Publications

See my Google Scholar or CV for a complete chronological list of publications.

Tissue and ex vivo cell atlases to dissect genetic drivers of human complex disease

Ota M., Spence J.P., Zeng T., Dann E., Marson A., Pritchard J.K. (2025) Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq. biorXiv | Full text

Dann E.*, Teeple E.*, Elmentaite R., Meyer K., Gaglia G., Nestle F., Savova V., Rinaldis E., Teichmann S.A. (2024) Estimating the impact of single-cell RNA sequencing of human tissues on drug target validation., medRxiv | Full text | code
^{*Equal Contribution}

Comparative methods and design of multi-condition single-cell genomics studies

Dann E., Cujba A.M., Oliver A.J., Meyer K., Teichmann S.A., Marioni J.C. (2023) Precise identification of cell states altered in disease with healthy single-cell references, Nature Genetics | Full text | code | python package

Dann E., Henderson N.C., Teichmann S.A., Morgan M.D., Marioni J.C. (2021) Differential abundance testing on single-cell data using k-nearest neighbor graphs, Nature Biotechnology | Full text | R package | python package

Heumos L., Ji Y., … , Dann E., … , Theis F.J. (2024) Pertpy: an end-to-end framework for perturbation analysis. biorXiv | Full text | python package

Missarova A., Dann E., … , J.C. Marioni (2024) Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome Biology | Full text | R package

Sumanaweera D., Suo C., Muraro D., Dann E., … , Teichmann S.A. (2023) Gene-level alignment of single cell trajectories. Nature Methods | Full text | python package

Lalchand V.*, Ravuri A.*, Dann E.*, … , Teichmann S.A., Lawrence N.D. (2022) Modelling Technical and Biological Effects in scRNA-seq data with Scalable GPLVMs. Proceedings of the 17th Machine Learning in Computational Biology meeting | Full text
^{*Equal Contribution}

Building the human cell atlas

Suo C.*, Dann E.*, … , Haniffa M., Teichmann S.A. (2022) Mapping the developing human immune system across organs. Science | Full text | code | data
^{*Equal Contribution}

Yayon N., Kedlian V., Boehme L., … , Dann E, … , Uhlmann V., Notarangelo L.D., Germain R.N., Radtke A.J., Marioni J.C., Taghon T., Teichmann S.A. (2024) A spatial human thymus cell atlas mapped to a continuous tissue axis. Nature | Full text

Oliver A.J., Ni H., … , Dann E., …, Elmentaite R., Teichmann S.A. (2024) Single-cell integration reveals metaplasia in inflammatory gut diseases. Nature | Full text

Barnes J. L., He P., … , Dann E., … , Teichmann S.A., Meyer K. B., Nikolic M. Z. (2022) Early human lung immune cell development and its role in epithelial cell fate. Science Immunology | Full text

He P., Lim K., Sun D., … , Dann E., … , Meyer K.B., Rawlins E.L. (2022) A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates, Cell | Full text

Botting R.A., Goh I., … , Dann E., … , Teichmann S.A. , Haniffa M. (2022) Multi-organ functions of yolk sac during human early development. biorXiv | Full text

Jardine L., Webb S., … , Dann E., … , Göttgens B., Roberts I., Teichmann S. and Haniffa M. (2021) Blood and immune development in human fetal bone marrow and Down syndrome, Nature | Full text

Elmentaite R., Kumasaka N., Roberts K., Fleming A., Dann E., … , James K.R., Teichmann S.A. (2021), Cells of the human intestinal tract mapped across space and time, Nature | Full text

Stephenson E., Reynolds G., Botting R.A., Calero-Nieto F.J., Morgan M.D., Tuong Z.K., Bach K., Sungnak W., … , Dann E., … , Duncan C.J.A, Smith K., Teichmann S.A., Clatworthy M.R., Marioni J.C., Gottgens B., Haniffa M. (2020) Single-cell multi-omics analysis of the immune response in COVID-19, Nature Medicine | Full text

Establishing best practices for single-cell analysis

Luecken M., Gigante S., Burkhardt D., Cannoodt R., … , Dann E., … , Saeys Y., Theis F., Krishnaswamy S. (2024) Defining and benchmarking open problems in single-cell analysis. Research Square | Full text

Heumos L., … Single-cell Best Practices Consortium, … , Theis F.J. (2023) Best practices for single-cell analysis across modalities. Nature Review Genetics | full text

Computational methods for single-cell multi-omics

Schuster V., Dann E., Krogh A., Teichmann S.A. (2023) multiDGD: A versatile deep generative model for multi-omics data. Nature Communications | Full text | python package

Suo C., Polanski K., Dann E., … , Tuong Z.K., Clatworthy M., Teichmann S.A. (2022) Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins, Nature Biotechnology | Full text | python package

Kleshchevnikov V., Shmatko A., Dann E., …, Stegle O., Bayraktar O.A. (2022) Cell2location maps fine-grained cell types in spatial transcriptomics. Nature Biotechnology | Full text | python package

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