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

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.

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

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...

STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport
->Nature | More from Lil Dr Glen EcoChat at BigEarthData.ai

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!

An Immuno-Linguistic Transformer for Multi-Scale Modeling of T-Cell Spatiotemporal Dynamics https://www.biorxiv.org/content/10.1101/2025.10.25.684555v1

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

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

Thank you for the wonderful opportunity to present here! Absolutely had a blast!

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.

🥂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

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.

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 🙏

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...

When 2 males have a baby that reaches adulthood
(mice with extensive genome editng))
www.cell.com/cell-stem-ce...

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...

wow! Atlas of the plasma proteome in health and disease in 53,026 adults

www.cell.com/cell/fulltex...

3D image of cardiomyocytes with high-throughput expansion microscopy

High-throughput expansion microscopy takes shape.
https://elifesciences.org/articles/96025?utm_source=bluesky&utm_medium=social&utm_campaign=organic

GitHub - jokergoo/rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions GREAT Analysis - Functional Enrichment on Genomic Regions - jokergoo/rGREAT

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 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...

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 - 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...

Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder - useful for 3D spatial transcriptomics www.nature.com/articles/s41...

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...

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

Unsupervised Deep Disentangled Representation of Single-Cell Omics www.biorxiv.org/content/10....

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm The molecular mechanisms that drive essential developmental patterning events in the mammalian embryo remain poorly understood. To generate a conceptual framework for gene regulatory processes during ...

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm www.biorxiv.org/content/10.1... #Epigenetics #Embryology #MouseDevelopment

detailed illustrations of arabidopsis roots showing the proposed effects of dPCD on plant-microbe interactions

How does programmed cell death and rapid corpse clearance of root cap cells affect their relationship with symbiotic organisms that want to colonise the roots?
https://buff.ly/49k4biq

A panoramic view of cell population dynamics in mammalian aging To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...

One more on #Aging
A panoramic view of cell population dynamics in mammalian aging

www.science.org/doi/10.1126/...

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling - Nature Biotechnology MultiPerturb-seq profiles gene expression and chromatin accessibility in single-cell pooled CRISPR screen.

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling www.nature.com/articles/s41...

Spatial transcriptomic landscape unveils immunoglobin-associated senescence as a hallmark of aging Spatial transcriptomic analysis of multiple tissues in male mice during aging identifies senescence-sensitive spots and immunoglobulin G accumulation as characteristic features of tissue aging and sug...

Spatial transcriptomic landscape unveils immunoglobin-associated senescence as a hallmark of aging www.cell.com/cell/fulltex... #Aging #SpatialTranscriptomics

Directionality of Transcriptional Regulatory Elements https://www.biorxiv.org/content/10.1101/2024.12.01.621925v1 Divergent transcription is a critical marker of active transcriptional regulatory elements (TREs), i

Directionality of Transcriptional Regulatory Elements https://www.biorxiv.org/content/10.1101/2024.12.01.621925v1

Assembloid models of cell-cell interaction to study tissue and disease biology Neurodevelopment involves the migration, projection, and integration of various cell types across different regions of the nervous system. Assembloids…

Assembloid models of cell-cell interaction to study tissue and disease biology www.sciencedirect.com/science/arti... #Assembloids #Organoids #stemcells

Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1 Mapping enhancers and their target genes in specific cell types is crucial for understanding gene re

Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1

Spatially restricted immune and microbiota-driven adaptation of the gut - Nature Intestinal regionalization is characterized by robust and resilient structural cell states and the intestine can adapt to environmental stress in a spatially controlled manner through crosstalk betwee...

#WeekendRead! #LocationLocationLocation! Amazing @Nature by @touficmayassi.bsky.social, Xavier &co showing regional specialization of the gut at the spatial (single cell) level! Strong resilience after inflammation & ILC2 are key in middle colon adaption to microbiota! www.nature.com/articles/s41...

I have constantly thought about this since I was a kid… #geology #poleshift #earth #magneticnorthpole #science

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...

Atlas of the plasma proteome in health and disease in 53,026 adults www.cell.com/cell/fulltex...