Research graph
References from CardamomOT: A mechanistic optimal transport-based framework for gene regulatory network inference, trajectory reconstruction and generative modeling. Local targets link to admitted publications; unresolved targets remain external evidence.
Cell Fate Decision as High-Dimensional Critical State Transition
10.1371/journal.pbio.2000640 · 2016 · External reference
Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
10.1371/journal.pbio.1002585 · 2016 · External reference
Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells
10.1038/s41467-017-01076-4 · 2017 · External reference
Stem Cell Differentiation as a Non-Markov Stochastic Process
2017 · External reference
The rise of the distributions: why non-normality is important for understanding the transcriptome and beyond
10.1007/s12551-018-0494-4 · 2019 · External reference
Cellular identity at the single-cell level
10.1039/c6mb00388e · 2016 · External reference
Gene Regulatory Network Inference: An Introductory Survey
10.1007/978-1-4939-8882-2_1 · 2019 · External reference
Inferring regulatory networks from expression data using tree-based methods
2010 · External reference
SCENIC: single-cell regulatory network inference and clustering
10.1038/nmeth.4463 · 2017 · External reference
dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data
10.1038/s41598-018-21715-0 · 2018 · External reference
Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe
2020 · External reference
Live-seq enables temporal transcriptomic recording of single cells
10.1038/s41586-022-05046-9 · 2022 · External reference
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA
10.1038/s41587-023-02082-2 · 2024 · External reference
10.1007/978-3-319-20828-2
10.1007/978-3-319-20828-2 · External reference
Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming
10.1016/j.cell.2019.01.006 · 2019 · External reference
Unresolved reference
External reference
Mapping transcriptomic vector fields of single cells
2022 · External reference
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo
10.1242/dev.198614 · 2021 · External reference
Simulation-free Schrödinger bridges via score and flow matching
2023 · External reference
Unresolved reference
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Unresolved reference
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From the Schrödinger problem to the Monge–Kantorovich problem
10.1016/j.jfa.2011.11.026 · 2012 · External reference
Cell trajectory inference based on Schrödinger problem and a mechanistic model of stochastic gene expression
2025 · External reference
A computational framework for solving wasserstein lagrangian flows
2023 · External reference
Unresolved reference
External reference
Dynamic gene regulatory network inference from single-cell data using optimal transport
10.1093/bioinformatics/btaf394 · 2025 · External reference
Unresolved reference
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A review of the current state of single-cell proteomics and future perspective
10.1007/s00216-023-04759-8 · 2023 · External reference
Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene
10.1038/msb.2010.96 · 2010 · External reference
Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells
10.1038/srep07125 · 2014 · External reference
Unresolved reference
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One model fits all: Combining inference and simulation of gene regulatory networks
10.1371/journal.pcbi.1010962 · 2023 · External reference
Inferring gene regulatory networks from single-cell data: a mechanistic approach
10.1186/s12918-017-0487-0 · 2017 · External reference
WASABI: a dynamic iterative framework for gene regulatory network inference
10.1186/s12859-019-2798-1 · 2019 · External reference
Reverse engineering of a mechanistic model of gene expression using metastability and temporal dynamics
10.3233/isb-210226 · 2021 · External reference
Trajectory inference from single-cell genomics data with a process time model
10.1371/journal.pcbi.1012752 · 2025 · External reference
Markovian Modeling of Gene-Product Synthesis
10.1006/tpbi.1995.1027 · 1995 · External reference
Inferring and simulating a gene regulatory network for the sympathoadrenal differentiation from single-cell transcriptomics in human
10.12688/f1000research.164530.1 · 2025 · External reference
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin
10.1038/s41588-021-00818-x · 2021 · External reference
Central dogma at the single-molecule level in living cells
10.1038/nature10315 · 2011 · External reference
Transcription in Living Cells: Molecular Mechanisms of Bursting
10.1146/annurev-biochem-011520-105250 · 2020 · External reference
Mammalian genes are transcribed with widely different bursting kinetics
10.1126/science.1198817 · 2011 · External reference
Validation of noise models for single-cell transcriptomics
10.1038/nmeth.2930 · 2014 · External reference
Reduction of a stochastic model of gene expression: Lagrangian dynamics gives access to basins of attraction as cell types and metastabilty
10.1007/s00285-021-01684-1 · 2021 · External reference
Generative modeling of single-cell time series with PRESCIENT enables prediction of cell trajectories with interventions
10.1038/s41467-021-23518-w · 2021 · External reference
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport
10.1038/s41592-025-02855-4 · 2026 · External reference
10.1007/978-3-031-42697-1_7
10.1007/978-3-031-42697-1_7 · External reference
Comprehensive Integration of Single-Cell Data
10.1016/j.cell.2019.05.031 · 2019 · External reference
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles
10.1093/bioinformatics/btx575 · 2018 · External reference
Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures
2017 · External reference
Maximum entropy determination of mammalian proteome dynamics
2024 · External reference
Global quantification of mammalian gene expression control
10.1038/nature10098 · 2011 · External reference
An atlas of protein turnover rates in mouse tissues
10.1038/s41467-021-26842-3 · 2021 · External reference
Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties
2018 · External reference
LineageOT is a unified framework for lineage tracing and trajectory inference
10.1038/s41467-021-25133-1 · 2021 · External reference
Visualizing structure and transitions in high-dimensional biological data
10.1038/s41587-019-0336-3 · 2019 · External reference
DNA methylation patterns and epigenetic memory
10.1101/gad.947102 · 2002 · External reference
OmniPath: guidelines and gateway for literature-curated signaling pathway resources
10.1038/nmeth.4077 · 2016 · External reference
10.1371/journal.pcbi.1013300 · 2025 · Admitted local publication
Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation
10.1371/journal.pcbi.1012476 · 2025 · External reference
Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability
10.1016/s0955-0674(02)00314-9 · 2002 · External reference
Two-State Stochastic Model of In Vivo Observations of Transcriptional Bursts
10.1007/s13538-025-01785-y · 2025 · External reference
Transcriptional burst frequency and burst size are equally modulated across the human genome
10.1073/pnas.1213530109 · 2012 · External reference
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Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage
10.7554/elife.100623.4 · 2026 · External reference
Trajectory inference for a branching SDE model of cell differentiation via lineage tracing
10.1007/s00285-026-02375-5 · 2026 · External reference
Scaling algorithms for unbalanced optimal transport problems
10.1090/mcom/3303 · 2018 · External reference
Convergence of the Sinkhorn algorithm when the Schrödinger problem has no solution
2025 · External reference
