RNA velocity unraveled

Cited by (176)

Items 101–176 of 176

1. Recovering biomolecular network dynamics from single-cell omics data requires three time points
   Shu Wang, M. Ali Al-Radhawi, Douglas A. Lauffenburger, Eduardo D. Sontag · 2024 · npj Systems Biology and Applications
2. Empirical methods that provide physical descriptions of dynamic cellular processes
   Ian Seim, Stephan W. Grill · 2024 · Biophysical Journal
3. Single-cell multiomics reveals the oscillatory dynamics of mRNA metabolism and chromatin accessibility during the cell cycle
   Maulik K. Nariya, David Santiago‐Algarra, Olivier Tassy, Marie Cerciat, Tao Ye, Andrea Riba, Nacho Molina · 2025 · Cell Reports
4. Integrating nowcasts into an ensemble of data-driven forecasting models for SARI hospitalizations in Germany
   Daniel Wolffram, Johannes Bracher, The RESPINOW Study Group, Melanie Schienle · 2026 · International Journal of Forecasting
5. Emergence of neuron types
   Louis Faure, Techameena Prach, Saïda Hadjab · 2022 · Current Opinion in Cell Biology
6. Decoding changes in tumor‐infiltrating leukocytes through dynamic experimental models and single‐cell technologies
   Colin Y.C. Lee, Menna Ruth Clatworthy, David R. Withers · 2024 · Immunology and Cell Biology
7. New wave theory
   Paul François · 2023 · Development
8. Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression
   Christopher A. Jackson, Maggie Beheler-Amass, Andreas Tjärnberg, Ina Suresh, Angela Shang-Mei Hickey, Richard Bonneau, David Gresham · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
9. Dynamic Gene Regulatory Network Inference with Interpretable, Biophysically-Motivated Neural ODEs
   Maggie Beheler-Amass, Chrisopher A Jackson, David Gresham, Richard Bonneau · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
10. ArchVelo: archetypal velocity modeling for single-cell multi-omic trajectories
    Maria Avdeeva, Sarah K. Walker, Joris van der Veeken, Alexander Yu Rudensky, Yuri Pritykin · 2026 · Nature Communications
11. STEER: decoupling kinetics with Spatial-Temporal Explainable Expert model for RNA velocity inference
    Zhiyuan Liu, Chen Li, Dafei Wu, Weiwei Zhai, Liang Ma · 2026 · National Science Review
12. Comprehensive benchmarking of RNA velocity methods across single-cell datasets
    Yida Wu, Chuihan Kong, Xu Liao, Zhixiang Lin, Xiaobo Sun, J H Liu · 2026 · Genome biology
13. A primer on single‐cell RNA ‐seq analysis using dendritic cells as a case study
    Giulia Protti, Roberto Spreafico · 2024 · FEBS Letters
14. Feature Clock: High-Dimensional Effects in Two-Dimensional Plots
    Olga Ovcharenko, Rita Sevastjanova, Valentina Boeva · 2024 · Visualization
15. Genome-wide chromatin recording resolves dynamic cell state changes
    Yodai Takei, Jordan A. Lay, James M. Linton, Duncan M. Chadly, Yoshiki Ochiai, Ron Hadas, Andrew A. Perez, Mario R. Blanco, Paola Laurino, Mitchell Guttman et al. · 2026 · Cell Systems
16. Deep dynamical models of single-cell multiomic velocities predict loss-of-function and rescue perturbations in B cells
    Alireza Karbalayghareh, Benedikt Pelzer, Christopher R. Chin, Ari M. Melnick, Darko Barišić, Christina S. Leslie · 2026 · Nature Biotechnology
17. Cascade Forest-Based Model for Prediction of RNA Velocity
    Zhiliang Zeng, Shouwei Zhao, Yu Peng, Xiang Hu, Zhixiang Yin · 2022 · Molecules
18. noSpliceVelo infers gene expression dynamics without separating unspliced and spliced transcripts
    Tarun Mahajan, Sergei Maslov · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
19. Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge
    Kazumitsu Maehara, Yasuyuki Ohkawa · 2025 · Nature Communications
20. Clonal analysis for understanding fate biases in developing embryos
    Sergey V. Isaev, Igor I. Adameyko · 2026 · Current Opinion in Genetics & Development
21. Quantifying stability via count splitting to guide model selection in RNA velocity analyses
    Yuhong Li, Zeyu Wei, Yen‐Chi Chen, Kevin Lin · 2026 · Bioinformatics Advances
22. Exploring transcription modalities from bimodal, single-cell RNA sequencing data
    Enikő Regényi, Mir‐Farzin Mashreghi, Christof Schütte, Vikram Sunkara · 2024 · NAR Genomics and Bioinformatics
23. Markov-bridge generation of transition paths and its application to cell-fate choice
    Guillaume Le Treut, Sarah Ancheta, Greg Huber, Henri Orland, David Yllanes · 2025 · Physical Review Research
24. Accurate quantification of spliced and unspliced transcripts for single-cell RNA sequencing with tidesurf
    Jan T. Schleicher, Doreen Klingler, Manfred Claassen · 2026 · PLoS ONE
25. Quantifying uncertainty in RNA velocity
    Huizi Zhang, Natalia Bochkina, Sara Wade · 2026 · Biometrics
26. Deciphering global transcriptional dynamics coordinated by gene-gene regulatory interactions using single-cell data
    Liying Zhou, Songhao Luo, Zhiwei Huang, Zhenquan Zhang, Zihao Wang, Jiajun Zhang · 2026 · Molecular Systems Biology
27. Early Detection of Transcriptomic State-Transition Dynamics in Cancer Through Nonlinear Dynamical Systems Analysis
    Hamid D. Ismail, Ahmad M. Harb, Basem William, Marwan U. Bikdash · 2026 · BioMedInformatics
28. Inferring Single-Cell RNA Kinetics from Various Biological Priors
    Yanshuo Chen, Zhengmian Hu, Ke Ni, Site Feng, Wei Chen, Heng Huang · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
29. TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
    Jiachen Li, Zhe Wang, Hong-Bin Shen, Ye Yuan · 2025 · eLife
30. Benchmarking algorithms for RNA velocity inference
    Kexin Huang, Yu Zhou, Tiangang Wang, Li Xiao, Xinlong Zhao, Xi Liu, Liyu Huang, Xiaobo Zhou, J Liu · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
31. Pyro-Velocity: Probabilistic RNA Velocity inference from single-cell data
    Luca Pinello, Eli Bingham, Qian Qin, David M. Langenau, Gioele La Manno · 2022 · Research Square
32. Beyond the Rainbow: A Review of Advanced Lineage Tracing Methodologies for Interrogating the Initiation, Evolution, and Recurrence of Brain Tumors
    Sara Sabet, Joshua J. Breunig · 2023 · Developmental Neuroscience
33. Unsupervised generative AI discovers pan-leukocyte dysregulated pathways in single-cell lupus data
    Hamid Bolouri, Karen M. Cerosaletti, Adam Lacy‐Hulbert · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
34. Presynaptic occlusion of NMDA receptor-dependent potentiation in Synaptophysin family knockouts
    Sergio del Olmo-Cabrera, Juan José Rodríguez Gotor, Rémy Verhaeghe, John F. Wesseling · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
35. mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities
    Satoshi Nomura, Yasuhiro Kojima, Kodai Minoura, Shuto Hayashi, Ko Abe, Haruka Hirose, Teppei Shimamura · 2026 · Bioinformatics
36. Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription, and splicing from single-cell RNA sequencing data with TSvelo
    Jiachen Li, Zhe Wang, Hong‐Bin Shen, Ye Yuan · 2025 · eLife
37. Beyond “Trapped Pets” and “Red Buttons”: Bioinformatics as an Experimental Discipline
    Emanuele Ratti, Giuseppe Alessandro D’Agostino · 2025 · Perspectives on Science
38. Alternative approaches to single-cell trajectory inference using a commute time matrix
    Douglas W. Houston · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
39. Extending Bayesian Modelling of RNA Velocity
    Elena Sabbioni, Enrico Bibbona, Gianluca Mastrantonio, Guido Sanguinetti · 2025 · Springer eBooks
40. Uncovering smooth structures in single-cell data with PCS-guided neighbor embeddings
    Rong Ma, Xi Li, Jingyuan Hu, Bin Yu · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
41. Exovelo: Cell States Velocity Estimation Without Parameter Fitting
    Yiftach Josef Kolb, Laleh Haghverdi · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
42. Modelling phenotypic heterogeneity and cell-state transitions during cancer progression
    Vishaka Gopalan, Sidhartha Goyal, Sumaiyah K. Rehman · 2025 · Oxford University Press eBooks
43. Emerging single-cell technologies and concepts to trace cancer progression and drug resistance
    Syeda Subia Ahmed, Danielle Pi, Nicholas Bodkin, Vito W. Rebecca, Yogesh Goyal · 2025 · Oxford University Press eBooks
44. Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches
    Javiera Cortés‐Ríos, María Rodriguez-Fernández, Peter Karl Sorger, Fabian Fröhlich · 2025 · PLoS Computational Biology
45. Tree Inference with Varifold Distances
    Elodie Maignant, Tim Conrad, Christoph von Tycowicz · 2025 · Lecture notes in computer science
46. velotest: Statistical assessment of RNA velocity embeddings reveals quality differences for reliable trajectory visualizations
    Sebastian Bischoff, Pavlin G. Poličar, Soham Mukherjee, Jakob H. Macke, Manfred Claassen, Cornelius Schröder · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
47. Characterizing Nonlinear Dynamics via Smooth Prototype Equivalences
    Roy Friedman, Noa Moriel, Matthew R. Ricci, Guy Pelc, Yair Weiss, Mor Nitzan · 2026 · PRX Life
48. Reviewer #3 (Public review): TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
    2025 · eLife
49. Author response: TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
    Jiachen Li, Zhe Wang, Hong-Bin Shen, Ye Yuan · 2025 · eLife
50. eLife Assessment: TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing
    Yongliang Yang · 2025 · eLife
51. Interspecific divergence of gene expression biophysics driven by both evolutionary systems drift and strong selective constraints on bursting rate
    Catherine Felce, Joshua G. Schraiber, Madhumitha Krishnaswamy, Alexander L. Cope, Lior S. Pachter, Matthew W. Pennell · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
52. RNA velocity in growing cells
    Vishal Shah, Hia Ming, Brian Cleary · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
53. Additional file 2 of Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates
    Zheng, Shijie C., Genevieve Stein-O’Brien, Leandros Boukas, Loyal A. Goff, Kasper D. Hansen · 2024 · Figshare
54. Additional file 1 of Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates
    Zheng, Shijie C., Genevieve Stein-O’Brien, Leandros Boukas, Loyal A. Goff, Kasper D. Hansen · 2024 · Figshare
55. Improved reconstruction of transcripts and coding sequences from RNA-seq data
    Jan Grau, Deborah Weise, Marika Panster, Martin Schattat, Jens Keilwagen · 2026 · Nucleic Acids Research
56. Experimental Time Points Guided Transcriptomic Velocity Inference
    Xinyuan Zang, Xin Shu, Zhang Nz, Yu Wu, Mingyue Deng, Xiaolong Zhou, Jie Yang, Chen‐Yu Zhang, Xiaoyong Wang, Zhen Zhou et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
57. Leveraging Twin Information for Inference of Gene Regulatory Networks
    Keerthana M. Arun, Yuval Scher, Yuhan D Zhang, Ida Büschel, Benjamin Kuznets-Speck, Carsten Marr, Yogesh Goyal · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
58. Optimal transport fate mapping resolves T cell differentiation dynamics across tissues
    Alec L. Plotkin, Genevieve Nicole Mullins, William D. Green, Huitong Shi, H. Kay Chung, Natalie Stanley, J. Justin Milner · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
59. Modelling molecular diffusion in the nucleus and its role in gene regulation
    Karen Amaral de Oliveira · 2023 · theses.fr (ABES)
60. Modelling the geometry of high-dimensional omics data : dimensionality, subspaces, trajectories
    Jonathan Bac · 2022 · theses.fr (ABES)
61. Image-informed modelling of microscale exchange in the human placenta
    Eleanor A. Doman, Richard Mcnair, Carl A. Whitfield, Megan C. Sharps, Oliver E. Jensen, Adam Stevens, Rohan M. Lewis, Igor L. Chernyavsky, Bram G. Sengers · 2026 · Placenta
62. Comparison between a conventional tool and deep learning models for RNA velocity analysis of scRNA-Seq data
    Matheus Rodrigues Sauda, Ana Beatriz Rodrigues, Maria Letícia de Oliveira Lyra, Rejane Maria Tommasini Grotto, Lei Gu, Tatiana de Campos Melo, Guilherme Targino Valente · 2026 · Molecular Genetics and Genomics
63. Information Geometry of Intracellular Compartment Coupling Reveals Transcriptomic State Transitions in Single Cells
    Ji‐Yong Sung, Jae‐Ho Cheong · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
64. VelOT: kinetic-free RNA velocity inference via optimal transport, flow-field smoothing, and VAMP coarse-graining of cellular dynamics
    Lucas Rincón de la Rosa, David Pérez-Garcı́a, Agustí Alentorn · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
65. PRIME: scalable, robust inference of mechanistic cell states from multimodal single-cell counts via probability generating functions
    Shiyue Li, Y M Wang, Qingchao Jiang, Ramon Grima, Zhixing Cao · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
66. Spatial RNA velocity reveals cellular state transitions and prognostic markers in the melanoma microenvironment
    Xiangjian Fang, Juntao Cheng, Zhiyi Wei, Biao Wang · 2026 · Frontiers in Oncology
67. Gene Regulatory Network Inference reveals TCF4 as a key a player in neuroblastoma gene expression circuitry
    Catherine Koering, Elodie Vallin, Franck Picard, Sandrine Gonin-Giraud, Olivier Gandrillon · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
68. PseudoVelo: Inferring Gene Expression Derivatives Along Pseudotime as Pseudo-Velocity
    Xinyuan Zang, Xin Shu, Zhen Zhou, Xiaoyong Wang, Jin Wang · 2026 · International Journal of Molecular Sciences
69. Multimodal single-cell profiling identifies nclTECs and links chromatin remodeling to TEC differentiation and self-antigen expression modes
    Hanne Sagsveen Hjorthaug, Marte Heimli, Siri T. Flåm, Benedicte Alexandra Lie · 2026 · iScience
70. Uncovering smooth structures in single-cell data with neighbor embeddings guided by predictability-computability-stability
    Rong Ma, Xi Li, Jingyuan Hu, Bin Yu · 2026 · Patterns
71. scATrans: annotating single-cell differential expression as transcription- or stabilization-weighted using unspliced RNA
    Zhao Li, Aaron Watkins James, S. Z. Li · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
72. Cell State, Not Cell Type, Should Anchor Computational Strategies for Therapeutic Target Discovery
    Ahmed Hamdy, Mona Khalil, Youssef Ibrahim · 2025 · Pharmacophore
73. Author response: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription, and splicing from single-cell RNA sequencing data with TSvelo
    Jiachen Li, Zhe Wang, Hong-Bin Shen, Ye Yuan · 2026 · eLife
74. The microglial lineage: from molecular states to context-dependent functions
    Cuihua Li, Zhisheng Wu, Xianyuan Xiang, Hanjie Li · 2026 · Cell Insight
75. Virtual lineages: in silico lineage tracing from single-cell and spatial transcriptomes
    Yongjie Lin, Yihan Lin · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
76. Joint representation of spliced and unspliced RNA expands information content in single-cell expression data
    Arya Jadhav, Zachary J. DeBruine · 2026 · Bioinformatics Advances