Rene V. Sit

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models

X-Cell predicts causal perturbation responses across diverse cellular contexts using a diffusion language model trained on a large CRISPRi Perturb-seq dataset.

Major cell type differences between larval and adult hemichordate body plans

The paper examines cellular changes during metamorphosis in hemichordates using single-cell RNA sequencing, revealing distinct transcriptional programs between larval and adult stages.

Fate mapping of peripherally derived macrophages reveals a long-lasting engrafted population that maintains a distinct transcriptomic profile for up to 8 months after Traumatic Brain Injury

This study tracks the fate of monocyte-derived macrophages (MDMs) after traumatic brain injury (TBI) and finds they persist in the brain for up to 8 months, maintaining a distinct transcriptomic profile and phagocytic activity.

X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models

The paper introduces a scalable Perturb-seq platform called FiCS Perturb-seq and releases X-Atlas/Orion, a large Perturb-seq atlas, to improve foundation model development through dose-dependent genetic effects.

Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism

The paper creates a comprehensive cell atlas of mouse lemurs using single-cell RNA sequencing, identifying over 750 cell types and comparing their molecular profiles to humans, mice, and macaques.

Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples

This study optimizes whole-genome sequencing of Plasmodium falciparum from low-density dried blood spots by evaluating DNA extraction, digestion, and amplification methods.

Molecular characterization of selectively vulnerable neurons in Alzheimer's Disease

The paper identifies molecular signatures of selectively vulnerable neurons in Alzheimer's Disease using single-nucleus RNA sequencing and validates findings with neuropathological methods.

A molecular cell atlas of the human lung from single cell RNA sequencing

The paper creates a comprehensive molecular cell atlas of the human lung using single-cell RNA sequencing, identifying 58 cell populations including 14 new types and revealing evolutionary changes in lung cell types.

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.

Single Cell RNAseq Reveals A Critical Role of Chloride Channels in Airway Development

This study uses single-cell RNAseq to identify chloride channel roles in airway development, showing their impact on differentiation and disease-like defects.

The murine transcriptome reveals global aging nodes with organ-specific phase and amplitude

The paper analyzes aging dynamics across 17 organs and plasma proteomics in mice, revealing consistent gene expression trajectories with organ-specific timing and amplitude.

Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris

The paper creates a single-cell transcriptomic atlas of 20 mouse organs and tissues, providing a resource for studying gene expression across cell types.