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

Zhu R.*, Dann E.*, Yan J., Retana J.R., Goto R., … , Pritchard J.K., Marson A. (2025) Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits. bioRxiv | Full text | code | data
^{*Equal Contribution}

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

Pett J.P., Prete M., Pham D., England N., … , Dann E., … , Teichmann S.A., Meyer K. (2025) An atlas of TF driven gene programs across human cells. bioRxiv | Full text

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

Deconinck L, Zappia L, Cannoodt R, Morgan M, scverse core, … , Saeys Y. (2025) anndataR improves interoperability between R and Python in single-cell transcriptomics. bioRxiv | Full text

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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