PerturbDB for unraveling gene functions and regulatory networks<? mode longmeta?>

B Yang, M Zhang, Y Shi, BQ Zheng, C Shi… - Nucleic Acids …, 2025 - academic.oup.com
Perturb-Seq combines CRISPR (clustered regularly interspaced short palindromic repeats)-
based genetic screens with single-cell RNA sequencing readouts for high-content …

Approximate Constrained Lumping of Polynomial Differential Equations

A Leguizamon-Robayo, A Jiménez-Pastor… - … Methods in Systems …, 2023 - Springer
In life sciences, deriving insights from dynamic models can be challenging due to the large
number of state variables involved. To address this, model reduction techniques can be …

[HTML][HTML] Efficient probabilistic inference in biochemical networks

A Le Coënt, B Barbot, N Pekergin - Computers in Biology and Medicine, 2024 - Elsevier
Biochemical networks are usually modeled by ordinary differential equations that describe
the time evolution of the concentrations of the interacting (biochemical) species for specific …

Exact linear reduction for rational dynamical systems

A Jiménez-Pastor, JP Jacob, G Pogudin - International Conference on …, 2022 - Springer
Detailed dynamical systems models used in life sciences may include dozens or even
hundreds of state variables. Models of large dimension are not only harder from the …

Proper Lumping for Positive Bilinear Control Systems

A Jiménez-Pastor, D Toller… - … on Automatic Control, 2024 - ieeexplore.ieee.org
Positive systems naturally arise in situations where the model tracks physical quantities.
Although the linear case is well understood, analysis and controller design for nonlinear …

Exact hierarchical reductions of dynamical models via linear transformations

A Demin, E Demitraki, G Pogudin - Communications in Nonlinear Science …, 2024 - Elsevier
Dynamical models described by ordinary differential equations (ODEs) are a fundamental
tool in the sciences and engineering. Exact reduction aims at producing a lower …

Forward and Backward Constrained Bisimulations for Quantum Circuits

A Jiménez-Pastor, KG Larsen, M Tribastone… - … Conference on Tools …, 2024 - Springer
Efficient methods for the simulation of quantum circuits on classic computers are crucial for
their analysis due to the exponential growth of the problem size with the number of qubits …

Approximate Constrained Lumping of Chemical Reaction Networks

A Leguizamon-Robayo, A Jiménez-Pastor… - arXiv preprint arXiv …, 2024 - arxiv.org
Gaining insights from realistic dynamical models of biochemical systems can be challenging
given their large number of state variables. Model reduction techniques can mitigate this by …

[PDF][PDF] Algorithm to find new identifiable reparametrizations of parametric rational ODE models

A Ovchinnikova, N Meshkatb… - arXiv preprint arXiv …, 2024 - math.berkeley.edu
Structural identifiability concerns the question of which unknown parameters of a model can
be recovered from (perfect) inputoutput data. If all of the parameters of a model can be …

A large-scale assessment of exact lumping of quantitative models in the BioModels repository

IC Perez-Verona, M Tribastone, A Vandin - Theoretical Computer Science, 2021 - Elsevier
Chemical reaction networks are a popular formalism for modeling biological processes
which supports both a deterministic and a stochastic interpretation based on ordinary …