26 citations · 47 across the 21 of their papers we have counts for
24 papers
Systematic pathway comparison on the powerset of rule-based biochemical systems
Anne-Susann Abel, Sissel Banke, Erika M. Herrera Machado +4
Computational pathway design often focuses on evaluating selected pathways or optimizing fluxes in a fixed network, but gives less direct access to the combinatorial question of wh…
A Collision-based strategy for Network-free Exploration of Complex Molecular Networks
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +2
This work presents a stochastic exploration framework for large, implicitly defined chemical reaction spaces that are too large to be generated and stored as explicit molecular net…
ChemRecon: a Consolidated Meta-Database Platform for Biochemical Data Integration
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg +1
In this paper, we present ChemRecon, a meta-database and Python interface for integrating and exploring biochemical data across multiple heterogeneous resources by consolidating co…
A Sensitivity Analysis Methodology for Rule-Based Stochastic Chemical Systems
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg +1
In this study, we introduce a sensitivity analysis methodology for stochastic systems in chemistry, where dynamics are often governed by random processes. Our approach is based on…
Rule-Based Gillespie Simulation of Chemical Systems
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg +3
The MØD computational framework implements rule-based generative chemistries as explicit transformations of graphs representing chemical structural formulae. Here, we expand MØD by…
Finding Pathways in Reaction Networks guided by Energy Barriers using Integer Linear Programming
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +2
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This…