Publications
Highlighted projects with more detail are on the Projects page. This is the full list.
- Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases. Nature Biotechnology, 2026. (corresponding author)
- Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states. Cell Systems, 2026. (corresponding author)
- AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents. arXiv, 2026.
- TGFb signaling instructs a conserved fibrosis-associated cell state marked by LRRC15. PNAS, 2026.
- Identification of markers for the isolation of neuron-specific extracellular vesicles. Nature Neuroscience, 2026.
- A cell atlas foundation model for scalable search of similar human cells. Nature, 2025. (first author)
- Considerations for building and using integrated single-cell atlases. Nature Methods, 2025.
- Inferring cellular communication through mapping cells in space using Tangram 2. bioRxiv, in review, Nature Methods, 2025.
- COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature, 2021. (co-first author)
- Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine, 2021. (co-first author)
- Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Reports Medicine, 2021.
- Low dimensionality in gene expression data enables the accurate extraction of transcriptional programs from shallow sequencing. Cell Systems, 2016. (first author)
- Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise. Cell Systems, 2015.