Julia Waldman

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.

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.

SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue

The paper develops a method for single nucleus RNA-Seq from FFPE tissues and applies it to a human lung adenocarcinoma sample.

Simultaneous single cell measurements of intranuclear proteins and gene expression

The paper introduces inCITE-seq, a method for simultaneous measurement of intranuclear proteins and gene expression in single cells, and demonstrates its application in analyzing neuronal activity in mouse brain tissue.

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.

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.

Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment

This study uses single-nucleus and spatial transcriptomics to analyze pancreatic cancer before and after neoadjuvant treatment, revealing changes in cell states and immune infiltration that may inform therapy.

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.

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

The paper introduces a method to multiplex single-nucleus RNA-seq using barcoded antibodies, reducing costs and enabling large-scale studies.

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.