3 citations · 7 across the 12 of their papers we have counts for
12 papers
Mixed-resolution hybrid modeling in an element-based framework
Kara Bocan, Natasa Miskov-Zivanov
Computational modeling of a complex system is limited by the parts of the system with the least information. While detailed models and high-resolution data may be available for par…
Automating Knowledge-Driven Model Recommendation: Methodology, Evaluation, and Key Challenges
Adam A. Butchy, Cheryl A. Telmer, Natasa Miskov-Zivanov
There is significant interest in using existing repositories of biological entities, relationships, and models to automate biological model assembly and extension. Current methods…
New advances in the automation of context-aware information selection and guided model assembly
Yasmine Ahmed, Adam A Butchy, Khaled Sayed +2
The automated assembly and extension of dynamic network models using information extracted from literature are challenging due to the amount and inconsistency in published literatu…
Guided assembly of cellular network models from knowledge in literature
Yasmine Ahmed, Natasa Miskov-Zivanov
Computational modeling is crucial for understanding and analyzing complex systems. In biology, model creation is a human dependent task that requires reading hundreds of papers and…
DiSH-trend: Intervention Modeling Simulator That Accounts for Trend Influences
Stefan Andjelkovic, Natasa Miskov-Zivanov
Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simul…
ACCORDION: Clustering and Selecting Relevant Data for Guided Network Extension and Query Answering
Yasmine Ahmed, Cheryl Telmer, Natasa Miskov-Zivanov
Querying new information from knowledge sources, in general, and published literature, in particular, aims to provide precise and quick answers to questions raised about a system u…
Intervention Pathway Discovery via Context-Dependent Dynamic Sensitivity Analysis
Gaoxiang Zhou, Kai-Wen Liang, Natasa Miskov-Zivanov
The sensitivity analysis of biological system models can significantly contribute to identifying and explaining influences of internal or external changes on model and its elements…
A Faster DiSH: Hardware Implementation of a Discrete Cell Signaling Network Simulator
Kevin Gilboy, Khaled Sayed, Niteesh Sundaram +2
Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. Howe…
Methods to Expand Cell Signaling Models using Automated Reading and Model Checking
Kai-Wen Liang, Qinsi Wang, Cheryl Telmer +3
Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproduci…
Recipes for Translating Big Data Machine Reading to Executable Cellular Signaling Models
Khaled Sayed, Cheryl A. Telmer, Adam A. Butchy +1
With the tremendous increase in the amount of biological literature, developing automated methods for extracting big data from papers, building models and explaining big mechanisms…
DiSH Simulator: Capturing Dynamics of Cellular Signaling with Heterogeneous Knowledge
Khaled Sayed, Yu-Hsin Kuo, Anuva Kulkarni +1
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both determinist…
Formal Modeling and Analysis of Pancreatic Cancer Microenvironment
Qinsi Wang, Natasa Miskov-Zivanov, Bing Liu +3
The focus of pancreatic cancer research has been shifted from pancreatic cancer cells towards their microenvironment, involving pancreatic stellate cells that interact with cancer…