updated references

theislab · Aug 26, 2024 · cddac32 · cddac32
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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
@@ -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:`Klein2023` [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE275562)"
+    "The studied dataset is mouse pancreatic endocrinogenesis multiome (paired scRNA- and scATAC-seq) {cite}`Klein2023`. Raw data available in [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE275562)"
    ]
   },
   {

diff --git a/docs/notebooks/single_cell/02_2_1_scrna_dentategyrus_train.ipynb b/docs/notebooks/single_cell/02_2_1_scrna_dentategyrus_train.ipynb
@@ -8,6 +8,13 @@
     "## Dentate gyrus (scRNA-seq) | Training with an RNA-dynamics kNN-graph"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The studied dataset for this tutorial is dentate gyrus (10X Genomics) {cite}`Hochgerner2018`, and it is loaded directly from `scvelo.datasets`."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 231,

diff --git a/docs/notebooks/single_cell/02_2_1_scrna_noack_priors_train.ipynb b/docs/notebooks/single_cell/02_2_1_scrna_noack_priors_train.ipynb
@@ -8,6 +8,13 @@
     "## Mouse neurogenesis scRNA-seq (Noack et al. 2022) | Training with an RNA-dynamics kNN-graph\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The studied dataset for this tutorial is mouse neurogenesis scRNA-seq {cite}`Noack2022`."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

diff --git a/docs/references.bib b/docs/references.bib
@@ -29,7 +29,7 @@ @article{Rube2022
 }
 
 
-@ARTICLE{Hochgerner2018,
+@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
@@ -52,6 +52,7 @@ @ARTICLE{Hochgerner2018
               the hippocampus and pinpoint the early postnatal transformation
               of radial glia from embryonic progenitors to adult quiescent stem
               cells.",
+  url = {https://doi.org/10.1038/s41593-017-0056-2},
   journal  = "Nat. Neurosci.",
   volume   =  21,
   number   =  2,
@@ -62,7 +63,7 @@ @ARTICLE{Hochgerner2018
 }
 
 
-@ARTICLE{Noack2022,
+@article{Noack2022,
   title    = "Multimodal profiling of the transcriptional regulatory landscape
               of the developing mouse cortex identifies Neurog2 as a key
               epigenome remodeler",
@@ -88,6 +89,7 @@ @ARTICLE{Noack2022
               looping in vivo. Our work provides a global view of the gene
               regulatory logic of lineage specification in the cerebral cortex.",
   journal  = "Nat. Neurosci.",
+  url = {https://doi.org/10.1038/s41593-021-01002-4},
   volume   =  25,
   number   =  2,
   pages    = "154--167",
@@ -96,7 +98,7 @@ @ARTICLE{Noack2022
   language = "en"
 }
 
-@UNPUBLISHED{Klein2023,
+@article{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,
@@ -138,6 +140,7 @@ @UNPUBLISHED{Klein2023
               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.",
+  url = {https://doi.org/10.1101/2023.05.11.540374},
   journal  = "bioRxiv",
   pages    = "2023.05.11.540374",
   month    =  may,