references into notebooks (pancreas)

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)"
    ]
   },
   {

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"
+}

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)