diff --git a/docs/notebooks/single_cell/02_2_1_scatac_multiome_pancreas_priors_train.ipynb b/docs/notebooks/single_cell/02_2_1_scatac_multiome_pancreas_priors_train.ipynb index 95a1aaa..1e2d62e 100644 --- a/docs/notebooks/single_cell/02_2_1_scatac_multiome_pancreas_priors_train.ipynb +++ b/docs/notebooks/single_cell/02_2_1_scatac_multiome_pancreas_priors_train.ipynb @@ -14,7 +14,7 @@ "source": [ "\n", "In this tutorial we demonstrate the applicability of mubind in a case where an arbitrarily complex graph is provided as a prior for the Graph Layer.\n", - "The utilized dataset is from mouse pancreatic endocrinogenesis multiome (paired scRNA- and scATAC-seq) {cite}pan:22 [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE275562)" + "The utilized dataset is from mouse pancreatic endocrinogenesis multiome (paired scRNA- and scATAC-seq) :cite:`Klein2023` [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE275562)" ] }, { diff --git a/docs/references.bib b/docs/references.bib index c901ccc..21d1aa8 100644 --- a/docs/references.bib +++ b/docs/references.bib @@ -27,3 +27,120 @@ @article{Rube2022 title = {Prediction of protein{\textendash}ligand binding affinity from sequencing data with interpretable machine learning}, journal = {Nature Biotechnology} } + + +@ARTICLE{Hochgerner2018, + title = "Conserved properties of dentate gyrus neurogenesis across + postnatal development revealed by single-cell {RNA} sequencing", + author = "Hochgerner, Hannah and Zeisel, Amit and L{\"o}nnerberg, Peter and + Linnarsson, Sten", + abstract = "The dentate gyrus of the hippocampus is a brain region in which + neurogenesis persists into adulthood; however, the relationship + between developmental and adult dentate gyrus neurogenesis has + not been examined in detail. Here we used single-cell RNA + sequencing to reveal the molecular dynamics and diversity of + dentate gyrus cell types in perinatal, juvenile, and adult mice. + We found distinct quiescent and proliferating progenitor cell + types, linked by transient intermediate states to neuroblast + stages and fully mature granule cells. We observed shifts in the + molecular identity of quiescent and proliferating radial glia and + granule cells during the postnatal period that were then + maintained through adult stages. In contrast, intermediate + progenitor cells, neuroblasts, and immature granule cells were + nearly indistinguishable at all ages. These findings demonstrate + the fundamental similarity of postnatal and adult neurogenesis in + the hippocampus and pinpoint the early postnatal transformation + of radial glia from embryonic progenitors to adult quiescent stem + cells.", + journal = "Nat. Neurosci.", + volume = 21, + number = 2, + pages = "290--299", + month = feb, + year = 2018, + language = "en" +} + + +@ARTICLE{Noack2022, + title = "Multimodal profiling of the transcriptional regulatory landscape + of the developing mouse cortex identifies Neurog2 as a key + epigenome remodeler", + author = "Noack, Florian and Vangelisti, Silvia and Raffl, Gerald and + Carido, Madalena and Diwakar, Jeisimhan and Chong, Faye and + Bonev, Boyan", + abstract = "How multiple epigenetic layers and transcription factors (TFs) + interact to facilitate brain development is largely unknown. + Here, to systematically map the regulatory landscape of neural + differentiation in the mouse neocortex, we profiled gene + expression and chromatin accessibility in single cells and + integrated these data with measurements of enhancer activity, DNA + methylation and three-dimensional genome architecture in purified + cell populations. This allowed us to identify thousands of new + enhancers, their predicted target genes and the temporal + relationships between enhancer activation, epigenome remodeling + and gene expression. We characterize specific neuronal + transcription factors associated with extensive and frequently + coordinated changes across multiple epigenetic modalities. In + addition, we functionally demonstrate a new role for Neurog2 in + directly mediating enhancer activity, DNA demethylation, + increasing chromatin accessibility and facilitating chromatin + looping in vivo. Our work provides a global view of the gene + regulatory logic of lineage specification in the cerebral cortex.", + journal = "Nat. Neurosci.", + volume = 25, + number = 2, + pages = "154--167", + month = feb, + year = 2022, + language = "en" +} + +@UNPUBLISHED{Klein2023, + title = "Mapping cells through time and space with moscot", + author = "Klein, Dominik and Palla, Giovanni and Lange, Marius and Klein, + Michal and Piran, Zoe and Gander, Manuel and Meng-Papaxanthos, + Laetitia and Sterr, Michael and Bastidas-Ponce, Aim{\'e}e and + Tarquis-Medina, Marta and Lickert, Heiko and Bakhti, Mostafa and + Nitzan, Mor and Cuturi, Marco and Theis, Fabian J", + abstract = "Single-cell genomics technologies enable multimodal profiling of + millions of cells across temporal and spatial dimensions. + Experimental limitations prevent the measurement of + all-encompassing cellular states in their native temporal + dynamics or spatial tissue niche. Optimal transport theory has + emerged as a powerful tool to overcome such constraints, enabling + the recovery of the original cellular context. However, most + algorithmic implementations currently available have not kept up + the pace with increasing dataset complexity, so that current + methods are unable to incorporate multimodal information or scale + to single-cell atlases. Here, we introduce multi-omics + single-cell optimal transport (moscot), a general and scalable + framework for optimal transport applications in single-cell + genomics, supporting multimodality across all applications. We + demonstrate moscot's ability to efficiently reconstruct + developmental trajectories of 1.7 million cells of mouse embryos + across 20 time points and identify driver genes for first heart + field formation. The moscot formulation can be used to transport + cells across spatial dimensions as well: To demonstrate this, we + enrich spatial transcriptomics datasets by mapping multimodal + information from single-cell profiles in a mouse liver sample, + and align multiple coronal sections of the mouse brain. We then + present moscot.spatiotemporal, a new approach that leverages gene + expression across spatial and temporal dimensions to uncover the + spatiotemporal dynamics of mouse embryogenesis. Finally, we + disentangle lineage relationships in a novel murine, + time-resolved pancreas development dataset using paired + measurements of gene expression and chromatin accessibility, + finding evidence for a shared ancestry between delta and epsilon + cells. Moscot is available as an easy-to-use, open-source python + package with extensive documentation at . \#\#\# Competing + Interest Statement F.J.T. consults for Immunai Inc., Singularity + Bio B.V., CytoReason Ltd, Cellarity, and Omniscope Ltd, and has + ownership interest in Dermagnostix GmbH and Cellarity. The + remaining authors declare no competing interests.", + journal = "bioRxiv", + pages = "2023.05.11.540374", + month = may, + year = 2023, + language = "en" +} diff --git a/docs/references.md b/docs/references.md index 6afee63..0f45dad 100644 --- a/docs/references.md +++ b/docs/references.md @@ -18,16 +18,19 @@ [BMC Bioinformatics](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04201-9) * **[Klein2023]** + Klein *et al.* (2023) *Klein, D. et al. Mapping cells through time and space with moscot.* [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2) * **[Hochgerner2018]** + Hochgerner *et al.* (2018) *Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing* [Nature Neuroscience](https://www.nature.com/articles/s41593-017-0056-2) * **[Noack2022]** + Noack *et al.* (2018) *Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler* [Nature Neuroscience](https://www.nature.com/articles/s41593-021-01002-4) \ No newline at end of file