Publications
Publications of 2023
The works of 2023 by the lab's members during their time here, from their ORCID records, Crossref and Europe PMC.
51 publications9 preprintsLater: 2024Earlier: 2022All publications
202351 publications
Topic: Benchmarks and best practices Deep Learning-Based Retinal Layer Segmentation in Optical Coherence Tomography Scans of Patients with Inherited Retinal Diseases
Exploratory electronic health record analysis with ehrapy
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis
Modeling fragment counts improves single-cell ATAC-seq analysis
Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus
Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies
A reversible state of hypometabolism in a human cellular model of sporadic Parkinson’s disease
flowVI: Flow Cytometry Variational Inference
Reporting electricity consumption is essential for sustainable AI
Human pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors
Reconstructing disease dynamics for mechanistic insights and clinical benefit
Scaling cross-tissue single-cell annotation models
Population-level integration of single-cell datasets enables multi-scale analysis across samples
Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment
Systematic analysis of drug combinations against Gram-positive bacteria
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
Identification of cell types, states and programs by learning gene set representations
Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis
A spatially resolved extracellular matrix proteome atlas of the distal human lung
Multi-omics regulatory network inference in the presence of missing data
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel
Distinct molecular profiles of skull bone marrow in health and neurological disorders
Progressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS
The neglected twin: Nummular eczema is a variant of atopic dermatitis with codominant TH2/TH17 immune response
Gene Expression–Based Molecular Test as Diagnostic Aid for the Differential Diagnosis of Psoriasis and Eczema in Formalin-Fixed and Paraffin-Embedded Tissue, Microbiopsies, and Tape Strips
hadge: a comprehensive pipeline for donor deconvolution in single cell
Unified fate mapping in multiview single-cell data
Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation
OME-Zarr: a cloud-optimized bioimaging file format with international community support
scARE: Attribution Regularization for Single Cell Representation Learning
Single-cell reference mapping to construct and extend cell-type hierarchies
Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome
Single‐cell biology: what does the future hold?
CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data
Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease
What do you most hope spatial molecular profiling will help us understand? Part 1
An integrated cell atlas of the lung in health and disease
394 Gene expression based molecular test proves clinical validity as diagnostic aid for the differential diagnosis of psoriasis and eczema in formalin fixed and paraffin embedded tissue
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps
Deciphering subcellular organization with multiplexed imaging and deep learning
Predicting cellular responses to complex perturbations in high‐throughput screens
The scverse project provides a computational ecosystem for single-cell omics data analysis
Epicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease
Best practices for single-cell analysis across modalities
Single-cell profiling to explore pancreatic cancer heterogeneity, plasticity and response to therapy
Synthetic enforcement of STING signaling in cancer cells appropriates the immune microenvironment for checkpoint inhibitor therapy
HBV rewires liver cancer signaling by altering PP2A complexes
Biologically informed deep learning to query gene programs in single-cell atlases
B-Cos Aligned Transformers Learn Human-Interpretable Features