Journal article
Mining, modeling, and evaluation of subnetworks from large biomolecular networks and its comparison study
IEEE transactions on information technology in biomedicine, v 13(2), pp 184-194
Mar 2009
PMID: 19272861
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
In this paper, we present a novel method to mine, model, and evaluate a regulatory system executing cellular functions that can be represented as a biomolecular network. Our method consists of two steps. First, a novel scale-free network clustering approach is applied to such a biomolecular network to obtain various subnetworks. Second, computational models are generated for the subnetworks and simulated to predict their behavior in the cellular context. We discuss and evaluate some of the advanced computational modeling approaches, in particular, state-space modeling, probabilistic Boolean network modeling, and fuzzy logic modeling. The modeling and simulation results represent hypotheses that are tested against high-throughput biological datasets (microarrays and/or genetic screens) under normal and perturbation conditions. Experimental results on time-series gene expression data for the human cell cycle indicate that our approach is promising for subnetwork mining and simulation from large biomolecular networks.
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Details
- Title
- Mining, modeling, and evaluation of subnetworks from large biomolecular networks and its comparison study
- Creators
- Xiaohua Hu - College of Information Science and Technology, Drexel University, Philadelphia, PA 19104, USA. thu@cis.drexel.eduMichael NgFang-Xiang WuBahrad A Sokhansanj
- Publication Details
- IEEE transactions on information technology in biomedicine, v 13(2), pp 184-194
- Publisher
- The Institute of Electrical and Electronics Engineers, Inc. (IEEE); United States
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Information Science; Electrical and Computer Engineering
- Web of Science ID
- WOS:000264059200006
- Scopus ID
- 2-s2.0-63349107248
- Other Identifier
- 991014878186804721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Computer Science, Information Systems
- Computer Science, Interdisciplinary Applications
- Mathematical & Computational Biology
- Medical Informatics