It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data

No abstract is available for this paper.

• Publication year

  2019

• Venue

  Briefings Bioinform.

• Publication date

  2019-07-19

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bib/bby014PMID 29490019PMCID PMC6931057
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A systems-level analysis of drug–target–disease associations for drug repositioning

  2018cited by this paper
• Identifying miRNA sponge modules using biclustering and regulatory scores

  2017cited by this paper
• Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell RNA-Seq Data Using a Biclustering Approach

  2017cited by this paper
• QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data

  2017cited by this paper
• BicPAMS: software for biological data analysis with pattern-based biclustering

  2017cited by this paper
• Additional file 7: of Identifying miRNA sponge modules using biclustering and regulatory scores

  2017cited by this paper
• Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data

  2017cited by this paper
• DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses

  2017cited by this paper
• A systematic comparative evaluation of biclustering techniques

  2017cited by this paper
• Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels

  2017cited by this paper
• Functional diversity of topological modules in human protein-protein interaction networks

  2017cited by this paper
• MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections

  2016cited by this paper
• Leveraging big data to transform target selection and drug discovery

  2016cited by this paper
• Pooling across cells to normalize single-cell RNA sequencing data with many zero counts

  2016cited by this paper
• Near-optimal probabilistic RNA-seq quantification

  2016cited by this paper
• BicNET: Flexible module discovery in large-scale biological networks using biclustering

  2016cited by this paper
• Applied Biclustering Methods for Big and High-Dimensional Data Using R

  2016cited by this paper
• Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

  2016cited by this paper
• Nitrogen remobilization and conservation, and underlying senescence‐associated gene expression in the perennial switchgrass Panicum virgatum

  2016cited by this paper
• Big Data Application in Biomedical Research and Health Care: A Literature Review

  2016cited by this paper
• BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge

  2016cited by this paper
• QUBIC: a bioconductor package for qualitative biclustering analysis of gene co‐expression data

  2016cited by this paper
• Population-level analysis of gut microbiome variation

  2016cited by this paper
• Erratum: Near-optimal probabilistic RNA-seq quantification

  2016cited by this paper
• PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

  2016cited by this paper
• Data mining with big data

  2016cited by this paper
• BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes

  2016cited by this paper
• Design and computational analysis of single-cell RNA-sequencing experiments

  2016cited by this paper
• Transformation and model choice for RNA-seq co-expression analysis

  2016cited by this paper
• Coming of age: ten years of next-generation sequencing technologies

  2016cited by this paper
• KEGG: new perspectives on genomes, pathways, diseases and drugs

  2016cited by this paper
• Statistical methods for studying disease subtype heterogeneity

  2016cited by this paper
• SC3 - consensus clustering of single-cell RNA-Seq data

  2016cited by this paper
• Exploring the Genetic Patterns of Complex Diseases via the Integrative Genome-Wide Approach

  2015cited by this paper
• Sparse group factor analysis for biclustering of multiple data sources

  2015cited by this paper
• RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

  2015cited by this paper
• Analysis of miRNA expression profiles in breast cancer using biclustering

  2015cited by this paper
• Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data

  2015cited by this paper
• Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

  2015cited by this paper
• Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models

  2015cited by this paper
• Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project.

  2015cited by this paper
• Biomarkers and subtypes of cancer

  2015cited by this paper
• cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

  2015cited by this paper
• Biclustering on expression data: A review

  2015cited by this paper
• A structured view on pattern mining-based biclustering

  2015cited by this paper
• Ten years of next-generation sequencing technology.

  2014cited by this paper
• Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq

  2014cited by this paper
• A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression

  2014cited by this paper
• A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

  2014cited by this paper
• Identification of transcription factors for drug-associated gene modules and biomedical implications

  2014cited by this paper
• Gene Ontology Consortium: going forward

  2014cited by this paper
• BicOverlapper 2.0: visual analysis for gene expression

  2014cited by this paper
• Identification of Clinical Phenotypes Using Cluster Analyses in COPD Patients with Multiple Comorbidities

  2014cited by this paper
• LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification

  2014cited by this paper
• Optimizing genome-scale network reconstructions

  2014cited by this paper
• BicPAM: Pattern-based biclustering for biomedical data analysis

  2014cited by this paper
• Sparse Biclustering of Transposable Data

  2014cited by this paper
• Tumour heterogeneity in the clinic

  2013cited by this paper
• A comparative analysis of biclustering algorithms for gene expression data

  2013cited by this paper
• A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

  2013cited by this paper
• Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns[C][W]

  2013cited by this paper
• Biclustering reveals breast cancer tumour subgroups with common clinical features and improves prediction of disease recurrence

  2013cited by this paper
• Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress

  2013cited by this paper
• Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

  2013cited by this paper
• PGMRA: a web server for (phenotype × genotype) many-to-many relation analysis in GWAS

  2013cited by this paper
• Discovery and visualization of miRNA–mRNA functional modules within integrated data using bicluster analysis

  2013cited by this paper
• The Quantified Self: Fundamental Disruption in Big Data Science and Biological Discovery

  2013cited by this paper
• Biclustering with heterogeneous variance

  2013cited by this paper
• Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions

  2013cited by this paper
• Intratumor heterogeneity: evolution through space and time.

  2012cited by this paper
• Next-generation phenotyping of electronic health records

  2012cited by this paper
• A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data

  2012cited by this paper
• Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks

  2012cited by this paper
• QServer: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters

  2012cited by this paper
• MetaMirClust: discovery of miRNA cluster patterns using a data-mining approach.

  2012cited by this paper
• Introduction to genetic association studies.

  2012cited by this paper
• “Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

  2012cited by this paper
• iBBiG: iterative binary bi-clustering of gene sets

  2012cited by this paper
• Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

  2012cited by this paper
• Computational methods for transcriptome annotation and quantification using RNA-seq

  2011cited by this paper
• Using Transcription Modules to Identify Expression Clusters Perturbed in Williams-Beuren Syndrome

  2011cited by this paper
• Models for transcript quantification from RNA-Seq

  2011cited by this paper
• An ensemble biclustering approach for querying gene expression compendia with experimental lists

  2011cited by this paper
• RNA sequencing: advances, challenges and opportunities

  2011cited by this paper
• Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series

  2011cited by this paper
• Identification of homogeneous genetic architecture of multiple genetically correlated traits by block clustering of genome‐wide associations

  2011cited by this paper
• Genome-wide discovery of missing genes in biological pathways of prokaryotes

  2011cited by this paper
• Query-based biclustering of gene expression data using Probabilistic Relational Models

  2011cited by this paper
• Powerful SNP-set analysis for case-control genome-wide association studies.

  2010cited by this paper
• Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms

  2010cited by this paper
• An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer

  2010cited by this paper
• The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

  2010cited by this paper
• Modular analysis of gene expression data with R

  2010cited by this paper
• Chronic obstructive pulmonary disease phenotypes: the future of COPD.

  2010cited by this paper
• Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm

  2010cited by this paper
• Title : Powerful SNP Set Analysis for Case-Control Genome Wide Association Studies Running Title : Powerful SNP Set Analysis

  2010cited by this paper
• which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Multi-species integrative biclustering

  2010cited by this paper
• Comparative analysis of biclustering algorithms

  2010cited by this paper
• Biclustering via Sparse Singular Value Decomposition

  2010cited by this paper
• Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

  2010cited by this paper

• Can environmental clustering reveal soil profile patterns? A depth-based approach at field scale

  2026cites this paper
• Evaluating internet accessibility and equity in Indonesia using integrated SUSENAS and OOKLA data

  2026cites this paper
• Biclustering-Based Analysis to Identify Fruit Production Potential in Indonesia Using Plaid Model Algorithm

  2025cites this paper
• Biclustering in bioinformatics using big data and High Performance Computing applications: challenges and perspectives, a review

  2025cites this paper
• Exhaustive biclustering driven by self-learning evolutionary approach for biomedical data

  2025cites this paper
• Using Biclustering to Detect Cheating in Real Time on Mixed-Format Tests

  2025cites this paper
• A formal explanation space for the simultaneous clustering of neurologic diseases based on their signs and symptoms

  2025cites this paper
• Finding Interpretable Data Pockets in Tabular Data

  2025cites this paper
• Biclustering Swiss In-home Food Consumption Across Consumer Groups and Foods

  2025cites this paper
• Model-based bi-clustering using multivariate Poisson-lognormal with general block-diagonal covariance matrix and its applications

  2025influential citation
• Bi-clustering of Binary Data via Neurodynamics-driven Binary Matrix Factorization

  2025cites this paper
• A personalized reinforcement learning recommendation algorithm using bi-clustering techniques

  2025cites this paper
• UnPaSt: unsupervised patient stratification by biclustering of omics data

  2024cites this paper
• Biclustering data analysis: a comprehensive survey

  2024influential citation
• Biclustering a dataset using photonic quantum computing

  2024cites this paper
• EnsemBic: An effective ensemble of biclustering to identify potential biomarkers of esophageal squamous cell carcinoma

  2024cites this paper
• Heterogeneity analysis provides evidence for a genetically homogeneous subtype of bipolar-disorder

  2024cites this paper
• Multiple clusterings: Recent advances and perspectives

  2024cites this paper
• bioScience: A new python science library for high-performance computing bioinformatics analytics

  2024cites this paper
• Integrating Statistical Significance and Discriminative Power in Pattern Discovery

  2024cites this paper
• Biclustering of Log Data: Insights from a Computer-Based Complex Problem Solving Assessment

  2024cites this paper
• Online–Offline Integrated Value Innovation Ecosystem: A Lead User Perspective

  2024cites this paper
• Heterogeneity analysis provides evidence for a genetically homogeneous subtype of bipolar-disorder

  2024cites this paper
• Outcome-guided spike-and-slab Lasso Biclustering: A Novel Approach for Enhancing Biclustering Techniques for Gene Expression Analysis

  2024cites this paper
• Identifying Poverty Vulnerability Patterns in Indonesia using Cheng and Chruch’s Algorithm

  2024cites this paper
• Co-clustering: A Survey of the Main Methods, Recent Trends, and Open Problems

  2024cites this paper
• HBIC: A Biclustering Algorithm for Heterogeneous Datasets

  2024cites this paper
• Optimization of dynamic bi-clustering based on improved genetic algorithm for microarray data

  2024cites this paper
• UnPaSt: unsupervised patient stratification by differentially expressed biclusters in omics data

  2024cites this paper
• Physical modeling of embryonic transcriptomes identifies collective modes of gene expression

  2024cites this paper
• Biclustering Performance Evaluation of Cheng and Church Algorithm and Iterative Signature Algorithm

  2023cites this paper
• MESBC: A novel mutually exclusive spectral biclustering method for cancer subtyping

  2023cites this paper
• G-bic: generating synthetic benchmarks for biclustering

  2023cites this paper
• Biarchetype Analysis: Simultaneous Learning of Observations and Features Based on Extremes

  2023cites this paper
• Pipeline for characterizing alternative mechanisms (PCAM) based on bi-clustering to study colorectal cancer heterogeneity.

  2023cites this paper
• Dual ICA to extract interacting sets of genes and conditions from transcriptomic data

  2023cites this paper
• Measuring organizational happiness in higher education - a data-driven approach

  2023cites this paper
• A New Binary Biclustering Algorithm Based on Weight Adjacency Difference Matrix for Analyzing Gene Expression Data

  2023cites this paper
• Metaheuristic Biclustering Algorithms: From State-of-the-art to Future Opportunities

  2023cites this paper
• Scaling pattern mining through non-overlapping variable partitioning

  2022cites this paper
• The Application of Bi-clustering and Bayesian Network for Gene Sets Network Construction in Breast Cancer Microarray Data

  2022cites this paper
• Biclustering Algorithms Based on Metaheuristics: A Review

  2022cites this paper
• A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans

  2022cites this paper
• Mutually exclusive spectral biclustering and its applications in cancer subtyping

  2022cites this paper
• Biclustering fMRI time series: a comparative study

  2022influential citation
• MSR-based algorithms for biclustering of microarray gene expression data

  2022cites this paper
• DESMOND 2.0: Identification of differentially expressed biclusters for unsupervised patient stratification

  2022cites this paper
• Topology and redescriptions detect multiple alternative biological pathways from clinical phenotypes

  2022cites this paper
• Topological biclustering ARTMAP for identifying within bicluster relationships

  2022cites this paper
• MSR based algorithms for biclustering of microarray gene expression data: a review

  2022cites this paper
• Scalability achievements for enumerative biclustering with online partitioning: Case studies involving mixed-attribute datasets

  2021cites this paper
• Precision medicine

  2021cites this paper
• Biclustering analysis of functionals via penalized fusion

  2021cites this paper
• Highly expressed centromere protein L indicates adverse survival and associates with immune infiltration in hepatocellular carcinoma

  2021cites this paper
• FuBiNFS - fuzzy biclustering neuro-fuzzy system

  2021cites this paper
• Large-scale miRNA-Target Data Analysis to Discover miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans

  2021cites this paper
• Maximal-Sum submatrix search using a hybrid contraint programming/linear programming approach

  2021cites this paper
• Penalized -regression-based bicluster localization

  2021cites this paper
• DISA tool: Discriminative and informative subspace assessment with categorical and numerical outcomes

  2021cites this paper
• Evolutionary Local Search Algorithm for the biclustering of gene expression data based on biological knowledge

  2021cites this paper
• Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

  2021cites this paper
• Integrative and sparse singular value decomposition method for biclustering analysis in multi-sources dataset

  2021cites this paper
• EBIC.JL: an efficient implementation of evolutionary biclustering algorithm in Julia

  2021cites this paper
• MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data

  2021cites this paper
• miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data

  2021cites this paper
• ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network

  2021cites this paper
• gMSR: A Multi-GPU Algorithm to Accelerate a Massive Validation of Biclusters

  2020cites this paper
• Identification Of Differentially Expressed Gene Modules In Heterogeneous Diseases.

  2020cites this paper
• A New Algorithm for Convex Biclustering and Its Extension to the Compositional Data

  2020cites this paper
• Iterative Multi-mode Discretization: Applications to Co-clustering

  2020cites this paper
• Spoken Language Interaction with Virtual Agents and Robots (SLIVAR): Towards Effective and Ethical Interaction (Dagstuhl Seminar 20021)

  2020cites this paper
• ORN: Extracting Latent Pathway Activities in Cancer with OR-gate Network

  2020cites this paper
• Identification of Differentially Expressed Gene Modules in Heterogeneous Diseases

  2020cites this paper
• BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization

  2020cites this paper
• Discovering Multiple Co-Clusterings in Subspaces

  2019cites this paper
• Co-clustering algorithm for the identification of cancer subtypes from gene expression data

  2019cites this paper
• A novel biclustering of gene expression data based on hybrid BAFS-BSA algorithm

  2019cites this paper
• The Interplay Between Solar Radiation, Climate Change and Immunotoxicants in Relation to Immune Response Modulation: A Concern for Outdoor Workers’ Health

  2019cites this paper
• Discovering a sparse set of pairwise discriminating features in high-dimensional data

  2019cites this paper
• Identifying gene-specific subgroups: an alternative to biclustering

  2019cites this paper
• Discovering Multiple Co-Clusterings With Matrix Factorization

  2019influential citation
• EBIC: a scalable biclustering method for large scale data analysis

  2019cites this paper
• Transcriptome Analysis

  2019cites this paper
• Scalable biclustering — the future of big data exploration?

  2019cites this paper
• QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data

  2019cites this paper
• Bi-clustering based biological and clinical characterization of colorectal cancer in complementary to CMS classification

  2018cites this paper
• Optimising allocation of marketing resources among offline channel retailers: A bi-clustering-based model

  year unknowncites this paper
• Identification of Differentially Expressed Gene Modules in Heterogeneous Diseases

  year unknowncites this paper