Monika Mohenska
@mmohenska.bsky.social
Bioinformatician at the Polo Lab. Interested in epigenetics and cell fate 🧬👩💻 Monash Biomedical Discovery Institute, Monash University, Adelaide Centre for Epigenetics, SAiGENCI, The University of Adelaide
Reposted by Monika Mohenska
Still my favorite 3D reconstruction of a pancreatic tissue.
Using the CODA workflow, we mapped a billion individual cells in 3D.
Red: pre-cancer lesions
Navy blue: ducts
Light blue: islets of Langerhans
Purple: acini
Green: blood vessels
Yellow: fat
More here: www.nature.com/articles/s41...
Using the CODA workflow, we mapped a billion individual cells in 3D.
Red: pre-cancer lesions
Navy blue: ducts
Light blue: islets of Langerhans
Purple: acini
Green: blood vessels
Yellow: fat
More here: www.nature.com/articles/s41...
November 20, 2025 at 6:34 PM
Still my favorite 3D reconstruction of a pancreatic tissue.
Using the CODA workflow, we mapped a billion individual cells in 3D.
Red: pre-cancer lesions
Navy blue: ducts
Light blue: islets of Langerhans
Purple: acini
Green: blood vessels
Yellow: fat
More here: www.nature.com/articles/s41...
Using the CODA workflow, we mapped a billion individual cells in 3D.
Red: pre-cancer lesions
Navy blue: ducts
Light blue: islets of Langerhans
Purple: acini
Green: blood vessels
Yellow: fat
More here: www.nature.com/articles/s41...
The TANK is almost in place!!! Get READY EMCRS!! #ABACBS2025 #bioinformatics #ai #computers #SharkTank
🎥 New teaser: 🦈 EMCR Shark Tank @ ABACBS 2025 (Adelaide Oval, Mon 24 Nov).
Level up your grant pitch with real-time feedback from our Sharks and compete for prizes.
Watch the video, then register: www.abacbs.org/sharktank2025
#ABACBS2025 #Bioinformatics #ResearchCareers #EMCR #Grants
Level up your grant pitch with real-time feedback from our Sharks and compete for prizes.
Watch the video, then register: www.abacbs.org/sharktank2025
#ABACBS2025 #Bioinformatics #ResearchCareers #EMCR #Grants
November 18, 2025 at 11:26 PM
The TANK is almost in place!!! Get READY EMCRS!! #ABACBS2025 #bioinformatics #ai #computers #SharkTank
Reposted by Monika Mohenska
Septins and the exocyst complex work together to guide membrane trafficking during cell division in fission yeast, revealing one of the most conserved functions of septins in exocytosis.
buff.ly/rkEfQZY
buff.ly/rkEfQZY
November 13, 2025 at 11:28 PM
Septins and the exocyst complex work together to guide membrane trafficking during cell division in fission yeast, revealing one of the most conserved functions of septins in exocytosis.
buff.ly/rkEfQZY
buff.ly/rkEfQZY
Reposted by Monika Mohenska
Multimodal learning enables chat-based exploration of single-cell data - @bocklab.bsky.social @cemm.oeaw.ac.at @meduniwien.ac.at go.nature.com/3WPGJnW
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
go.nature.com
November 11, 2025 at 4:58 PM
Multimodal learning enables chat-based exploration of single-cell data - @bocklab.bsky.social @cemm.oeaw.ac.at @meduniwien.ac.at go.nature.com/3WPGJnW
Reposted by Monika Mohenska
Late-Onset Preeclampsia is characterised by Accelerated Placental Aging https://www.biorxiv.org/content/10.1101/2025.11.12.687933v1
November 14, 2025 at 5:33 AM
Late-Onset Preeclampsia is characterised by Accelerated Placental Aging https://www.biorxiv.org/content/10.1101/2025.11.12.687933v1
Reposted by Monika Mohenska
A new AI model integrates single-cell and spatial transcriptomics data, enabling large-scale reconstruction of cell organization and interactions within tissues for advanced biological analysis. doi.org/g982z4
Foundation model reveals how cells are organized in tissues
Researchers at Helmholtz Munich and the Technical University of Munich (TUM) have developed Nicheformer, the first large-scale foundation model that integrates single-cell analysis with spatial transcriptomics.
phys.org
November 3, 2025 at 4:30 PM
A new AI model integrates single-cell and spatial transcriptomics data, enabling large-scale reconstruction of cell organization and interactions within tissues for advanced biological analysis. doi.org/g982z4
Get excited!! Jam packed week of bioinformatics, science and FUN! #ABACBS2025 #bioinformatics #AI #machinelearning #science conference of the season 💻🧬
Walkthrough of the conference centre ahead of #ABACBS2025 later this month. Bit overcast in Adelaide today but hoping for clear skies at the conference ☀️🕶️
November 13, 2025 at 4:56 AM
Get excited!! Jam packed week of bioinformatics, science and FUN! #ABACBS2025 #bioinformatics #AI #machinelearning #science conference of the season 💻🧬
Reposted by Monika Mohenska
A model of apical-out human first trimester trophoblast organoids to study regeneration after syncytial damage https://www.biorxiv.org/content/10.1101/2025.10.21.683405v1
October 22, 2025 at 9:31 PM
A model of apical-out human first trimester trophoblast organoids to study regeneration after syncytial damage https://www.biorxiv.org/content/10.1101/2025.10.21.683405v1
Reposted by Monika Mohenska
A new preprint from our lab is up on bioRxiv! We used trophoblast stem cell model to compare the innate immune response between LPS and IFNB between cell types and cell lines.
Trophoblast stem cells and syncytiotrophoblasts lack inflammatory responses to LPS but retain robust interferon-mediated antiviral immunity https://www.biorxiv.org/content/10.1101/2025.10.23.684222v1
October 27, 2025 at 1:48 PM
A new preprint from our lab is up on bioRxiv! We used trophoblast stem cell model to compare the innate immune response between LPS and IFNB between cell types and cell lines.
Reposted by Monika Mohenska
link 📈🤖
Spatially Regularized Gaussian Mixtures for Clustering Spatial Transcriptomic Data (Sottosanti, Risso, Denti) Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investi
Spatially Regularized Gaussian Mixtures for Clustering Spatial Transcriptomic Data (Sottosanti, Risso, Denti) Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investi
October 23, 2025 at 4:12 PM
link 📈🤖
Spatially Regularized Gaussian Mixtures for Clustering Spatial Transcriptomic Data (Sottosanti, Risso, Denti) Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investi
Spatially Regularized Gaussian Mixtures for Clustering Spatial Transcriptomic Data (Sottosanti, Risso, Denti) Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investi
Reposted by Monika Mohenska
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport
->Nature | More from Lil Dr Glen EcoChat at BigEarthData.ai
->Nature | More from Lil Dr Glen EcoChat at BigEarthData.ai
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport
Zebrafish For the training and validation sets, we used the five first time points shown in Fig. 2a of the original publication6: 3.3 hpf slice 1, 5.25 hpf slice 10, 10 hpf slice 11, 12 hpf slice 8 and 18...
www.nature.com
November 4, 2025 at 10:01 AM
Reposted by Monika Mohenska
Our Genome Biology paper on wheat spike development integrating single cell and spatial transcriptomics is now published! Check out the paper here: doi.org/10.1186/s130... and enjoy the beautiful pictures (including our 44 supplementary figures)! Be sure to check out some of our tools below!
October 13, 2025 at 7:04 PM
Our Genome Biology paper on wheat spike development integrating single cell and spatial transcriptomics is now published! Check out the paper here: doi.org/10.1186/s130... and enjoy the beautiful pictures (including our 44 supplementary figures)! Be sure to check out some of our tools below!
Reposted by Monika Mohenska
An Immuno-Linguistic Transformer for Multi-Scale Modeling of T-Cell Spatiotemporal Dynamics https://www.biorxiv.org/content/10.1101/2025.10.25.684555v1
October 27, 2025 at 5:47 PM
An Immuno-Linguistic Transformer for Multi-Scale Modeling of T-Cell Spatiotemporal Dynamics https://www.biorxiv.org/content/10.1101/2025.10.25.684555v1
Reposted by Monika Mohenska
New 3D reconstructions of Drosophila sensory neurons reveal striking diversity in dendrite shape, even among neurons of the same type. These findings open up new questions about how neuron structure relates to sensory function.
buff.ly/dfRVVsm
buff.ly/dfRVVsm
August 21, 2025 at 1:44 PM
New 3D reconstructions of Drosophila sensory neurons reveal striking diversity in dendrite shape, even among neurons of the same type. These findings open up new questions about how neuron structure relates to sensory function.
buff.ly/dfRVVsm
buff.ly/dfRVVsm
Reposted by Monika Mohenska
We're excited to highlight the EMCR Shark Tank 🦈 A new event to be held as part of the ABACBS 2025
Level up your grant pitch & get real-time feedback from leading "Sharks" — with a prize to be won! Details ➜: lnkd.in/gffKiu3h
#Bioinformatics #ResearchCareers #EMCR #Grants #ABACBS
Level up your grant pitch & get real-time feedback from leading "Sharks" — with a prize to be won! Details ➜: lnkd.in/gffKiu3h
#Bioinformatics #ResearchCareers #EMCR #Grants #ABACBS
August 15, 2025 at 4:51 AM
We're excited to highlight the EMCR Shark Tank 🦈 A new event to be held as part of the ABACBS 2025
Level up your grant pitch & get real-time feedback from leading "Sharks" — with a prize to be won! Details ➜: lnkd.in/gffKiu3h
#Bioinformatics #ResearchCareers #EMCR #Grants #ABACBS
Level up your grant pitch & get real-time feedback from leading "Sharks" — with a prize to be won! Details ➜: lnkd.in/gffKiu3h
#Bioinformatics #ResearchCareers #EMCR #Grants #ABACBS
Thank you for the wonderful opportunity to present here! Absolutely had a blast!
We hope you’re loving #ozsinglecell2025. Some amazing single cell science and technology on display!
May 25, 2025 at 5:18 AM
Thank you for the wonderful opportunity to present here! Absolutely had a blast!
Reposted by Monika Mohenska
🥂Congratulations to Petropoulos & co for their new Open Access study in our journal (@naturecellbiology.bsky.social): single-cell #transcriptomics, spatial, functional and comparative analyses show that the guinea pig presents high similarity with early human #embryogenesis.
bit.ly/3RaRwWY
bit.ly/3RaRwWY
The guinea pig serves as an alternative model to study human preimplantation development - Nature Cell Biology
Petropoulos and colleagues perform single-cell transcriptomics, spatial, functional and comparative analyses, and show that the guinea pig presents high similarity with early human embryogenesis.
bit.ly
April 9, 2025 at 8:21 PM
🥂Congratulations to Petropoulos & co for their new Open Access study in our journal (@naturecellbiology.bsky.social): single-cell #transcriptomics, spatial, functional and comparative analyses show that the guinea pig presents high similarity with early human #embryogenesis.
bit.ly/3RaRwWY
bit.ly/3RaRwWY
Reposted by Monika Mohenska
Out in @natureneuro.bsky.social today 🥂
Cytoarchitecture, wiring and signal flow of the human default mode network
Combining 3D histology, 7T MRI, and connectomics to explore DMN structure-function associations
Led by Casey Paquola, @themindwanders.bsky.social & a terrific team of colleagues 🙏
Cytoarchitecture, wiring and signal flow of the human default mode network
Combining 3D histology, 7T MRI, and connectomics to explore DMN structure-function associations
Led by Casey Paquola, @themindwanders.bsky.social & a terrific team of colleagues 🙏
The architecture of the human default mode network explored through cytoarchitecture, wiring and signal flow - Nature Neuroscience
The default mode network (DMN) is implicated in cognition and behavior. Here, the authors show that the DMN is cytoarchitecturally heterogeneous, it contains regions receptive to input from the sensory cortex and a core relatively insulated from environmental input, and it uniquely balances its output across sensory hierarchies.
www.nature.com
January 28, 2025 at 2:24 PM
Out in @natureneuro.bsky.social today 🥂
Cytoarchitecture, wiring and signal flow of the human default mode network
Combining 3D histology, 7T MRI, and connectomics to explore DMN structure-function associations
Led by Casey Paquola, @themindwanders.bsky.social & a terrific team of colleagues 🙏
Cytoarchitecture, wiring and signal flow of the human default mode network
Combining 3D histology, 7T MRI, and connectomics to explore DMN structure-function associations
Led by Casey Paquola, @themindwanders.bsky.social & a terrific team of colleagues 🙏
Reposted by Monika Mohenska
When 2 males have a baby that reaches adulthood
(mice with extensive genome editng))
www.cell.com/cell-stem-ce...
(mice with extensive genome editng))
www.cell.com/cell-stem-ce...
Adult bi-paternal offspring generated through direct modification of imprinted genes in mammals
Li and colleagues successfully generated bi-paternal mice that developed to adulthood
by targeting 20 key imprinted loci. This study underscores imprinting gene abnormalities
as the primary barrier to...
www.cell.com
January 28, 2025 at 4:50 PM
When 2 males have a baby that reaches adulthood
(mice with extensive genome editng))
www.cell.com/cell-stem-ce...
(mice with extensive genome editng))
www.cell.com/cell-stem-ce...
wow! Atlas of the plasma proteome in health and disease in 53,026 adults
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Atlas of the plasma proteome in health and disease in 53,026 adults
A large-scale proteomics study involving 53,026 individuals maps 2,920 plasma proteins
to 406 prevalent diseases, 660 incident diseases, and 986 health-related traits, identifying
promising biomarkers...
www.cell.com
January 29, 2025 at 12:34 PM
wow! Atlas of the plasma proteome in health and disease in 53,026 adults
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Monika Mohenska
High-throughput expansion microscopy takes shape.
https://elifesciences.org/articles/96025?utm_source=bluesky&utm_medium=social&utm_campaign=organic
https://elifesciences.org/articles/96025?utm_source=bluesky&utm_medium=social&utm_campaign=organic
January 28, 2025 at 9:01 PM
High-throughput expansion microscopy takes shape.
https://elifesciences.org/articles/96025?utm_source=bluesky&utm_medium=social&utm_campaign=organic
https://elifesciences.org/articles/96025?utm_source=bluesky&utm_medium=social&utm_campaign=organic
Great to see GREAT (Genomic Regions Enrichment of Annotations Tool) in R github.com/jokergoo/rGR...
GitHub - jokergoo/rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions
GREAT Analysis - Functional Enrichment on Genomic Regions - jokergoo/rGREAT
github.com
January 22, 2025 at 4:02 AM
Great to see GREAT (Genomic Regions Enrichment of Annotations Tool) in R github.com/jokergoo/rGR...
Modeling early gastrulation in human blastoids with DNA methylation patterns of natural blastocysts www.cell.com/cell-stem-ce...
Modeling early gastrulation in human blastoids with DNA methylation patterns of natural blastocysts
Xie et al. generate 4CL blastoids with morphology, transcriptional profiles, and DNA
methylation patterns similar to those of blastocysts while maintaining gene imprinting
and showing potential for po...
www.cell.com
January 20, 2025 at 5:28 AM
Modeling early gastrulation in human blastoids with DNA methylation patterns of natural blastocysts www.cell.com/cell-stem-ce...
Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder - useful for 3D spatial transcriptomics www.nature.com/articles/s41...
Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder - Nature Communications
Breakthrough technologies for spatially resolved transcriptomics have enabled genome-wide profiling of gene expressions in captured locations. Here the authors integrate gene expressions and spatial l...
www.nature.com
January 5, 2025 at 11:12 PM
Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder - useful for 3D spatial transcriptomics www.nature.com/articles/s41...
ESC, TSC, XEN, EPISC regulation in mouse: Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression
www.biorxiv.org/content/10.1... #epigenetics #3dchrom
www.biorxiv.org/content/10.1... #epigenetics #3dchrom
Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expressi...
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages, the trophectoderm (TE), the epiblast (EPI) and the primitive endoderm (PrE...
www.biorxiv.org
December 15, 2024 at 11:48 PM
ESC, TSC, XEN, EPISC regulation in mouse: Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression
www.biorxiv.org/content/10.1... #epigenetics #3dchrom
www.biorxiv.org/content/10.1... #epigenetics #3dchrom