References#

[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, Oct 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.

[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.

[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.

[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, Dec 2018. doi:10.1038/s41586-018-0744-4.

[Bra02]

Jan H Brandts. Matlab code for sorting real schur forms. Numerical linear algebra with applications, 9(3):249–261, 2002. doi:10.1002/nla.274.

[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.

[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.

[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.

[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.

[HButtnerW+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.

[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.

[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.

[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.

[NSK+19]

Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Vincent Liu, Vidur Garg, Roshan Sharma, Claire S Simon, Nestor Saiz, Rui Gardner, Stéphane C Boutet, and others. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature, 569(7756):361–367, 2019. doi:10.1038/s41586-019-1127-1.

[PZH+19]

Jonathan S Packer, Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim, and others. A lineage-resolved molecular atlas of c. elegans embryogenesis at single-cell resolution. Science, 365(6459):eaax1971, 2019.

[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.

[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:https://doi.org/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, Mar 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.

[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, Feb 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, Apr 2019. doi:10.1038/s41587-019-0068-4.

[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.

[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.

[TIP+16]

Itay Tirosh, Benjamin Izar, Sanjay M. Prakadan, Marc H. Wadsworth, Daniel Treacy, John J. Trombetta, Asaf Rotem, Christopher Rodman, Christine Lian, George Murphy, Mohammad Fallahi-Sichani, Ken Dutton-Regester, Jia-Ren Lin, Ofir Cohen, Parin Shah, Diana Lu, Alex S. Genshaft, Travis K. Hughes, Carly G. K. Ziegler, Samuel W. Kazer, Aleth Gaillard, Kellie E. Kolb, Alexandra-Chloé Villani, Cory M. Johannessen, Aleksandr Y. Andreev, Eliezer M. Van Allen, Monica Bertagnolli, Peter K. Sorger, Ryan J. Sullivan, Keith T. Flaherty, Dennie T. Frederick, Judit Jané-Valbuena, Charles H. Yoon, Orit Rozenblatt-Rosen, Alex K. Shalek, Aviv Regev, and Levi A. Garraway. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell rna-seq. Science, 352(6282):189–196, 2016. doi:10.1126/science.aad0501.

[TVH+16]

Itay Tirosh, Andrew S. Venteicher, Christine Hebert, Leah E. Escalante, Anoop P. Patel, Keren Yizhak, Jonathan M. Fisher, Christopher Rodman, Christopher Mount, Mariella G. Filbin, Cyril Neftel, Niyati Desai, Jackson Nyman, Benjamin Izar, Christina C. Luo, Joshua M. Francis, Aanand A. Patel, Maristela L. Onozato, Nicolo Riggi, Kenneth J. Livak, Dave Gennert, Rahul Satija, Brian V. Nahed, William T. Curry, Robert L. Martuza, Ravindra Mylvaganam, A. John Iafrate, Matthew P. Frosch, Todd R. Golub, Miguel N. Rivera, Gad Getz, Orit Rozenblatt-Rosen, Daniel P. Cahill, Michelle Monje, Bradley E. Bernstein, David N. Louis, Aviv Regev, and Mario L. Suvà. Single-cell rna-seq supports a developmental hierarchy in human oligodendroglioma. Nature, 539(7628):309–313, Nov 2016. doi:10.1038/nature20123.

[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, Apr 2017. doi:10.1038/ncb3493.

[WAT18]

F. Alexander Wolf, Philipp Angerer, and Fabian J. Theis. Scanpy: large-scale single-cell gene expression data analysis. Genome Biology, 19(1):15, Feb 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, Mar 2019. doi:10.1186/s13059-019-1663-x.

[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.