Marcin Tabaka

Identifying multimodal molecular programs with mTopic.

This paper introduces mTopic, a topic modeling framework for analyzing multimodal molecular data across single-cell and spatial contexts, enabling identification of coherent molecular programs and cross-modality associations.

Ocelli: an open-source tool for the visualization of developmental multimodal single-cell data

Ocelli is a Python tool for visualizing developmental multimodal single-cell data using diffusion-based modeling, improving computational efficiency and low-dimensional representation quality.

spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content

spinDrop improves single-cell sequencing by reducing noise and increasing detection rates, enabling high-quality molecular atlases of mouse brain development and organogenesis.

A newly-recognized population of residual neural crest cells in the adult leptomeninges is re-activated for vascular repair

The paper identifies residual neural crest stem cells in adult mouse meninges that are reactivated for vascular repair after injury.

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.

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.

Genetic predisposition to myeloproliferative neoplasms implicates hematopoietic stem cell biology

This study identifies 14 genome-wide significant loci and a polygenic signature for myeloproliferative neoplasms, implicating hematopoietic stem cell function and self-renewal in disease risk.

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.

scSVA: an interactive tool for big data visualization and exploration in single-cell omics

scSVA provides a lightweight R package for interactive visualization and exploration of large single-cell omics datasets using efficient 3D embedding methods.

Genetic determinants of co-accessible chromatin regions in T cell activation across humans

The paper identifies genetic variants affecting chromatin accessibility in T cells and links them to gene expression and autoimmune disease.

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming.

Optimal transport converts a 65,781-cell reprogramming time course into probabilistic fates and trajectories, exposing alternative cell fates and a gene, Obox6, that improves reprogramming efficiency.