Artür Manukyan
@arturmansl.bsky.social
Network (Graph) Scientist. Computational and Spatial Biology. Statistical Learning for Bioinformatics.
Reposted by Artür Manukyan
Switzerland is joining Horizon Europe!
We are uniting two research powerhouses.
For cutting-edge innovation that will boost our energy security, digital transformation, health and so much more.
Today is a good day for science, and for our EU-Switzerland partnership.
We are uniting two research powerhouses.
For cutting-edge innovation that will boost our energy security, digital transformation, health and so much more.
Today is a good day for science, and for our EU-Switzerland partnership.
November 10, 2025 at 2:58 PM
Switzerland is joining Horizon Europe!
We are uniting two research powerhouses.
For cutting-edge innovation that will boost our energy security, digital transformation, health and so much more.
Today is a good day for science, and for our EU-Switzerland partnership.
We are uniting two research powerhouses.
For cutting-edge innovation that will boost our energy security, digital transformation, health and so much more.
Today is a good day for science, and for our EU-Switzerland partnership.
Reposted by Artür Manukyan
After years of hard work we're thrilled to announce our new Nature Methods paper:
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.
Another milestone for everyone working with Giotto!
www.nature.com/articles/s41...
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.
Another milestone for everyone working with Giotto!
www.nature.com/articles/s41...
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem - Nature Methods
Giotto Suite provides a comprehensive, flexible and scalable platform for technology-agnostic spatial omics analysis using R.
www.nature.com
October 2, 2025 at 1:37 PM
After years of hard work we're thrilled to announce our new Nature Methods paper:
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.
Another milestone for everyone working with Giotto!
www.nature.com/articles/s41...
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.
Another milestone for everyone working with Giotto!
www.nature.com/articles/s41...
Reposted by Artür Manukyan
🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
September 28, 2025 at 5:50 PM
🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
#EuroBioC2025 just started at @prbb.org in beautiful Barcelona. Looking forward to meeting friends and collaborators to discuss new generation of data structures and file formats for spatial/single-cell biology.
September 17, 2025 at 1:08 PM
#EuroBioC2025 just started at @prbb.org in beautiful Barcelona. Looking forward to meeting friends and collaborators to discuss new generation of data structures and file formats for spatial/single-cell biology.
Reposted by Artür Manukyan
Very honored to receive the 2025 ISCB Innovator Award at #ISMBECCB2025 and present our lab’s journey—from mapping cells to modeling their future.
Thanks to my amazing team and collaborators—this is our award! 🙌
📽️ Keynote: Atlases, AI & virtual cells
📝 doi.org/10.1093/bioi...
Thanks to my amazing team and collaborators—this is our award! 🙌
📽️ Keynote: Atlases, AI & virtual cells
📝 doi.org/10.1093/bioi...
July 25, 2025 at 9:13 AM
Very honored to receive the 2025 ISCB Innovator Award at #ISMBECCB2025 and present our lab’s journey—from mapping cells to modeling their future.
Thanks to my amazing team and collaborators—this is our award! 🙌
📽️ Keynote: Atlases, AI & virtual cells
📝 doi.org/10.1093/bioi...
Thanks to my amazing team and collaborators—this is our award! 🙌
📽️ Keynote: Atlases, AI & virtual cells
📝 doi.org/10.1093/bioi...
Reposted by Artür Manukyan
🚀 Reminder: Bioconductor Developer Forum is this Monday!
🧵 Topic: R & Rust in Bioinformatics
🗓️ July 28 | 🕚 11am EDT / 5pm CEST
🔗 Details + Zoom: blog.bioconductor.org/posts/2025-0...
#Bioconductor #RStats #RustLang #OpenSource
🧵 Topic: R & Rust in Bioinformatics
🗓️ July 28 | 🕚 11am EDT / 5pm CEST
🔗 Details + Zoom: blog.bioconductor.org/posts/2025-0...
#Bioconductor #RStats #RustLang #OpenSource
Exploring R and Rust in Bioinformatics – Online Developer Forum, 28 July 2025 – Bioconductor community blog
A blog for the Bioconductor community!
blog.bioconductor.org
July 25, 2025 at 11:54 AM
🚀 Reminder: Bioconductor Developer Forum is this Monday!
🧵 Topic: R & Rust in Bioinformatics
🗓️ July 28 | 🕚 11am EDT / 5pm CEST
🔗 Details + Zoom: blog.bioconductor.org/posts/2025-0...
#Bioconductor #RStats #RustLang #OpenSource
🧵 Topic: R & Rust in Bioinformatics
🗓️ July 28 | 🕚 11am EDT / 5pm CEST
🔗 Details + Zoom: blog.bioconductor.org/posts/2025-0...
#Bioconductor #RStats #RustLang #OpenSource
Reposted by Artür Manukyan
We’re happy to share our new preprint form
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...
Spatiotemporal dynamics of tumor microenvironment remodeling
During tumorigenesis, interactions between tumor and stromal cells progressively remodel the tumor microenvironment (TME) towards pro-tumoral functions. Understanding early TME remodeling dynamics is ...
biorxiv.org
July 22, 2025 at 9:48 AM
We’re happy to share our new preprint form
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...
Reposted by Artür Manukyan
🧬🖥️🧪 Interested in single-cell-informed cell-type #deconvolution? Have a look at our enhanced benchmarking study and #omnideconv ecosystem!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
July 15, 2025 at 2:25 PM
🧬🖥️🧪 Interested in single-cell-informed cell-type #deconvolution? Have a look at our enhanced benchmarking study and #omnideconv ecosystem!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Artür Manukyan
🔬Hands-on workshops kick off the Berlin Summer Meeting 2025 #BSM2025! Attendees dove into real-time sequence search, nucleic acid analysis of environmental samples, spatial transcriptomics for infectious diseases, AI-assisted genomics, and a behind-the-scenes tour of single-cell omics 🧬🧑🔬
#mdcBerlin
#mdcBerlin
June 18, 2025 at 2:32 PM
🔬Hands-on workshops kick off the Berlin Summer Meeting 2025 #BSM2025! Attendees dove into real-time sequence search, nucleic acid analysis of environmental samples, spatial transcriptomics for infectious diseases, AI-assisted genomics, and a behind-the-scenes tour of single-cell omics 🧬🧑🔬
#mdcBerlin
#mdcBerlin
Reposted by Artür Manukyan
I sometimes overhear conversations about tool choice in bioinformatics, where implementation language is stated as the primary criterion. Such thinking stands in the way of scientific quality and productivity. It is a form of self-harm.
What should one really care about?
(1/5)
What should one really care about?
(1/5)
June 13, 2025 at 5:23 PM
I sometimes overhear conversations about tool choice in bioinformatics, where implementation language is stated as the primary criterion. Such thinking stands in the way of scientific quality and productivity. It is a form of self-harm.
What should one really care about?
(1/5)
What should one really care about?
(1/5)
Reposted by Artür Manukyan
What a special atmosphere! #ELMI2025 Poster Session 1 on Helix A last night. The perfect environment to exchange with friends & colleagues about #bioimaging #RDM:
- OMERO-vitessce
- IO-FAST initiative
- @nfdi4bioimage.bsky.social Data Stewardship
Talks, Workshops & Poster Session 2 up ahead today!🔬
- OMERO-vitessce
- IO-FAST initiative
- @nfdi4bioimage.bsky.social Data Stewardship
Talks, Workshops & Poster Session 2 up ahead today!🔬
June 5, 2025 at 8:01 AM
What a special atmosphere! #ELMI2025 Poster Session 1 on Helix A last night. The perfect environment to exchange with friends & colleagues about #bioimaging #RDM:
- OMERO-vitessce
- IO-FAST initiative
- @nfdi4bioimage.bsky.social Data Stewardship
Talks, Workshops & Poster Session 2 up ahead today!🔬
- OMERO-vitessce
- IO-FAST initiative
- @nfdi4bioimage.bsky.social Data Stewardship
Talks, Workshops & Poster Session 2 up ahead today!🔬
Reposted by Artür Manukyan
As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...
False positives in study of memory-related gene expression - Nature
Nature - False positives in study of memory-related gene expression
www.nature.com
June 4, 2025 at 5:59 PM
As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...
Sums up a day in my life at the lab ...
May 31, 2025 at 7:51 PM
Sums up a day in my life at the lab ...
Reposted by Artür Manukyan
Just wrapped up 2 inspiring days at ISCO – Innovations in Single Cell Omics! A great community came together to share science and fun. A big THANK YOU to all our fantastic speakers and interactive participants
May 13, 2025 at 9:16 PM
Just wrapped up 2 inspiring days at ISCO – Innovations in Single Cell Omics! A great community came together to share science and fun. A big THANK YOU to all our fantastic speakers and interactive participants
Reposted by Artür Manukyan
The Innovations in Single Cell Omics conference in Berlin was amazing! Great talks and we even had a Night Science workshop! 🙏 @stefaniegrosswendt.bsky.social, Ashley Sanders, @simonhaas.bsky.social, @leifludwig.bsky.social, @elimereu.bsky.social, @larsplus.bsky.social & @alejofraticelli.bsky.social
Just wrapped up 2 inspiring days at ISCO – Innovations in Single Cell Omics! A great community came together to share science and fun. A big THANK YOU to all our fantastic speakers and interactive participants
May 13, 2025 at 9:52 PM
The Innovations in Single Cell Omics conference in Berlin was amazing! Great talks and we even had a Night Science workshop! 🙏 @stefaniegrosswendt.bsky.social, Ashley Sanders, @simonhaas.bsky.social, @leifludwig.bsky.social, @elimereu.bsky.social, @larsplus.bsky.social & @alejofraticelli.bsky.social
Reposted by Artür Manukyan
📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...
Call for abstracts and registrations coming soon!
Call for abstracts and registrations coming soon!
scverse conference 2025
Follow us on our channels to learn more details in the coming weeks
scverse.org
May 12, 2025 at 10:47 PM
📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...
Call for abstracts and registrations coming soon!
Call for abstracts and registrations coming soon!
Reposted by Artür Manukyan
To supplement my students' learning, I made this brief explanation + demo on how to analyze #spatialtranscriptomics data to identify spatially variable genes using Moran's I #dataanalysis #Rstats
Code along: www.youtube.com/watch?v=aaAN...
#AcademicSky #codetutorials #Bioinformatics
Code along: www.youtube.com/watch?v=aaAN...
#AcademicSky #codetutorials #Bioinformatics
May 12, 2025 at 4:15 PM
To supplement my students' learning, I made this brief explanation + demo on how to analyze #spatialtranscriptomics data to identify spatially variable genes using Moran's I #dataanalysis #Rstats
Code along: www.youtube.com/watch?v=aaAN...
#AcademicSky #codetutorials #Bioinformatics
Code along: www.youtube.com/watch?v=aaAN...
#AcademicSky #codetutorials #Bioinformatics
Reposted by Artür Manukyan
Another semester done 🥳🥂
In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i...
#AcademicSky
In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i...
#AcademicSky
Jean Fan | Personal site
Personal website of Prof. Jean Fan
jean.fan
May 5, 2025 at 8:00 PM
Another semester done 🥳🥂
In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i...
#AcademicSky
In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i...
#AcademicSky
Reposted by Artür Manukyan
Time to join GESTALT – Global Alliance for Spatial Technologies – GESTALT – Global Alliance for Spatial Technologies
Together we do more …
www.nature.com/articles/s41...
globalspatial.org
Together we do more …
www.nature.com/articles/s41...
globalspatial.org
GESTALT – Global Alliance for Spatial Technologies – GESTALT – Global Alliance for Spatial Technologies
globalspatial.org
April 10, 2025 at 8:25 AM
Time to join GESTALT – Global Alliance for Spatial Technologies – GESTALT – Global Alliance for Spatial Technologies
Together we do more …
www.nature.com/articles/s41...
globalspatial.org
Together we do more …
www.nature.com/articles/s41...
globalspatial.org
Reposted by Artür Manukyan
⏰ Final Reminder — EuroBioC2025 abstract submissions close today, 24 April! Don't miss the chance to share your work in Barcelona this September. Submit here: eurobioc2025.bioconductor.org/pages/submis...
April 24, 2025 at 8:56 AM
⏰ Final Reminder — EuroBioC2025 abstract submissions close today, 24 April! Don't miss the chance to share your work in Barcelona this September. Submit here: eurobioc2025.bioconductor.org/pages/submis...
Reposted by Artür Manukyan
⏳ Time’s running out! Submit your abstract for #EuroBioC2025 by 24 April.
Join us this Sept in Barcelona to share your research, meet the #Bioconductor community & explore all things #Bioinformatics + #RStats.
👉 eurobioc2025.bioconductor.org/pages/submis...
Join us this Sept in Barcelona to share your research, meet the #Bioconductor community & explore all things #Bioinformatics + #RStats.
👉 eurobioc2025.bioconductor.org/pages/submis...
April 22, 2025 at 9:59 AM
⏳ Time’s running out! Submit your abstract for #EuroBioC2025 by 24 April.
Join us this Sept in Barcelona to share your research, meet the #Bioconductor community & explore all things #Bioinformatics + #RStats.
👉 eurobioc2025.bioconductor.org/pages/submis...
Join us this Sept in Barcelona to share your research, meet the #Bioconductor community & explore all things #Bioinformatics + #RStats.
👉 eurobioc2025.bioconductor.org/pages/submis...
Reposted by Artür Manukyan
Accurate cell segmentation remains a major issue for spatial transcriptomics.
Elyas Heidari and colleagues from the Gerstung, Pe'er and Stegle Labs released Segger, a new algorithm that uses GNN to model both transcripts and cells. More details in their preprint: www.biorxiv.org/content/10.1...
Elyas Heidari and colleagues from the Gerstung, Pe'er and Stegle Labs released Segger, a new algorithm that uses GNN to model both transcripts and cells. More details in their preprint: www.biorxiv.org/content/10.1...
Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data
The accurate assignment of transcripts to their cells of origin remains the Achilles heel of imaging-based spatial transcriptomics, despite being critical for nearly all downstream analyses. Current c...
www.biorxiv.org
March 17, 2025 at 12:06 PM
Accurate cell segmentation remains a major issue for spatial transcriptomics.
Elyas Heidari and colleagues from the Gerstung, Pe'er and Stegle Labs released Segger, a new algorithm that uses GNN to model both transcripts and cells. More details in their preprint: www.biorxiv.org/content/10.1...
Elyas Heidari and colleagues from the Gerstung, Pe'er and Stegle Labs released Segger, a new algorithm that uses GNN to model both transcripts and cells. More details in their preprint: www.biorxiv.org/content/10.1...
Reposted by Artür Manukyan
Postdoc - Statistics and machine learning with spatial omics and single-cell perturbation data
www.huber.embl.de/group/posts/...
www.huber.embl.de/group/posts/...
Postdoc - Statistics and machine learning with spatial omics and single-cell perturbation data – Huber Group @ EMBL
Precision Oncology and Multiomics
www.huber.embl.de
March 12, 2025 at 1:08 PM
Postdoc - Statistics and machine learning with spatial omics and single-cell perturbation data
www.huber.embl.de/group/posts/...
www.huber.embl.de/group/posts/...
Reposted by Artür Manukyan
STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance www.biorxiv.org/content/10....
March 12, 2025 at 2:15 PM
STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance www.biorxiv.org/content/10....
Reposted by Artür Manukyan
🧪 Finally!!! A single-cell atlas of the mouse seminal vesicle!!! (seriously though, it just might be the last major mammalian organ to undergo single cell sequencing). Check it out! pubmed.ncbi.nlm.nih.gov/40036847/#fu... @arturmansl.bsky.social @anashin.bsky.social @epididymosome.bsky.social
March 7, 2025 at 4:35 PM
🧪 Finally!!! A single-cell atlas of the mouse seminal vesicle!!! (seriously though, it just might be the last major mammalian organ to undergo single cell sequencing). Check it out! pubmed.ncbi.nlm.nih.gov/40036847/#fu... @arturmansl.bsky.social @anashin.bsky.social @epididymosome.bsky.social