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

Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell RNA-Seq Data Using a Biclustering Approach

(2017) Funan Shi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections

(2017) Robert B. Bentham et al.   NUCLEIC ACIDS RESEARCH

Functional diversity of topological modules in human protein-protein interaction networks

(2017) Guangming Liu et al.   Scientific Reports

Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO 2 Levels

(2017) Jennifer Levering et al.   mSystems

BicNET: Flexible module discovery in large-scale biological networks using biclustering

(2016) Rui Henriques et al.   Algorithms for Molecular Biology

BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge

(2016) Rui Henriques et al.   Algorithms for Molecular Biology

Sparse group factor analysis for biclustering of multiple data sources

(2016) Kerstin Bunte et al.   BIOINFORMATICS

Leveraging big data to transform target selection and drug discovery

(2016) B Chen et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Exploring the Genetic Patterns of Complex Diseases via the Integrative Genome-Wide Approach

(2016) Ben Teng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Erratum: Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum

(2016) Jiading Yang et al.   NEW PHYTOLOGIST

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

(2016) Bingqiang Liu et al.   Scientific Reports

BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes

(2016) Amir Lakizadeh et al.   PLoS One

Biomarkers and subtypes of cancer

(2015) Maud H.W. Starmans et al.   Aging-US

Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data

(2015) Xin Chen et al.   BioEnergy Research

Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models

(2015) Andrea Rau et al.   BIOINFORMATICS

Analysis of miRNA expression profiles in breast cancer using biclustering

(2015) Antonino Fiannaca et al.   BMC BIOINFORMATICS

Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project

(2015) Bie Verbist et al.   DRUG DISCOVERY TODAY

Biclustering on expression data: A review

(2015) Beatriz Pontes et al.   JOURNAL OF BIOMEDICAL INFORMATICS

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

(2015) David J. Reiss et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

A structured view on pattern mining-based biclustering

(2015) Rui Henriques et al.   PATTERN RECOGNITION

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Statistical methods for studying disease subtype heterogeneity

(2015) Molin Wang et al.   STATISTICS IN MEDICINE

BicPAM: Pattern-based biclustering for biomedical data analysis

(2014) Rui Henriques et al.   Algorithms for Molecular Biology

BicOverlapper 2.0: visual analysis for gene expression

(2014) R. Santamaria et al.   BIOINFORMATICS

A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression

(2014) Yiyi Liu et al.   BMC BIOINFORMATICS

Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq

(2014) Jeremy A Miller et al.   BMC GENOMICS

LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification

(2014) Joana P. Goncalves et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

(2014) Eliza J.R. Peterson et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Identification of Clinical Phenotypes Using Cluster Analyses in COPD Patients with Multiple Comorbidities

(2014) Pierre-Régis Burgel et al.   Biomed Research International

Identification of transcription factors for drug-associated gene modules and biomedical implications

(2013) Min Xiong et al.   BIOINFORMATICS

Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress

(2013) Charlotte M Wilson et al.   Biotechnology for Biofuels

Biclustering reveals breast cancer tumour subgroups with common clinical features and improves prediction of disease recurrence

(2013) Yi Kan Wang et al.   BMC GENOMICS

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

(2013) Sung Ho Yoon et al.   GENOME RESEARCH

Data mining with big data

(2013) Xindong Wu et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Sparse Biclustering of Transposable Data

(2013) Kean Ming Tan et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

(2013) M. Iskar et al.   Molecular Systems Biology

Tumour heterogeneity in the clinic

(2013) Philippe L. Bedard et al.   NATURE

Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions

(2013) Qin Ma et al.   NUCLEIC ACIDS RESEARCH

Discovery and visualization of miRNA–mRNA functional modules within integrated data using bicluster analysis

(2013) Kenneth Bryan et al.   NUCLEIC ACIDS RESEARCH

PGMRA: a web server for (phenotype x genotype) many-to-many relation analysis in GWAS

(2013) J. Arnedo et al.   NUCLEIC ACIDS RESEARCH

Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns

(2013) Ruolin Yang et al.   PLANT CELL

Biclustering with heterogeneous variance

(2013) G. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Quantified Self: Fundamental Disruption in Big Data Science and Biological Discovery

(2013) Melanie Swan   Big Data

iBBiG: iterative binary bi-clustering of gene sets

(2012) Daniel Gusenleitner et al.   BIOINFORMATICS

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

(2012) Shan Wang et al.   BMC PLANT BIOLOGY

A comparative analysis of biclustering algorithms for gene expression data

(2012) K. Eren et al.   BRIEFINGS IN BIOINFORMATICS

Intratumor Heterogeneity: Evolution through Space and Time

(2012) C. Swanton   CANCER RESEARCH

MetaMirClust: Discovery of miRNA cluster patterns using a data-mining approach

(2012) Wen-Ching Chan et al.   GENOMICS

Next-generation phenotyping of electronic health records

(2012) G. Hripcsak et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

QServer: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters

(2012) Fengfeng Zhou et al.   PLoS One

Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks

(2012) Joana P. Gonçalves et al.   PLoS One

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

(2012) Jesse Gillis et al.   PLoS Computational Biology

A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data

(2012) Li Li et al.   BioData Mining

An ensemble biclustering approach for querying gene expression compendia with experimental lists

(2011) R. De Smet et al.   BIOINFORMATICS

Genome-wide discovery of missing genes in biological pathways of prokaryotes

(2011) Yong Chen et al.   BMC BIOINFORMATICS

Query-based biclustering of gene expression data using Probabilistic Relational Models

(2011) Hui Zhao et al.   BMC BIOINFORMATICS

Identification of homogeneous genetic architecture of multiple genetically correlated traits by block clustering of genome-wide associations

(2011) Mayetri Gupta et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Using Transcription Modules to Identify Expression Clusters Perturbed in Williams-Beuren Syndrome

(2011) Charlotte N. Henrichsen et al.   PLoS Computational Biology

Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms

(2010) Burton Chia et al.   Algorithms for Molecular Biology

Powerful SNP-Set Analysis for Case-Control Genome-wide Association Studies

(2010) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Chronic Obstructive Pulmonary Disease Phenotypes

(2010) MeiLan K. Han et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Modular analysis of gene expression data with R

(2010) G. Csardi et al.   BIOINFORMATICS

FABIA: factor analysis for bicluster acquisition

(2010) Sepp Hochreiter et al.   BIOINFORMATICS

Biclustering via Sparse Singular Value Decomposition

(2010) Mihee Lee et al.   BIOMETRICS

Expander: from expression microarrays to networks and functions

(2010) Igor Ulitsky et al.   Nature Protocols

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer

(2010) Juan Cui et al.   NUCLEIC ACIDS RESEARCH

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Patterns of HIV-1 Protein Interaction Identify Perturbed Host-Cellular Subsystems

(2010) Jamie I. MacPherson et al.   PLoS Computational Biology

Multi-species integrative biclustering

(2010) Peter Waltman et al.   GENOME BIOLOGY

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

(2009) Sara C Madeira et al.   Algorithms for Molecular Biology

Finding large average submatrices in high dimensional data

(2009) Andrey A. Shabalin et al.   Annals of Applied Statistics

Detailing regulatory networks through large scale data integration

(2009) C. Huttenhower et al.   BIOINFORMATICS

Breast Cancer Subtypes as Defined by the Estrogen Receptor (ER), Progesterone Receptor (PR), and the Human Epidermal Growth Factor Receptor 2 (HER2) among Women with Invasive Breast Cancer in California, 1999-2004

(2009) Carol A. Parise et al.   Breast Journal

Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm

(2009) S.C. Madeira et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

The second wave of synthetic biology: from modules to systems

(2009) Priscilla E. M. Purnick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

(2009) Guojun Li et al.   NUCLEIC ACIDS RESEARCH

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

(2008) Yuji Zhang et al.   BMC BIOINFORMATICS

Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome

(2008) Jason G Mezey et al.   BMC EVOLUTIONARY BIOLOGY

Bayesian biclustering of gene expression data

(2008) Jiajun Gu et al.   BMC GENOMICS

Gene module level analysis: identification to networks and dynamics

(2008) Xuewei Wang et al.   CURRENT OPINION IN BIOTECHNOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

The liver pharmacological and xenobiotic gene response repertoire

(2008) Georges Natsoulis et al.   Molecular Systems Biology

A modular approach for integrative analysis of large-scale gene-expression and drug-response data

(2008) Zoltán Kutalik et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis

(2008) K. Horan et al.   PLANT PHYSIOLOGY

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Biclustering in data mining

(2007) Stanislav Busygin et al.   COMPUTERS & OPERATIONS RESEARCH