相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Mapping transcriptomic vector fields of single cells
Xiaojie Qiu et al.
CELL (2022)
Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data
Qi Jiang et al.
PLOS COMPUTATIONAL BIOLOGY (2022)
Uncovering the cell fate decision in lysis-lysogeny transition and stem cell development via Markov state modeling
Xiaoguang Li et al.
JOURNAL OF CHEMICAL PHYSICS (2021)
Quantifying the Landscape of Decision Making From Spiking Neural Networks
Leijun Ye et al.
FRONTIERS IN COMPUTATIONAL NEUROSCIENCE (2021)
A Dimension Reduction Approach for Energy Landscape: Identifying Intermediate States in Metabolism-EMT Network
Xin Kang et al.
ADVANCED SCIENCE (2021)
Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics
Peijie Zhou et al.
NATURE COMMUNICATIONS (2021)
Quantifying cell transitions in C. elegans with data-fitted landscape models
Elena Camacho-Aguilar et al.
PLOS COMPUTATIONAL BIOLOGY (2021)
Inference of high-resolution trajectories in single-cell RNA-seq data by using RNA velocity
Ziqi Zhang et al.
CELL REPORTS METHODS (2021)
On the Mathematics of RNA Velocity I: Theoretical Analysis
Tiejun Li et al.
CSIAM TRANSACTIONS ON APPLIED MATHEMATICS (2021)
The Physics of Cellular Decision Making During Epithelial–Mesenchymal Transition
Shubham Tripathi et al.
Annual Review of Biophysics (2020)
Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies
Nico Battich et al.
SCIENCE (2020)
Learning dynamical information from static protein and sequencing data
Philip Pearce et al.
NATURE COMMUNICATIONS (2019)
Discrete flux and velocity fields of probability and their global maps in reaction systems
Anna Terebus et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
Reversed graph embedding resolves complex single-cell trajectories
Xiaojie Qiu et al.
NATURE METHODS (2017)
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape
Jing Guo et al.
BIOINFORMATICS (2017)
Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond
Peijie Zhou et al.
JOURNAL OF CHEMICAL PHYSICS (2016)
Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM
Joachim Frank et al.
METHODS (2016)
Broken detailed balance at mesoscopic scales in active biological systems
Christopher Battle et al.
SCIENCE (2016)
Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory
Hao Ge et al.
PHYSICAL REVIEW E (2016)
Landscape and flux theory of non-equilibrium dynamical systems with application to biology
Jin Wang
ADVANCES IN PHYSICS (2015)
Stem cell differentiation as a many-body problem
Bin Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Landscape and flux reveal a new global view and physical quantification of mammalian cell cycle
Chunhe Li et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Non-equilibrium transition state rate theory
Haidong Feng et al.
CHEMICAL SCIENCE (2014)
Predicting rates of cell state change caused by stochastic fluctuations using a data-driven landscape model
Daniel R. Sisan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
A new mechanism of stem cell differentiation through slow binding/unbinding of regulators to genes
Haidong Feng et al.
SCIENTIFIC REPORTS (2012)
Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells
Piyush B. Gupta et al.
CELL (2011)
Quantifying the Waddington landscape and biological paths for development and differentiation
Jin Wang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
Weinan E et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 61 (2010)
The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation
Jin Wang et al.
BIOPHYSICAL JOURNAL (2010)
Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective
Sui Huang et al.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2009)
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data
Regina Samaga et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Emerging of stochastic dynamical equalities and steady state thermodynamics from Darwinian dynamics
P. Ao
COMMUNICATIONS IN THEORETICAL PHYSICS (2008)
A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination
Vijay Chickarmane et al.
PLOS ONE (2008)
Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations
Jin Wang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Bifurcation dynamics in lineage-commitment in bipotent progenitor cells
Sui Huang et al.
DEVELOPMENTAL BIOLOGY (2007)
Towards an understanding of lineage specification in hematopoietic stem cells: A mathematical model for the interaction of transcription factors GATA-1 and PU.1
Ingo Roeder et al.
JOURNAL OF THEORETICAL BIOLOGY (2006)
Derivation of midbrain dopamine neurons from human embryonic stem cells
AL Perrier et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Intrinsic and extrinsic contributions to stochasticity in gene expression
PS Swain et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
The chemical Langevin equation
DT Gillespie
JOURNAL OF CHEMICAL PHYSICS (2000)