Nothing Special   »   [go: up one dir, main page]

Hashemikhabir et al., 2012 - Google Patents

Large-scale signaling network reconstruction

Hashemikhabir et al., 2012

Document ID
3284548666047736235
Author
Hashemikhabir S
Ayaz E
Kavurucu Y
Can T
Kahveci T
Publication year
Publication venue
IEEE/ACM Transactions on Computational Biology and Bioinformatics

External Links

Snippet

Reconstructing the topology of a signaling network by means of RNA interference (RNAi) technology is an underdetermined problem especially when a single gene in the network is knocked down or observed. In addition, the exponential search space limits the existing …
Continue reading at ieeexplore.ieee.org (other versions)

Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30386—Retrieval requests
    • G06F17/30424—Query processing
    • G06F17/30533—Other types of queries
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/12—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for modelling or simulation in systems biology, e.g. probabilistic or dynamic models, gene-regulatory networks, protein interaction networks or metabolic networks
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/24—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/16—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for molecular structure, e.g. structure alignment, structural or functional relations, protein folding, domain topologies, drug targeting using structure data, involving two-dimensional or three-dimensional structures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/30—Medical informatics, i.e. computer-based analysis or dissemination of patient or disease data
    • G06F19/34—Computer-assisted medical diagnosis or treatment, e.g. computerised prescription or delivery of medication or diets, computerised local control of medical devices, medical expert systems or telemedicine
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computer systems based on biological models
    • G06N3/02—Computer systems based on biological models using neural network models
    • G06N3/04—Architectures, e.g. interconnection topology
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N99/00—Subject matter not provided for in other groups of this subclass
    • G06N99/005—Learning machines, i.e. computer in which a programme is changed according to experience gained by the machine itself during a complete run
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computer systems based on biological models
    • G06N3/12—Computer systems based on biological models using genetic models
    • G06N3/126—Genetic algorithms, i.e. information processing using digital simulations of the genetic system
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00—Computer systems utilising knowledge based models
    • G06N5/04—Inference methods or devices
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F15/00—Digital computers in general; Data processing equipment in general
    • G06F15/18—Digital computers in general; Data processing equipment in general in which a programme is changed according to experience gained by the computer itself during a complete run; Learning machines
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N7/00—Computer systems based on specific mathematical models
    • G06N7/005—Probabilistic networks
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F11/00—Error detection; Error correction; Monitoring

Similar Documents

Publication Publication Date Title
Wu et al. Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
Patro et al. Predicting protein interactions via parsimonious network history inference
Hashemikhabir et al. Large-scale signaling network reconstruction
Statnikov et al. Ultra-scalable and efficient methods for hybrid observational and experimental local causal pathway discovery
Amin et al. Top-k similar graph matching using TraM in biological networks
Madeddu et al. A feature-learning-based method for the disease-gene prediction problem
Elhesha et al. Identification of co-evolving temporal networks
Knapp et al. Reconstruction of cellular signal transduction networks using perturbation assays and linear programming
Ahmed et al. ACCORDION: clustering and selecting relevant data for guided network extension and query answering
Hwang et al. Construction of large-scale Bayesian networks by local to global search
Weinstein Generative Statistical Methods for Biological Sequences
Ozsoy et al. A divide and conquer approach for construction of large-scale signaling networks from PPI and RNAi data using linear programming
Arrais et al. Using biomedical networks to prioritize gene–disease associations
Woicik et al. Gemini: memory-efficient integration of hundreds of gene networks with high-order pooling
Pyne et al. Rapid reconstruction of Time-varying gene regulatory networks with limited main memory
Singh Algorithms for the analysis of protein interaction networks
Milenković et al. Topological characteristics of molecular networks
Cai et al. SADA: A general framework to support robust causation discovery with theoretical guarantee
Djordjilović et al. An empirical comparison of popular structure learning algorithms with a view to gene network inference
Nakajima et al. Exact and heuristic methods for network completion for time‐varying genetic networks
Marino Algorithms for biological graphs: analysis and enumeration
Zhao et al. Deep pathway analysis incorporating mutation information and gene expression data
Zhang et al. An graph-based algorithm for prioritizing cancer susceptibility genes from gene fusion data
Pardo Computational method for the inference of therapeutic targets and sequence of treatments
Federico et al. Structure learning for gene regulatory networks