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