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- Franziska Hinkelmann, Madison Brandon, +4 authors Reinhard C. Laubenbacher
- BMC Bioinformatics
- 2011

Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding ofâ€¦ (More)

- Alan Veliz-Cuba, Boris Aguilar, Franziska Hinkelmann, Reinhard C. Laubenbacher
- BMC Bioinformatics
- 2014

A key problem in the analysis of mathematical models of molecular networks is the determination of their steady states. The present paper addresses this problem for Boolean network models, anâ€¦ (More)

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 different entities ofâ€¦ (More)

- Franziska Hinkelmann, David Murrugarra, Abdul Salam Jarrah, Reinhard C. Laubenbacher
- Bulletin of mathematical biology
- 2011

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 agreed-upon standard wayâ€¦ (More)

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 Boolean models areâ€¦ (More)

This dissertation develops algebraic theory for discrete models in systems biology. Many discrete model types can be translated into the framework of polynomial dynamical systems (PDS), that is,â€¦ (More)

- Elena S. Dimitrova, Luis David GarcÃa-Puente, +5 authors Paola Vera-Licona
- Theor. Comput. Sci.
- 2011

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, offered as a webâ€¦ (More)

- Franziska Hinkelmann, Elizabeth Arnold
- ArXiv
- 2010

We introduce the Macaulay2 package BooleanGB, which computes a GrÃ¶bner basis for Boolean polynomials using a binary representation rather than symbolic. We compare the runtime of several Booleanâ€¦ (More)

- Antara Sengupta, Camellia Ray, +8 authors Abdul Salam
- 2014

miRNAs are small, non-coding RNAs and of 21-25 nucleotide in size. They negatively regulate protein-coding mRNAs at the post-transcriptional level. miRNAs play very important roles in variousâ€¦ (More)

- Jayanta Kumar Das, Pabitra Pal Choudhury, +5 authors Ranjeet Kumar Rout
- 2014

In this article, a noble approach is presented to classify n-variable Boolean functions in logical way such that each function belonging to a particular class can be traced with respect to a singleâ€¦ (More)

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