60 citations · 194 across the 6 of their papers we have counts for
6 papers
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
Franziska Hinkelmann, Madison Brandon, Bonny Guang +4
Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, with…
Inferring Biologically Relevant Models: Nested Canalyzing Functions
Franziska Hinkelmann, Abdul Salam Jarrah
Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the di…
Fast Gröbner Basis Computation for Boolean Polynomials
Franziska Hinkelmann, Elizabeth Arnold
We introduce the Macaulay2 package BooleanGB, which computes a Gröbner basis for Boolean polynomials using a binary representation rather than symbolic. We compare the runtime of s…
A Mathematical Framework for Agent Based Models of Complex Biological Networks
Franziska Hinkelmann, David Murrugarra, Abdul Salam Jarrah +1
Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agree…
Boolean Models of Bistable Biological Systems
Franziska Hinkelmann, Reinhard Laubenbacher
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often B…
Parameter estimation for Boolean models of biological networks
Elena Dimitrova, Luis David Garcia-Puente, Franziska Hinkelmann +5
Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome,…