Nowicka et al., 2020 - Google Patents

A framework for designing miRNA-based distributed cell classifier circuits

Nowicka et al., 2020

View PDF
Document ID
9695069019362607349
Author
Nowicka M
Siebert H
Publication year
Publication venue
bioRxiv

External Links

Snippet

Motivation Cell classifiers are synthetic bio-devices performing type-specific in vivo classification. The circuits identify a cell state based on its molecular fingerprint. In particular, the classifiers may be designed to recognize cancerous cells and trigger their apoptosis …
Continue reading at www.biorxiv.org (PDF) (other versions)

Classifications

    • 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
    • G06F19/30—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
    • G06F19/345—Medical expert systems, neural networks or other automated diagnosis
    • 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
    • G06F19/28—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
    • 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
    • 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
    • G06F19/18—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
    • 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
    • G06F19/20—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
    • 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
    • G06N—COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00—Computer systems utilising knowledge based models
    • G06N5/02—Knowledge representation
    • G06N5/022—Knowledge engineering, knowledge acquisition
    • G06N5/025—Extracting rules from data
    • 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
    • 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
    • G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
    • G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
    • G06K9/62—Methods or arrangements for recognition using electronic means
    • G06K9/6267—Classification techniques
    • G06K9/6268—Classification techniques relating to the classification paradigm, e.g. parametric or non-parametric approaches
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
    • G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
    • G06K9/62—Methods or arrangements for recognition using electronic means
    • G06K9/6217—Design or setup of recognition systems and techniques; Extraction of features in feature space; Clustering techniques; Blind source separation
    • G06K9/6261—Design or setup of recognition systems and techniques; Extraction of features in feature space; Clustering techniques; Blind source separation partitioning the feature space
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06K—RECOGNITION OF DATA; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
    • G06K9/00—Methods or arrangements for reading or recognising printed or written characters or for recognising patterns, e.g. fingerprints
    • G06K9/62—Methods or arrangements for recognition using electronic means
    • G06K9/6267—Classification techniques
    • G06K9/6279—Classification techniques relating to the number of classes

Similar Documents

Publication Publication Date Title
Lee et al. Review of statistical methods for survival analysis using genomic data
Ram et al. Classification and biomarker genes selection for cancer gene expression data using random forest
Jabeen et al. Machine learning-based state-of-the-art methods for the classification of rna-seq data
Berestovsky et al. An evaluation of methods for inferring Boolean networks from time-series data
Khalsan et al. A survey of machine learning approaches applied to gene expression analysis for cancer prediction
Zararsız et al. A comprehensive simulation study on classification of RNA-Seq data
Singh et al. DIABLO–an integrative, multi-omics, multivariate method for multi-group classification
Badwan et al. Machine learning approaches to predict drug efficacy and toxicity in oncology
US11574718B2 (en) Outcome driven persona-typing for precision oncology
Le et al. Machine learning for cell type classification from single nucleus RNA sequencing data
Doostparast Torshizi et al. Graph-based semi-supervised learning with genomic data integration using condition-responsive genes applied to phenotype classification
Bhandari et al. A comprehensive survey on computational learning methods for analysis of gene expression data
Noorbakhsh et al. Machine learning in biology and medicine
Zararsiz et al. voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data
Bugnon et al. Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning
Yin et al. scIAE: an integrative autoencoder-based ensemble classification framework for single-cell RNA-seq data
Park et al. Machine learning-based identification of genetic interactions from heterogeneous gene expression profiles
Seifert et al. Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study
Wise et al. SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data
Kim et al. Bayesian evolutionary hypergraph learning for predicting cancer clinical outcomes
Osseni et al. MOT: a Multi-Omics Transformer for multiclass classification tumour types predictions
Nowicka et al. A framework for designing miRNA-based distributed cell classifier circuits
Kusonmano et al. Effects of pooling samples on the performance of classification algorithms: a comparative study
Yang et al. Deep-BGCpred: A unified deep learning genome-mining framework for biosynthetic gene cluster prediction
Brbić et al. Discovering novel cell types across heterogeneous single-cell experiments