References

AFB+18

Anna Alemany, Maria Florescu, Chloé S Baron, Josi Peterson-Maduro, and Alexander Van Oudenaarden. Whole-organism clone tracing using single-cell sequencing. Nature, 556(7699):108–112, 2018. doi:10.1038/nature25969.

BBSP+19

Yael Baran, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz, and Amos Tanay. Metacell: analysis of single-cell rna-seq data using k-nn graph partitions. Genome Biology, 20(1):206, 2019. doi:10.1186/s13059-019-1812-2.

BIRI+21

Melania Barile, Ivan Imaz-Rosshandler, Isabella Inzani, Shila Ghazanfar, Jennifer Nichols, John C Marioni, Carolina Guibentif, and Berthold Göttgens. Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. Genome biology, 22(1):1–22, 2021. doi:10.1186/s13059-021-02414-y.

BPTD+19

A. Bastidas-Ponce, S. Tritschler, L. Dony, K. Scheibner, M. Tarquis-Medina, C. Salinno, S. Schirge, I. Burtscher, A. Böttcher, F.J. Theis, H. Lickert, and M. Bakhti. Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis. Development, 2019. doi:10.1242/dev.173849.

BPRB+17

Aimée Bastidas-Ponce, Sara S Roscioni, Ingo Burtscher, Erik Bader, Michael Sterr, Mostafa Bakhti, and Heiko Lickert. Foxa2 and pdx1 cooperatively regulate postnatal maturation of pancreatic β-cells. Molecular metabolism, 6(6):524–534, 2017. doi:10.1016/j.molmet.2017.03.007.

BBdB+20

Nico Battich, Joep Beumer, Buys de Barbanson, Lenno Krenning, Chloé S Baron, Marvin E Tanenbaum, Hans Clevers, and Alexander van Oudenaarden. Sequencing metabolically labeled transcripts in single cells reveals mrna turnover strategies. Science, 367(6482):1151–1156, 2020. doi:10.1126/science.aax3072.

BMH+19

Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel WH Kwok, Lai Guan Ng, Florent Ginhoux, and Evan W Newell. Dimensionality reduction for visualizing single-cell data using umap. Nature biotechnology, 37(1):38–44, 2019. doi:10.1038/nbt.4314.

BDA+14

Sean C Bendall, Kara L Davis, El-ad David Amir, Michelle D Tadmor, Erin F Simonds, Tiffany J Chen, Daniel K Shenfeld, Garry P Nolan, and Dana Pe’er. Single-cell trajectory detection uncovers progression and regulatory coordination in human b cell development. Cell, 157(3):714–725, 2014. doi:10.1016/j.cell.2014.04.005.

BLP+20

V. Bergen, M. Lange, S. Peidli, F.A. Wolf, and F.J. Theis. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol., 38:1408?1414, 2020. doi:10.1038/s41587-020-0591-3.

BSKT21

Volker Bergen, Ruslan A Soldatov, Peter V Kharchenko, and Fabian J Theis. Rna velocity—current challenges and future perspectives. Molecular systems biology, 17(8):e10282, 2021. doi:10.15252/msb.202110282.

BKK+18

Brent A. Biddy, Wenjun Kong, Kenji Kamimoto, Chuner Guo, Sarah E. Waye, Tao Sun, and Samantha A. Morris. Single-cell mapping of lineage and identity in direct reprogramming. Nature, 564(7735):219–224, 2018. doi:10.1038/s41586-018-0744-4.

BWS+18

Lauren E Byrnes, Daniel M Wong, Meena Subramaniam, Nathaniel P Meyer, Caroline L Gilchrist, Sarah M Knox, Aaron D Tward, Chun J Ye, and Julie B Sneddon. Lineage dynamics of murine pancreatic development at single-cell resolution. Nature communications, 9(1):3922, 2018. doi:10.1038/s41467-018-06176-3.

CPSV18

Lenaic Chizat, Gabriel Peyré, Bernhard Schmitzer, and François-Xavier Vialard. Scaling algorithms for unbalanced optimal transport problems. Mathematics of Computation, 87(314):2563–2609, 2018. URL: https://www.ams.org/journals/mcom/2018-87-314/S0025-5718-2018-03303-8/home.html.

CLL+05

R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker. Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps. Proceedings of the National Academy of Sciences, 102(21):7426–7431, 2005. doi:10.1073/pnas.0500334102.

Cut13

Marco Cuturi. Sinkhorn distances: lightspeed computation of optimal transport. Advances in neural information processing systems, 2013. URL: https://proceedings.neurips.cc/paper/2013/hash/af21d0c97db2e27e13572cbf59eb343d-Abstract.html.

DP12

Gökhan Dalgin and Victoria E Prince. Mnx1: a gatekeeper of β cell fate. Islets, 4(4):320–322, 2012. doi:10.4161/isl.21984.

DeS70

J. S. DeSalvo. Standard error of forecast in multiple regression: proof of a useful result. 1970. URL: https://www.rand.org/pubs/papers/P4365.html.

DHS+11

Frederique Diraison, K Hayward, Kelly L Sanders, F Brozzi, Sophie Lajus, J Hancock, JE Francis, E Ainscow, UA Bommer, E Molnar, and others. Translationally controlled tumour protein (tctp) is a novel glucose-regulated protein that is important for survival of pancreatic beta cells. Diabetologia, 54:368–379, 2011. doi:10.1007/s00125-010-1958-7.

EBK+19

Florian Erhard, Marisa AP Baptista, Tobias Krammer, Thomas Hennig, Marius Lange, Panagiota Arampatzi, Christopher S Jürges, Fabian J Theis, Antoine-Emmanuel Saliba, and Lars Dölken. Scslam-seq reveals core features of transcription dynamics in single cells. Nature, 571(7765):419–423, 2019. doi:10.1038/s41586-019-1369-y.

FWR+18

Jeffrey A. Farrell, Yiqun Wang, Samantha J. Riesenfeld, Karthik Shekhar, Aviv Regev, and Alexander F. Schier. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science, 2018. doi:10.1126/science.aar3131.

Fis21

R. A. Fisher. On the “probable error” of a coefficient of correlation deduced from a small sample. 1921.

FS21

Aden Forrow and Geoffrey Schiebinger. Lineageot is a unified framework for lineage tracing and trajectory inference. Nature communications, 12(1):4940, 2021. doi:10.1038/s41467-021-25133-1.

GSW+20

Gunsagar S. Gulati, Shaheen S. Sikandar, Daniel J. Wesche, Anoop Manjunath, Anjan Bharadwaj, Mark J. Berger, Francisco Ilagan, Angera H. Kuo, Robert W. Hsieh, Shang Cai, Maider Zabala, Ferenc A. Scheeren, Neethan A. Lobo, Dalong Qian, Feiqiao B. Yu, Frederick M. Dirbas, Michael F. Clarke, and Aaron M. Newman. Single-cell transcriptional diversity is a hallmark of developmental potential. Science, 367(6476):405–411, 2020. doi:10.1126/science.aax0249.

HBW+16

L. Haghverdi, M. Büttner, F.A. Wolf, F. Buettner, and F.J. Theis. Diffusion pseudotime robustly reconstructs lineage branching. Nat. Methods, 13(10):845–848, 2016. doi:10.1038/nmeth.3971.

HBT15

Laleh Haghverdi, Florian Buettner, and Fabian J Theis. Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics, 31(18):2989–2998, 2015. doi:10.1093/bioinformatics/btv325.

JKKS+14

Diego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren-Shaul, Naama Elefant, Franziska Paul, Irina Zaretsky, Alexander Mildner, Nadav Cohen, Steffen Jung, Amos Tanay, and others. Massively parallel single-cell rna-seq for marker-free decomposition of tissues into cell types. Science, 343(6172):776–779, 2014. URL: https://www.science.org/doi/full/10.1126/science.1247651.

KPL+23

Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Aimée Bastidas-Ponce, Marta Tarquis-Medina, Heiko Lickert, Mostafa Bakhti, Mor Nitzan, Marco Cuturi, and Fabian J. Theis. Mapping cells through time and space with moscot. bioRxiv, 2023. URL: https://www.biorxiv.org/content/early/2023/05/12/2023.05.11.540374, doi:10.1101/2023.05.11.540374.

LMSZ+18

Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E. Kastriti, Peter Lönnerberg, Alessandro Furlan, Jean Fan, Lars E. Borm, Zehua Liu, David van Bruggen, Jimin Guo, Xiaoling He, Roger Barker, Erik Sundström, Gonçalo Castelo-Branco, Patrick Cramer, Igor Adameyko, Sten Linnarsson, and Peter V. Kharchenko. RNA velocity of single cells. Nature, 2018. doi:10.1038/s41586-018-0414-6.

LBK+22

Marius Lange, Volker Bergen, Michal Klein, Manu Setty, Bernhard Reuter, Mostafa Bakhti, Heiko Lickert, Meshal Ansari, Janine Schniering, Herbert B. Schiller, Dana Pe'er, and Fabian J. Theis. Cellrank for directed single-cell fate mapping. Nat. Methods, 2022. doi:10.1038/s41592-021-01346-6.

LPK+23

Marius Lange, Zoe Piran, Michal Klein, Bastiaan Spanjaard, Dominik Klein, Jan Philipp Junker, Fabian J Theis, and Mor Nitzan. Mapping lineage-traced cells across time points with moslin. bioRxiv, pages 2023–04, 2023. doi:10.1101/2023.04.14.536867.

LSWZ21

Tiejun Li, Jifan Shi, Yichong Wu, and Peijie Zhou. On the mathematics of rna velocity i: theoretical analysis. CSIAM Transactions on Applied Mathematics, 2(1):1–55, 2021. doi:10.4208/csiam-am.SO-2020-0001.

MBS+15

Evan Z. Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R. Bialas, Nolan Kamitaki, Emily M. Martersteck, John J. Trombetta, David A. Weitz, Joshua R. Sanes, Alex K. Shalek, Aviv Regev, and Steven A. McCarroll. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell, 161(5):1202–1214, 2015. doi:10.1016/j.cell.2015.05.002.

MHM18

Leland McInnes, John Healy, and James Melville. Umap: uniform manifold approximation and projection for dimension reduction. arXiv preprint arXiv:1802.03426, 2018. doi:10.48550/arXiv.1802.03426.

MMC+21

Markus Mittnenzweig, Yoav Mayshar, Saifeng Cheng, Raz Ben-Yair, Ron Hadas, Yoach Rais, Elad Chomsky, Netta Reines, Anna Uzonyi, Lior Lumerman, Aviezer Lifshitz, Zohar Mukamel, Ayelet-Hashahar Orenbuch, Amos Tanay, and Yonatan Stelzer. A single-embryo, single-cell time-resolved model for mouse gastrulation. Cell, 184(11):2825–2842.e22, 2021. doi:10.1016/j.cell.2021.04.004.

MB19

Abu Saleh Md Moin and Alexandra E Butler. Alterations in beta cell identity in type 1 and type 2 diabetes. Current diabetes reports, 19:1–12, 2019. doi:10.1007/s11892-019-1194-6.

NAC+15

Tiziana Napolitano, Fabio Avolio, Monica Courtney, Andhira Vieira, Noémie Druelle, Nouha Ben-Othman, Biljana Hadzic, Sergi Navarro, and Patrick Collombat. Pax4 acts as a key player in pancreas development and plasticity. In Seminars in cell & developmental biology, volume 44, 107–114. Elsevier, 2015. doi:10.1016/j.semcdb.2015.08.013.

PSK+21

Giovanni Palla, Hannah Spitzer, Michal Klein, David Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle, Sergei Rybakov, Ignacio L. Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, and Fabian J. Theis. Squidpy: a scalable framework for spatial single cell analysis. bioRxiv, 2021. doi:10.1101/2021.02.19.431994.

PBP+15

Fong Cheng Pan, Marcela Brissova, Alvin C Powers, Samuel Pfaff, and Christopher VE Wright. Inactivating the permanent neonatal diabetes gene mnx1 switches insulin-producing β-cells to a δ-like fate and reveals a facultative proliferative capacity in aged β-cells. Development, 142(21):3637–3648, 2015. doi:10.1242/dev.126011.

PC+19

Gabriel Peyré, Marco Cuturi, and others. Computational optimal transport: with applications to data science. Foundations and Trends® in Machine Learning, 11(5-6):355–607, 2019. doi:10.1561/2200000073.

QHQ+20

Qi Qiu, Peng Hu, Xiaojie Qiu, Kiya W Govek, Pablo G Cámara, and Hao Wu. Massively parallel and time-resolved rna sequencing in single cells with scnt-seq. Nature methods, 17(10):991–1001, 2020. doi:10.1038/s41592-020-0935-4.

QZMR+22

Xiaojie Qiu, Yan Zhang, Jorge D Martin-Rufino, Chen Weng, Shayan Hosseinzadeh, Dian Yang, Angela N Pogson, Marco Y Hein, Kyung Hoi Joseph Min, Li Wang, and others. Mapping transcriptomic vector fields of single cells. Cell, 185(4):690–711, 2022. doi:10.1016/j.cell.2021.12.045.

RWM+18

Bushra Raj, Daniel E Wagner, Aaron McKenna, Shristi Pandey, Allon M Klein, Jay Shendure, James A Gagnon, and Alexander F Schier. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nature biotechnology, 36(5):442–450, 2018. doi:10.1038/nbt.4103.

RFW19

Bernhard Reuter, Konstantin Fackeldey, and Marcus Weber. Generalized markov modeling of nonreversible molecular kinetics. The Journal of Chemical Physics, 150(17):174103, 2019. doi:10.1063/1.5064530.

RKL22

Bernhard Reuter, Michal Klein, and Marius Lange. Pygpcca - python gpcca: generalized perron cluster cluster analysis package to coarse-grain reversible and non-reversible markov state models. 2022. URL: https://github.com/msmdev/pyGPCCA, doi:10.5281/zenodo.6914001.

RWF+18

Bernhard Reuter, Marcus Weber, Konstantin Fackeldey, Susanna Röblitz, and Martin E. Garcia. Generalized markov state modeling method for nonequilibrium biomolecular dynamics: exemplified on amyloid β conformational dynamics driven by an oscillating electric field. Journal of Chemical Theory and Computation, 14(7):3579–3594, 2018. PMID: 29812922. doi:10.1021/acs.jctc.8b00079.

RO10

Mark D. Robinson and Alicia Oshlack. A scaling normalization method for differential expression analysis of rna-seq data. Genome Biology, 11(3):R25, 2010. doi:10.1186/gb-2010-11-3-r25.

SCTS19

Wouter Saelens, Robrecht Cannoodt, Helena Todorov, and Yvan Saeys. A comparison of single-cell trajectory inference methods. Nature biotechnology, 37(5):547–554, 2019. doi:10.1038/s41587-019-0071-9.

SST+19

Geoffrey Schiebinger, Jian Shu, Marcin Tabaka, Brian Cleary, Vidya Subramanian, Aryeh Solomon, Joshua Gould, Siyan Liu, Stacie Lin, Peter Berube, Lia Lee, Jenny Chen, Justin Brumbaugh, Philippe Rigollet, Konrad Hochedlinger, Rudolf Jaenisch, Aviv Regev, and Eric S. Lander. Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming. Cell, 176(4):928–943.e22, 2019. doi:10.1016/j.cell.2019.01.006.

SKL+19

Manu Setty, Vaidotas Kiseliovas, Jacob Levine, Adam Gayoso, Linas Mazutis, and Dana Pe'er. Characterization of cell fate probabilities in single-cell data with palantir. Nature Biotechnology, 37(4):451–460, 2019. doi:10.1038/s41587-019-0068-4.

SPCT+97

Beatriz Sosa-Pineda, Kamal Chowdhury, Miguel Torres, Guillermo Oliver, and Peter Gruss. The pax4 gene is essential for differentiation of insulin-producing β cells in the mammalian pancreas. Nature, 386(6623):399–402, 1997. doi:10.1038/386399a0.

SHM+18

Bastiaan Spanjaard, Bo Hu, Nina Mitic, Pedro Olivares-Chauvet, Sharan Janjuha, Nikolay Ninov, and Jan Philipp Junker. Simultaneous lineage tracing and cell-type identification using crispr–cas9-induced genetic scars. Nature biotechnology, 36(5):469–473, 2018. doi:10.1038/nbt.4124.

SYW+21

Shobana V. Stassen, Gwinky G. K. Yip, Kenneth K. Y. Wong, Joshua W. K. Ho, and Kevin K. Tsia. Via: generalized and scalable trajectory inference in single-cell omics data. bioRxiv, 2021. doi:10.1101/2021.02.10.430705.

SRF+18

Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, and Sandrine Dudoit. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC genomics, 19(1):1–16, 2018. doi:10.1186/s12864-018-4772-0.

SSA+20

M. Strunz, L. Simon, M. Ansari, J.J. Kathiriya, I. Angelidis, C. Mayr, G. Tsidiridis, M. Lange, L. Mattner, M. Yee, P. Ogar, A. Sengupta, I. Kukhtevich, R. Schneider, Z. Zhao, C. Voss, T. Stöger, J.H.L. Neumann, A. Hilgendorff, J. Behr, M. O'Reilly, M. Lehmann, G. Burgstaller, M. Königshoff, H.A. Chapman, F.J. Theis, and H. B. Schiller. Alveolar regeneration through a Krt8+transitional stem cell state that persists in human lung fibrosis. Nat. Commun., 2020. doi:10.1038/s41467-020-17358-3.

TCG+14

Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, and John L Rinn. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature biotechnology, 32(4):381–386, 2014. doi:10.1038/nbt.2859.

TYYC+14

Ming-Jen Tsai, Hsin-Fang Yang-Yen, Ming-Ko Chiang, Mei-Jen Wang, Shiou-Shian Wu, and Sung-Ho Chen. Tctp is essential for β-cell proliferation and mass expansion during development and β-cell adaptation in response to insulin resistance. Endocrinology, 155(2):392–404, 2014. doi:10.1210/en.2013-1663.

VdMH08

Laurens Van der Maaten and Geoffrey Hinton. Visualizing data using t-sne. Journal of machine learning research, 2008.

vDSN+18

David van Dijk, Roshan Sharma, Juozas Nainys, Kristina Yim, Pooja Kathail, Ambrose J. Carr, Cassandra Burdziak, Kevin R. Moon, Christine L. Chaffer, Diwakar Pattabiraman, Brian Bierie, Linas Mazutis, Guy Wolf, Smita Krishnaswamy, and Dana Pe'er. Recovering gene interactions from single-cell data using data diffusion. Cell, 174(3):716–729.e27, 2018. doi:10.1016/j.cell.2018.05.061.

VHR+17

Lars Velten, Simon F. Haas, Simon Raffel, Sandra Blaszkiewicz, Saiful Islam, Bianca P. Hennig, Christoph Hirche, Christoph Lutz, Eike C. Buss, Daniel Nowak, Tobias Boch, Wolf-Karsten Hofmann, Anthony D. Ho, Wolfgang Huber, Andreas Trumpp, Marieke A. G. Essers, and Lars M. Steinmetz. Human haematopoietic stem cell lineage commitment is a continuous process. Nature Cell Biology, 19(4):271–281, 2017. doi:10.1038/ncb3493.

WLK+23

Philipp Weiler, Marius Lange, Michal Klein, Dana Pe\textquotesingle er, and Fabian Theis. Unified fate mapping in multiview single-cell data. bioRxiv, 2023. URL: https://doi.org/10.1101/2023.07.19.549685, doi:10.1101/2023.07.19.549685.

WTW+13

Crystal L Wilcox, Natalie A Terry, Erik R Walp, Randall A Lee, and Catherine Lee May. Pancreatic α-cell specific deletion of mouse arx leads to α-cell identity loss. PloS one, 8(6):e66214, 2013. doi:10.1371/journal.pone.0066214.

WAT18

F. Alexander Wolf, Philipp Angerer, and Fabian J. Theis. Scanpy: large-scale single-cell gene expression data analysis. Genome Biology, 19(1):15, 2018. doi:10.1186/s13059-017-1382-0.

WHP+19

F. Alexander Wolf, Fiona K. Hamey, Mireya Plass, Jordi Solana, Joakim S. Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, and Fabian J. Theis. Paga: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biology, 20(1):59, 2019. doi:10.1186/s13059-019-1663-x.

ZMBK14

Jia Zhang, Lindsay B McKenna, Clifford W Bogue, and Klaus H Kaestner. The diabetes gene hhex maintains δ-cell differentiation and islet function. Genes & development, 28(8):829–834, 2014. doi:10.1101/gad.235499.113.

ZAG+21

Stephen Zhang, Anton Afanassiev, Laura Greenstreet, Tetsuya Matsumoto, and Geoffrey Schiebinger. Optimal transport analysis reveals trajectories in steady-state systems. bioRxiv, 2021. doi:10.1101/2021.03.02.433630.

ZOG+21

Xiaodong Zhu, Alexis Oguh, Morgan A Gingerich, Scott A Soleimanpour, Doris A Stoffers, and Maureen Gannon. Cell cycle regulation of the pdx1 transcription factor in developing pancreas and insulin-producing β-cells. Diabetes, 70(4):903–916, 2021. doi:10.2337/db20-0599.