About me 👩‍💻

I’m a PhD student in computational biology in the Cellular Genetics programme at the Wellcome Sanger Institute and the University of Cambridge, working between the groups of Sarah Teichmann and John Marioni.

I work on comparative analyses between single-cell datasets and efficient use of cell atlases, in the context of human development.

I like open source software, reproducible analyses, board games and slow movies.

Software 💻

miloR | MarioniLab/miloR | primary developer | R/Bioconductor package for the identification of differential cell abundance in KNN graphs for single-cell data

milopy | emdann/milopy | primary developer | python package for the identification of differential cell abundance in KNN graphs for single-cell data

cell2location | BayraktarLab/cell2location | contributor | python package for mapping of tissue cell types via integration of single cell RNA-seq and spatial transcriptomics data

SingleCellOpenProblems | singlecellopenproblems/SingleCellOpenProblems | contributor

Publications 📜

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

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

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, bioRxiv
Full text

💥 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

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

Beltran H., Romanel A., … , Dann E., … , Benelli M., and Demichelis F. (2020) Circulating Tumor DNA Profile Recognizes Transformation to Castration-Resistant Neuroendocrine Prostate Cancer, Journal of Clinical Investigation
Full text

Emma Dann


About me 👩‍💻

I’m a PhD student in computational biology in the Cellular Genetics programme at the Wellcome Sanger Institute and the University of Cambridge, working between the groups of Sarah Teichmann and John Marioni.

I work on comparative analyses between single-cell datasets and efficient use of cell atlases, in the context of human development.

I like open source software, reproducible analyses, board games and slow movies.

Software 💻

miloR | MarioniLab/miloR | primary developer | R/Bioconductor package for the identification of differential cell abundance in KNN graphs for single-cell data

milopy | emdann/milopy | primary developer | python package for the identification of differential cell abundance in KNN graphs for single-cell data

cell2location | BayraktarLab/cell2location | contributor | python package for mapping of tissue cell types via integration of single cell RNA-seq and spatial transcriptomics data

SingleCellOpenProblems | singlecellopenproblems/SingleCellOpenProblems | contributor

Publications 📜

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

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

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, bioRxiv
Full text

💥 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

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

Beltran H., Romanel A., … , Dann E., … , Benelli M., and Demichelis F. (2020) Circulating Tumor DNA Profile Recognizes Transformation to Castration-Resistant Neuroendocrine Prostate Cancer, Journal of Clinical Investigation
Full text