Michal Slyper

SlideCNA: Spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data

SlideCNA detects spatial copy number alterations from Slide-seq data to identify sub-clones in metastatic breast cancer.

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

This study creates a single-nucleus and spatial transcriptomic atlas of the COVID-19 liver, revealing cellular and functional disruptions associated with organ damage.

Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis

Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)

SCHAF generates spatially resolved single-cell transcriptomes from H&E histology images using vision transformers and adversarial learning, showing good agreement with ground-truth data.

Accelerated cognitive decline in obese mouse model of Alzheimer's disease is linked to sialic acid-driven immune deregulation

This study shows that obesity accelerates cognitive decline in Alzheimer's mice via sialic acid-driven immune changes.

Intrinsic and extrinsic regulation of human fetal bone marrow haematopoiesis and perturbations in Down syndrome

This study uses single-cell RNA-sequencing to analyze fetal bone marrow development and identifies disruptions in hematopoiesis in Down syndrome.

Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution

The paper identifies obesity-related TREM2high macrophages in diabetic mouse and human kidney through single-cell transcriptomics and cross-species comparison.

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

ExSeq enables multiplexed RNA mapping at nanoscale resolution by expanding biological specimens for in situ sequencing.

Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq

Cumulus is a cloud-based framework for analyzing large-scale sc/snRNA-seq data, improving efficiency and scalability while maintaining result quality.

RAAS blockade, kidney disease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells

The paper examines ACE2 expression in kidney cells in relation to RAAS blockers and age/sex, finding age-related differences and associations with drug use.

A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors

The paper develops a toolbox for scRNA-Seq and snRNA-Seq of fresh and frozen human tumors, testing it across eight tumor types and optimizing protocols for different tissue characteristics.

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.

Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics

The paper uses single-cell RNA-Seq to assess kidney organoid reproducibility across iPSC lines and shows transplantation reduces off-target cells.

Decoding the development of the blood and immune systems during human fetal liver haematopoiesis

The paper uses single-cell transcriptomics to map hematopoiesis in human fetal liver, identifying cell differentiation trajectories and shifts in hematopoietic composition during development.

Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis

The paper was withdrawn due to the inclusion of confidential information about a third party.