Molecular Networks · Quantitative Biology
Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art
David J. Warne, Ruth E. Baker, Matthew J. Simpson
2019-03-04
Computational Engineering, Finance, and Science · Computer Science
Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach
Seung Woo Shin, Chris Thachuk, Erik Winfree
2019-10-01
Formal Languages and Automata Theory · Computer Science
The many roads to the simulation of reaction systems
Claudio Ferretti, Alberto Leporati, Luca Manzoni, Antonio E. Porreca
2020-08-05
Quantum Physics · Physics
A modular quantum-classical framework for simulating chemical reaction pathways accurately
Nirmal M R, Shampa Sarkar, Manoj Nambiar, Sriram Goverapet Srinivasan
2022-10-18
Chemical Physics · Physics
Integrated Reaction Path Processing from Sampled Structure Sequences
Michael A. Heuer, Alain C. Vaucher, Moritz P. Haag, Markus Reiher
2018-04-25
Quantitative Methods · Quantitative Biology
Design of Experiments for Verifying Biomolecular Networks
Ruby Sedgwick, John Goertz, Molly Stevens, Ruth Misener +1
2020-11-26
Quantitative Methods · Quantitative Biology
RuleVis: Constructing Patterns and Rules for Rule-Based Models
David Abramov, Jasmine Otto, Mahika Dubey, Cassia Artanegara +3
2019-11-13
Molecular Networks · Quantitative Biology
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017-12-08
Discrete Mathematics · Computer Science
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions
Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
2016-04-22
Molecular Networks · Quantitative Biology
Symbolic dynamics of biochemical pathways as finite states machines
Ovidiu Radulescu, Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev +1
2015-07-07
Computational Engineering, Finance, and Science · Computer Science
Finding Pathways in Reaction Networks guided by Energy Barriers using Integer Linear Programming
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen, Peter Dittrich +1
2026-03-31
Molecular Networks · Quantitative Biology
Reduction of dynamical biochemical reaction networks in computational biology
Ovidiu Radulescu, Alexander N. Gorban, Andrei Zinovyev, Vincent Noel
2014-10-15