Updated publications

Author: Pseudomanifold

config.toml

@@ -17,6 +17,9 @@ ignoreFiles = ['publications.md$']
   [markup.goldmark.extensions]
     typographer = true
 
+  [markup.tableOfContents]
+    endLevel = 3
+
 [[menu.main]]
   name    = "Welcome"
   pageRef = "/"

content/publications.md

@@ -1,5 +1,9 @@
 ### 2025
 
+- [*Defining and Benchmarking Open Problems in Single-Cell Analysis*](https://dx.doi.org/10.1038/s41587-025-02694-w)<br />
+M.&thinsp;D.&nbsp;Luecken<sup>&dagger;</sup>, S.&nbsp;Gigante<sup>&dagger;</sup>, D.&thinsp;B.&nbsp;Burkhardt<sup>&dagger;</sup>, R.&nbsp;Cannoodt<sup>&dagger;</sup>, D.&thinsp;C.&nbsp;Strobl, N.&thinsp;S.&nbsp;Markov, L.&nbsp;Zappia, G.&nbsp;Palla, W.&nbsp;Lewis, D.&nbsp;Dimitrov, M.&thinsp;E.&nbsp;Vinyard, D.&thinsp;S.&nbsp;Magruder, M.&thinsp;F.&nbsp;Mueller, A.&nbsp;Andersson, E.&nbsp;Dann, Q.&nbsp;Qin, D.&thinsp;J.&nbsp;Otto, M.&nbsp;Klein, O.&thinsp;B.&nbsp;Botvinnik, L.&nbsp;Deconinck, K.&nbsp;Waldrant, S.&thinsp;N.&nbsp;Yasa, A.&nbsp;Szałata, A.&nbsp;Benz, Z.&nbsp;Li, O.&thinsp;P.&nbsp;Members, B.&nbsp;Rieck, C.&nbsp;Ahlmann-Eltze, E.&nbsp;da Veiga Beltrame, C.&thinsp;B.&nbsp;González-Blas, A.&thinsp;T.&nbsp;Chen, B.&nbsp;DeMeo, C.&nbsp;Ergen, S.&nbsp;Floc'hlay, A.&nbsp;Gayoso, S.&nbsp;Hicks, Y.&nbsp;Ji, V.&nbsp;Kleshchevnikov, G.&nbsp;La Manno, M.&thinsp;G.&nbsp;Lombardo, R.&nbsp;Lopez, D.&nbsp;Righelli, H.&nbsp;Sarkar, V.&nbsp;Svensson, A.&nbsp;Tong, G.&nbsp;Xing, C.&nbsp;Xu, J.&thinsp;M.&nbsp;Bloom, A.&thinsp;O.&nbsp;Pisco, J.&nbsp;Saez-Rodriguez, D.&nbsp;Wulsin, L.&nbsp;Pinello, Y.&nbsp;Saeys, F.&thinsp;J.&nbsp;Theis<sup>&Dagger;</sup>, and S.&nbsp;Krishnaswamy<sup>&Dagger;</sup><br />
+Nature Biotechnology, 2025<br />
+        <small>[\[BibTeX\]](Luecken25a.bib)</small>
 - [*Geometry-Aware Edge Pooling for Graph Neural Networks*](https://arxiv.org/abs/2506.11700)<br />
 K.&nbsp;Limbeck<sup>&dagger;</sup>, L.&nbsp;Mezrag<sup>&dagger;</sup>, G.&nbsp;Wolf<sup>&Dagger;</sup>, and B.&nbsp;Rieck<sup>&Dagger;</sup><br />
 Preprint, 2025<br />
@@ -24,7 +28,7 @@ Preprint, 2025<br />
 D.&nbsp;Bhaskar<sup>&dagger;</sup>, Y.&nbsp;Zhang<sup>&dagger;</sup>, J.&nbsp;Moore, F.&nbsp;Gao, B.&nbsp;Rieck, G.&nbsp;Wolf, F.&nbsp;Khasawneh, E.&nbsp;Munch, J.&thinsp;A.&nbsp;Noah, H.&nbsp;Pushkarskaya, C.&nbsp;Pittenger, V.&nbsp;Greco, and S.&nbsp;Krishnaswamy<br />
 Preprint, 2025<br />
         <small>[\[Preprint\]](https://biorxiv.org/content/10.1101/2023.03.22.533807v3) &bull; [\[BibTeX\]](Bhaskar25a.bib)</small>
-- [*Characterizing Physician Referral Networks With Ricci Curvature*](https://arxiv.org/abs/2408.16022)<br />
+- [*Characterizing Physician Referral Networks With Ricci Curvature*](https://dx.doi.org/10.1007/978-3-031-88346-0_1)<br />
 J.&nbsp;Wayland, R.&thinsp;J.&nbsp;Funk, and B.&nbsp;Rieck<br />
 Pediatric and Lifespan Data Science, pp. 1--16, 2025<br />
         <small>[\[Preprint\]](https://arxiv.org/abs/2408.16022) &bull; [\[BibTeX\]](Wayland25a.bib)</small>
@@ -293,7 +297,7 @@ S.&nbsp;Horoi<sup>&dagger;</sup>, J.&nbsp;Huang<sup>&dagger;</sup>, B.&nbsp;Riec
 Montreal AI Symposium, 2021<br />
         <small>[\[BibTeX\]](Horoi21a.bib)</small>
 - [*A Sandbox for Prediction and Integration of DNA, RNA, and Proteins in Single Cells*](https://openreview.net/forum?id=gN35BGa1Rt)<br />
-M.&thinsp;D.&nbsp;Lücken<sup>&dagger;</sup>, D.&thinsp;B.&nbsp;Burkhardt<sup>&dagger;</sup>, R.&nbsp;Cannoodt<sup>&dagger;</sup>, C.&nbsp;Lance<sup>&dagger;</sup>, A.&nbsp;Agrawal, H.&nbsp;Aliee, A.&thinsp;T.&nbsp;Chen, L.&nbsp;Deconinck, A.&thinsp;M.&nbsp;Detweiler, A.&thinsp;A.&nbsp;Granados, S.&nbsp;Huynh, L.&nbsp;Isacco, Y.&thinsp;J.&nbsp;Kim, B.&nbsp;De Kumar, S.&nbsp;Kuppasani, H.&nbsp;Lickert, A.&nbsp;McGeever, J.&thinsp;C.&nbsp;Melgarejo, H.&nbsp;Mekonen, M.&nbsp;Morri, M.&nbsp;Müller, N.&nbsp;Neff, S.&nbsp;Paul, B.&nbsp;Rieck, K.&nbsp;Schneider, S.&nbsp;Steelman, M.&nbsp;Sterr, D.&thinsp;J.&nbsp;Treacy, A.&nbsp;Tong, A.&nbsp;Villani, G.&nbsp;Wang, J.&nbsp;Yan, C.&nbsp;Zhang, A.&thinsp;O.&nbsp;Pisco<sup>&Dagger;</sup>, S.&nbsp;Krishnaswamy<sup>&Dagger;</sup>, F.&thinsp;J.&nbsp;Theis<sup>&Dagger;</sup>, and J.&thinsp;M.&nbsp;Bloom<sup>&Dagger;</sup><br />
+M.&thinsp;D.&nbsp;Luecken<sup>&dagger;</sup>, D.&thinsp;B.&nbsp;Burkhardt<sup>&dagger;</sup>, R.&nbsp;Cannoodt<sup>&dagger;</sup>, C.&nbsp;Lance<sup>&dagger;</sup>, A.&nbsp;Agrawal, H.&nbsp;Aliee, A.&thinsp;T.&nbsp;Chen, L.&nbsp;Deconinck, A.&thinsp;M.&nbsp;Detweiler, A.&thinsp;A.&nbsp;Granados, S.&nbsp;Huynh, L.&nbsp;Isacco, Y.&thinsp;J.&nbsp;Kim, B.&nbsp;De Kumar, S.&nbsp;Kuppasani, H.&nbsp;Lickert, A.&nbsp;McGeever, J.&thinsp;C.&nbsp;Melgarejo, H.&nbsp;Mekonen, M.&nbsp;Morri, M.&nbsp;Müller, N.&nbsp;Neff, S.&nbsp;Paul, B.&nbsp;Rieck, K.&nbsp;Schneider, S.&nbsp;Steelman, M.&nbsp;Sterr, D.&thinsp;J.&nbsp;Treacy, A.&nbsp;Tong, A.&nbsp;Villani, G.&nbsp;Wang, J.&nbsp;Yan, C.&nbsp;Zhang, A.&thinsp;O.&nbsp;Pisco<sup>&Dagger;</sup>, S.&nbsp;Krishnaswamy<sup>&Dagger;</sup>, F.&thinsp;J.&nbsp;Theis<sup>&Dagger;</sup>, and J.&thinsp;M.&nbsp;Bloom<sup>&Dagger;</sup><br />
 Advances in Neural Information Processing
 Systems&nbsp;(Datasets and Benchmarks Track), 2021<br />
         <small>[\[BibTeX\]](Luecken21a.bib)</small>

content/research.md

@@ -39,4 +39,4 @@ Here is a collection of tools that have been developed by the AIDOS Lab, in orde
 Here are all publications of lab members, sorted by year. Publications
 appear in the order in which they are accepted.
 
-{{< include "publications.md" "publications" >}}
+{{% include "publications.md" "publications" %}}

static/research/Luecken21a.bib

@@ -1,5 +1,5 @@
 @inproceedings{Luecken21a,
-	author = {Malte D. L{\"u}cken and Daniel Bernard Burkhardt and
+	author = {Malte D. Luecken and Daniel Bernard Burkhardt and
 Robrecht Cannoodt and Christopher Lance and Aditi
 Agrawal and Hananeh Aliee and Ann T. Chen and Louise
 Deconinck and Angela M. Detweiler and Alejandro A.

static/research/Luecken25a.bib

@@ -0,0 +1,10 @@
+@article{Luecken25a,
+	author = {Luecken, Malte D. and Gigante, Scott and Burkhardt, Daniel B. and Cannoodt, Robrecht and Strobl, Daniel C. and Markov, Nikolay S. and Zappia, Luke and Palla, Giovanni and Lewis, Wesley and Dimitrov, Daniel and Vinyard, Michael E. and Magruder, D. S. and Mueller, Michaela F. and Andersson, Alma and Dann, Emma and Qin, Qian and Otto, Dominik J. and Klein, Michal and Botvinnik, Olga Borisovna and Deconinck, Louise and Waldrant, Kai and Yasa, Sai Nirmayi and Sza{\l}ata, Artur and Benz, Andrew and Li, Zhijian and {Open Problems Jamboree Members} and Rieck, Bastian and Ahlmann-Eltze, Constantin and da Veiga Beltrame, Eduardo and Bravo Gonz{\'a}lez-Blas, Carmen and Chen, Ann T. and DeMeo, Benjamin and Ergen, Can and Floc'hlay, Swann and Gayoso, Adam and Hicks, Stephanie and Ji, Yuge and Kleshchevnikov, Vitalii and La Manno, Gioele and Lombardo, Maximilian G. and Lopez, Romain and Righelli, Dario and Sarkar, Hirak and Svensson, Valentine and Tong, Alexander and Xing, Galen and Xu, Chenling and Bloom, Jonathan M. and Pisco, Angela Oliveira and Saez-Rodriguez, Julio and Wulsin, Drausin and Pinello, Luca and Saeys, Yvan and Theis, Fabian J. and Krishnaswamy, Smita},
+	author+an = {1=first; 2=first; 3=first; 4=first; 27=highlight; 54=last; 55=last},
+	doi = {10.1038/s41587-025-02694-w},
+	issn = {1546-1696},
+	journal = {Nature Biotechnology},
+	month = {July},
+	title = {Defining and benchmarking open problems in single-cell analysis},
+	year = {2025},
+}

static/research/Wayland25a.bib

@@ -4,6 +4,7 @@ @inproceedings{Wayland25a
 	author = {Jeremy Wayland and Russel J. Funk and Bastian Rieck},
 	author+an = {3=highlight},
 	booktitle = {Pediatric and Lifespan Data Science},
+	doi = {10.1007/978-3-031-88346-0_1},
 	editor = {Ehwerhemuepha, Louis and Hoffman, Mark and Kalawi, Adam and Sanger, Terence},
 	eprint = {2408.16022},
 	isbn = {978-3-031-88346-0},