A network synthesis model for generating protein interaction network families
SME Sahraeian, BJ Yoon - 2012 - journals.plos.org
In this work, we introduce a novel network synthesis model that can generate families of
evolutionarily related synthetic protein–protein interaction (PPI) networks. Given an …
evolutionarily related synthetic protein–protein interaction (PPI) networks. Given an …
GASOLINE: a greedy and stochastic algorithm for optimal local multiple alignment of interaction networks
The analysis of structure and dynamics of biological networks plays a central role in
understanding the intrinsic complexity of biological systems. Biological networks have been …
understanding the intrinsic complexity of biological systems. Biological networks have been …
Comparative analysis of biological networks: Hidden markov model and markov chain-based approach
This study reviewed the application of Markov models to various comparative network
analysis problems which provides a powerful means of gaining novel system-level …
analysis problems which provides a powerful means of gaining novel system-level …
Biological network querying techniques: analysis and comparison
Research in systems biology has made available large amounts of data about interactions
among cell building blocks (eg, proteins, genes). To properly look up these data and mine …
among cell building blocks (eg, proteins, genes). To properly look up these data and mine …
Characterizing co-expression networks underpinning maize stalk rot virulence in Fusarium verticillioides through computational subnetwork module analyses
Fusarium verticillioides is recognized as an important stalk rot pathogen of maize worldwide,
but our knowledge of genetic mechanisms underpinning this pathosystem is limited …
but our knowledge of genetic mechanisms underpinning this pathosystem is limited …
Effective identification of conserved pathways in biological networks using hidden Markov models
Background The advent of various high-throughput experimental techniques for measuring
molecular interactions has enabled the systematic study of biological interactions on a …
molecular interactions has enabled the systematic study of biological interactions on a …
RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks
Motivation: Recent technological advances in measuring molecular interactions have
resulted in an increasing number of large-scale biological networks. Translation of these …
resulted in an increasing number of large-scale biological networks. Translation of these …
Asymmetric comparison and querying of biological networks
Comparing and querying the protein-protein interaction (PPI) networks of different
organisms is important to infer knowledge about conservation across species. Known …
organisms is important to infer knowledge about conservation across species. Known …
An efficient network querying method based on conditional random fields
Motivation: A large amount of biomolecular network data for multiple species have been
generated by high-throughput experimental techniques, including undirected and directed …
generated by high-throughput experimental techniques, including undirected and directed …
Private predictions on hidden Markov models
Abstract Hidden Markov models (HMMs) are widely used in practice to make predictions.
They are becoming increasingly popular models as part of prediction systems in finance …
They are becoming increasingly popular models as part of prediction systems in finance …