Linas Mažutis

Cell-in-drop genotyping detects megabase-scale loss of heterozygosity as a quantitative marker for CRISPR-Cas9 on-target toxicity

Hierarchical classification of immune cell transcriptomes at population-scale

The paper introduces Suco and Compocyte to classify immune cells from 3,965 patients, identifying new macrophage and monocyte states and T cell memory erosion in metastases.

High-throughput single cell -omics using semi-permeable capsules

This paper introduces a semi-permeable capsule technology for high-throughput single-cell -omics, demonstrating its utility in scRNA-Seq of hematopoietic disorders and uncovering transcriptome changes in AML.

Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer

The paper analyzes transcriptomic changes in metastatic pancreatic cancer using a patient's autopsy data to identify site-specific gene programs and clonal phylogeny.

Im-seq: Multimodal droplet barcoding enables high-throughput linking of single-cell imaging and gene expression

The paper introduces a method to link single-cell imaging and gene expression data through multimodal droplet barcoding, identifying genes correlated with phenotypic features.

Joint representation and visualization of derailed cell states with Decipher

Decipher is a deep generative model that integrates single-cell RNA-seq data to visualize and characterize transitions between normal and perturbed cell states across different diseases.

Scalable single-cell metagenomic analysis with Bascet and Zorn

This paper introduces Bascet and Zorn, tools for scalable single-cell metagenomic analysis, demonstrating their utility on mock and human saliva samples.

inDrops-2: a flexible, versatile and cost-efficient droplet microfluidics approach for high-throughput scRNA-seq of fresh and preserved clinical samples

The paper introduces inDrops-2, a cost-efficient scRNA-seq platform that profiles clinical samples with sensitivity comparable to commercial systems and demonstrates its utility in analyzing lung carcinoma samples.

Single Cell Analysis of Treatment-Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies

The paper uses single-cell analysis to study how cell surface antigen expression changes in treatment-resistant prostate cancer, revealing transcriptional heterogeneity and shared gene regulatory networks between NEPC and SCLC.

RNA cytometry of single-cells using semi-permeable microcapsules

This paper introduces a high-throughput RNA cytometry method using semi-permeable microcapsules to enable digital profiling of single-cell gene expression.

A unified atlas of CD8 T cell dysfunctional states in cancer and infection

The paper defines a shared differentiation trajectory of CD8 T cell dysfunction across cancer and infection using ATAC-seq and RNA-seq data from multiple studies.

AD-linked R47H-TREM2 mutation induces disease-enhancing proinflammatory microglial states in mice and humans

This study identifies R47H-TREM2 mutation-induced proinflammatory microglial states in human AD and tauopathy mice, showing Akt pathway involvement and potential therapeutic targets.

Palantir characterizes cell fate continuities in human hematopoiesis

Palantir models cell fate as a probabilistic process using entropy to analyze differentiation trajectories in human hematopoiesis, identifying key transcription factors and terminal states.

MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data

MAGIC improves single-cell RNA-seq data by imputing missing values and revealing gene-gene interactions through a diffusion-based method.