re-upping this with a Bluetorial in a shameless act of self-promotion. 1/n
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors
Wei Wang, @lionlchristiaen.bsky.social and colleagues
www.embopress.org/doi/full/10....
Wei Wang, @lionlchristiaen.bsky.social and colleagues
www.embopress.org/doi/full/10....
November 15, 2025 at 8:15 AM
Re-upping this with a Bluetorial in a shameless act of self-promotion. 1/n
Reposted by Noah Bruderer
Crowding more proteins per cytoplasm unit volume would hamper processes such as diffusion, which is already about ten fold slower inside the cell than in pure water.
Source: book.bionumbers.org/what-is-the-...
Source: book.bionumbers.org/what-is-the-...
» What is the macromolecular composition of the cell?Cell Biology by the Numbers
Vignettes that reveal how numbers serve as a sixth sense to understanding our cells
book.bionumbers.org
November 10, 2025 at 12:57 PM
Crowding more proteins per cytoplasm unit volume would hamper processes such as diffusion, which is already about ten fold slower inside the cell than in pure water.
Source: book.bionumbers.org/what-is-the-...
Source: book.bionumbers.org/what-is-the-...
Reposted by Noah Bruderer
Intestinal villus cells extrude living, following a calcium pulse. Unlike from extruding apoptotic cells, Ca2+ messaging stops at the first neighbors! #FluorescenceFriday
Part of our TrepatLab preprint: www.biorxiv.org/content/10.1...
Video by @ronjahoutekamer.bsky.social @gloerichlab.bsky.social
Part of our TrepatLab preprint: www.biorxiv.org/content/10.1...
Video by @ronjahoutekamer.bsky.social @gloerichlab.bsky.social
November 7, 2025 at 2:40 PM
Intestinal villus cells extrude living, following a calcium pulse. Unlike from extruding apoptotic cells, Ca2+ messaging stops at the first neighbors! #FluorescenceFriday
Part of our TrepatLab preprint: www.biorxiv.org/content/10.1...
Video by @ronjahoutekamer.bsky.social @gloerichlab.bsky.social
Part of our TrepatLab preprint: www.biorxiv.org/content/10.1...
Video by @ronjahoutekamer.bsky.social @gloerichlab.bsky.social
Reposted by Noah Bruderer
Our latest on how cells get ready for fate transition! @noahbruderer.bsky.social @margauxfailla.bsky.social @lionlchristiaen.bsky.social
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors www.embopress.org/doi/full/10....
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors www.embopress.org/doi/full/10....
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors | The EMBO Journal
imageimageDuring development, multipotent cardiopharyngeal progenitors express both cardiac
and pharyngeal muscle transcriptional programs. This study in the tunicate Ciona shows that cell cycle-regul...
www.embopress.org
November 4, 2025 at 12:05 PM
Our latest on how cells get ready for fate transition! @noahbruderer.bsky.social @margauxfailla.bsky.social @lionlchristiaen.bsky.social
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors www.embopress.org/doi/full/10....
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors www.embopress.org/doi/full/10....
Reposted by Noah Bruderer
💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵
1/6 #iccv2025
1/6 #iccv2025
October 23, 2025 at 6:01 PM
💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵
1/6 #iccv2025
1/6 #iccv2025
Reposted by Noah Bruderer
Happy to share the last version of our story @currentbiology.bsky.social on the role of interfacial tension in mechanical cell competition led by @leovalon.bsky.social and Alexis Matamoro Vidal
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
October 9, 2025 at 3:27 PM
Happy to share the last version of our story @currentbiology.bsky.social on the role of interfacial tension in mechanical cell competition led by @leovalon.bsky.social and Alexis Matamoro Vidal
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Noah Bruderer
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
October 5, 2025 at 10:35 AM
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
Reposted by Noah Bruderer
🧬🔬🧪 🎉 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...
Reposted by Noah Bruderer
Morphogenesis alert! A unifying physical principle links gastrulation in frogs, fish and flies! Stoked to be part of this new paper with Xin Li in Dave Thirumalai's lab and Robert Huebner in my group and a co-lab with @peiferlabunc.bsky.social and Margot Williams.
1/n
www.nature.com/articles/s41...
1/n
www.nature.com/articles/s41...
Emergence of cellular nematic order is a conserved feature of gastrulation in animal embryos - Nature Communications
The morphogenetic events that occur during gastrulation involve dramatic cell- and tissue-level changes. Here they show that propagation of nematic order, leading to long-range spatial correlation, is...
www.nature.com
July 2, 2025 at 1:20 PM
Morphogenesis alert! A unifying physical principle links gastrulation in frogs, fish and flies! Stoked to be part of this new paper with Xin Li in Dave Thirumalai's lab and Robert Huebner in my group and a co-lab with @peiferlabunc.bsky.social and Margot Williams.
1/n
www.nature.com/articles/s41...
1/n
www.nature.com/articles/s41...
Reposted by Noah Bruderer
We are thrilled to announce the launch of the Michael Sars Visitors Program! ✨🧪 To spark new connections, we are opening our doors to visiting researchers who wish to conduct a project in #SunnyBergen. Applications are open, help us spread the word!
Introducing the Michael Sars Visitors Program
The Michael Sars Centre is launching a Visitors Program designed to foster scientific exchange and collaborations across disciplines.
tinyurl.com
June 26, 2025 at 1:13 PM
We are thrilled to announce the launch of the Michael Sars Visitors Program! ✨🧪 To spark new connections, we are opening our doors to visiting researchers who wish to conduct a project in #SunnyBergen. Applications are open, help us spread the word!
Reposted by Noah Bruderer
What a fantastic morning at #MSS2025 🤩 After an opening by BIO Dept. head @unibergen.bsky.social Ståle Ellingsen, three amazing talks by @lowelab.bsky.social, Georgia Rapti @embl.org and Camila Esguerra @ncmbm.bsky.social on System Evolution 👏
June 6, 2025 at 11:14 AM
What a fantastic morning at #MSS2025 🤩 After an opening by BIO Dept. head @unibergen.bsky.social Ståle Ellingsen, three amazing talks by @lowelab.bsky.social, Georgia Rapti @embl.org and Camila Esguerra @ncmbm.bsky.social on System Evolution 👏
Reposted by Noah Bruderer
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse...
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
May 3, 2025 at 7:12 PM
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse...
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
Reposted by Noah Bruderer
📣 New article out in @cp-cellreports.bsky.social 🤩 Zonglai Liang and colleagues from the @mchatzigeorgiou.bsky.social group reveal a dual role for Anoctamins in sensory perception & metamorphosis in #Ciona larvae 🧪 Take a peek behind the scenes ⤵️
Conserved proteins link sensory input and metamorphosis in a marine chordate
Anoctamins play a key role in sensory perception in mammals. A new article by the Chatzigeorgiou group reveals their dual role in perception and larval metamorphosis in the chordate Ciona.
tinyurl.com
April 25, 2025 at 11:58 AM
📣 New article out in @cp-cellreports.bsky.social 🤩 Zonglai Liang and colleagues from the @mchatzigeorgiou.bsky.social group reveal a dual role for Anoctamins in sensory perception & metamorphosis in #Ciona larvae 🧪 Take a peek behind the scenes ⤵️
Reposted by Noah Bruderer
🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us!
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍
job-boards.greenhouse.io/chanzuckerbe...
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍
job-boards.greenhouse.io/chanzuckerbe...
Scientist, Spatial Molecular Cartography (Jacobo/Royer Group - Biohub SF)
San Francisco, California, United States
job-boards.greenhouse.io
April 15, 2025 at 6:27 PM
🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us!
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍
job-boards.greenhouse.io/chanzuckerbe...
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍
job-boards.greenhouse.io/chanzuckerbe...
Reposted by Noah Bruderer
Loïc Royer @loicaroyer.bsky.social presented today the impressive work of his team @czbiohub.bsky.social in optical engineering and developing analysis tools to explore vertebrate development 🐟🧪 Thank you for an inspiring and visually stunning talk! 🤩
March 28, 2025 at 3:49 PM
Loïc Royer @loicaroyer.bsky.social presented today the impressive work of his team @czbiohub.bsky.social in optical engineering and developing analysis tools to explore vertebrate development 🐟🧪 Thank you for an inspiring and visually stunning talk! 🤩
Reposted by Noah Bruderer
We are in for a mindblowing treat today at @msarscentre.bsky.social with @loicaroyer.bsky.social from @czbiohub.bsky.social hosted by @noahbruderer.bsky.social for a seminar on “Building a virtual embryo, a single cell at a time”.
March 28, 2025 at 9:04 AM
We are in for a mindblowing treat today at @msarscentre.bsky.social with @loicaroyer.bsky.social from @czbiohub.bsky.social hosted by @noahbruderer.bsky.social for a seminar on “Building a virtual embryo, a single cell at a time”.
Reposted by Noah Bruderer
Applying LLMs to biomedical research today can go one of two ways: we either use a closed-source web app, or we get coding ourselves. Many researchers lack training for the latter, so their only choice is the former. We want to change that. www.nature.com/articles/s41...
February 5, 2025 at 9:15 AM
Applying LLMs to biomedical research today can go one of two ways: we either use a closed-source web app, or we get coding ourselves. Many researchers lack training for the latter, so their only choice is the former. We want to change that. www.nature.com/articles/s41...
Reposted by Noah Bruderer
We are excited to announce that registration for the Michael Sars Symposium 2025 is now open! 🤩 Join us on June 6th at Media City Bergen for a day of exceptional talks 🧪 #MSS2025
✨Learn more and register here: tinyurl.com/yc4jxdvz
✨Learn more and register here: tinyurl.com/yc4jxdvz
January 29, 2025 at 8:55 AM
We are excited to announce that registration for the Michael Sars Symposium 2025 is now open! 🤩 Join us on June 6th at Media City Bergen for a day of exceptional talks 🧪 #MSS2025
✨Learn more and register here: tinyurl.com/yc4jxdvz
✨Learn more and register here: tinyurl.com/yc4jxdvz
Search is changing, using LLMs to reliably query your own data and public data bases will become the norm. Amongst other tools we use @langchain.bsky.social to drastically reduce hallucinations of LLMs.
AI has the potential to transform the way we access and handle datasets. Meet BioChatter: an open large language model framework designed to support biomedical research 💻 An exciting project by @ebi.embl.org with contributions from @noahbruderer.bsky.social, out now in @naturebiotech.bsky.social 👏
BioChatter: making large language models accessible for biomedical research
A team led by researchers at EMBL's European Bioinformatics Institute (EMBL-EBI), in collaboration with a PhD candidate in the Christiaen group, developed an open-source large language model (LLM) fra...
tinyurl.com
January 22, 2025 at 2:35 PM
Search is changing, using LLMs to reliably query your own data and public data bases will become the norm. Amongst other tools we use @langchain.bsky.social to drastically reduce hallucinations of LLMs.
Reposted by Noah Bruderer
I’m delighted to share that I will be starting my lab @univmiami.bsky.social in Spring 2025! We will study cellular and developmental biology in non-bilaterian animals – cnidarians, ctenophores, placozoans, and sponges – to explore early animal evolution.
November 27, 2024 at 4:26 PM
I’m delighted to share that I will be starting my lab @univmiami.bsky.social in Spring 2025! We will study cellular and developmental biology in non-bilaterian animals – cnidarians, ctenophores, placozoans, and sponges – to explore early animal evolution.
Find me at #CBIAS2024 in London!
Come to chat about image-to-single-cell morphology and how morphosnaker 🧊🐍🧊 can help.
Also come to play around with our virtual embryo.
#morphosnaker #singlecell #morphology
Come to chat about image-to-single-cell morphology and how morphosnaker 🧊🐍🧊 can help.
Also come to play around with our virtual embryo.
#morphosnaker #singlecell #morphology
November 25, 2024 at 1:15 PM
Find me at #CBIAS2024 in London!
Come to chat about image-to-single-cell morphology and how morphosnaker 🧊🐍🧊 can help.
Also come to play around with our virtual embryo.
#morphosnaker #singlecell #morphology
Come to chat about image-to-single-cell morphology and how morphosnaker 🧊🐍🧊 can help.
Also come to play around with our virtual embryo.
#morphosnaker #singlecell #morphology
Reposted by Noah Bruderer
November 25, 2024 at 8:32 AM
Reposted by Noah Bruderer
Ciona intestinalis in situ @ 25m around Sotra island,🇳🇴!
@msarscentre.bsky.social
I am trying to understand how chemical cues lead to these mass aggregations!
@msarscentre.bsky.social
I am trying to understand how chemical cues lead to these mass aggregations!
November 21, 2024 at 10:34 AM
Ciona intestinalis in situ @ 25m around Sotra island,🇳🇴!
@msarscentre.bsky.social
I am trying to understand how chemical cues lead to these mass aggregations!
@msarscentre.bsky.social
I am trying to understand how chemical cues lead to these mass aggregations!