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Clustering short time series gene expression data

https://doi.org/10.1093/bioinformatics/bti1022
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection
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Cluster analysis and display of genome-wide expression patterns
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Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
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Continuous Representations of Time-Series Gene Expression Data
inferredcites →https://doi.org/10.1091/mbc.11.12.4241openalex-snapshot
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
inferredcites →https://doi.org/10.1093/bioinformatics/18.11.1477openalex-snapshot
Statistical analysis of a small set of time-ordered gene expression data using linear splines
inferredcites →https://doi.org/10.1093/bioinformatics/btg093openalex-snapshot
Gene selection and clustering for time-course and dose–response microarray experiments using order-restricted inference
inferredcites →https://doi.org/10.1093/bioinformatics/btg1036openalex-snapshot
Using hidden Markov models to analyze gene expression time course data
inferredcites →https://doi.org/10.1093/nar/gkg078openalex-snapshot
The Stanford Microarray Database: data access and quality assessment tools
inferredcites →https://doi.org/10.1093/nar/gkh205openalex-snapshot
Statistical resynchronization and Bayesian detection of periodically expressed genes
inferredcites →https://doi.org/10.1093/nar/gng052openalex-snapshot
Testing for differentially expressed genes with microarray data
inferredcites →https://doi.org/10.1126/science.1072152openalex-snapshot
Gene Expression During the Life Cycle of Drosophila melanogaster
inferredcites →https://doi.org/10.1126/science.294.5543.870openalex-snapshot
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What points at this work

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Inferring transcriptomic cell states and transitions only from time series transcriptome data
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Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer
inferred← citeshttps://doi.org/10.1038/srep08984openalex-snapshot
A weighted relative difference accumulation algorithm for dynamic metabolomics data: long-term elevated bile acids are risk factors for hepatocellular carcinoma
inferred← citeshttps://doi.org/10.1038/srep40131openalex-snapshot
DynOmics to identify delays and co-expression patterns across time course experiments
inferred← citeshttps://doi.org/10.1039/b913690hopenalex-snapshot
Finding explained groups of time-course gene expression profiles with predictive clustering trees
inferred← citeshttps://doi.org/10.1039/c8ra05122dopenalex-snapshot
Gene function prediction based on combining gene ontology hierarchy with multi-instance multi-label learning
inferred← citeshttps://doi.org/10.1049/iet-syb.2015.0042openalex-snapshot
Retrieving relevant time‐course experiments: a study on Arabidopsis microarrays
inferred← citeshttps://doi.org/10.1073/pnas.0914285107openalex-snapshot
Model-based method for transcription factor target identification with limited data
inferred← citeshttps://doi.org/10.1073/pnas.1006283107openalex-snapshot
Reverse engineering dynamic temporal models of biological processes and their relationships
inferred← citeshttps://doi.org/10.1073/pnas.1211130110openalex-snapshot
Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia
inferred← citeshttps://doi.org/10.1074/mcp.ra117.000108openalex-snapshot
Systematic and Quantitative Assessment of Hydrogen Peroxide Reactivity With Cysteines Across Human Proteomes
inferred← citeshttps://doi.org/10.1080/00207160701203419openalex-snapshot
A novel pattern based clustering methodology for time-series microarray data
inferred← citeshttps://doi.org/10.1080/02664763.2020.1772733openalex-snapshot
Bayesian modeling of factorial time-course data with applications to a bone aging gene expression study
inferred← citeshttps://doi.org/10.1080/03610918.2016.1206929openalex-snapshot
Bayesian Fourier clustering of gene expression data
inferred← citeshttps://doi.org/10.1080/03610918.2020.1839092openalex-snapshot
An evaluation of a novel approach for clustering genes with dissimilar replicates
inferred← citeshttps://doi.org/10.1080/03610918.2023.2170409openalex-snapshot
On clustering of periodically correlated processes based on Hilbert-Schmidt inner product of Fourier transforms
inferred← citeshttps://doi.org/10.1080/10495398.2020.1824920openalex-snapshot
Temporal microRNA expression profile of pig peripheral blood during postnatal development
inferred← citeshttps://doi.org/10.1088/1758-5090/acb107openalex-snapshot
One-step generation of core–shell biomimetic microspheres encapsulating double-layer cells using microfluidics for hair regeneration
inferred← citeshttps://doi.org/10.1089/cmb.2008.0201openalex-snapshot
K-Boost: A Scalable Algorithm for High-Quality Clustering of Microarray Gene Expression Data
inferred← citeshttps://doi.org/10.1089/cmb.2008.13ttopenalex-snapshot
Timing of Gene Expression Responses to Environmental Changes
inferred← citeshttps://doi.org/10.1089/cmb.2009.0270openalex-snapshot
Wavelet-Based Functional Clustering for Patterns of High-Dimensional Dynamic Gene Expression
inferred← citeshttps://doi.org/10.1089/omi.2010.0005openalex-snapshot
A New Symbolic Representation for the Identification of Informative Genes in Replicated Microarray Experiments
inferred← citeshttps://doi.org/10.1093/bib/bbac415openalex-snapshot
Integrating bioinformatic strategies in spatial life science research
inferred← citeshttps://doi.org/10.1093/bib/bbr032openalex-snapshot
How to cluster gene expression dynamics in response to environmental signals
inferred← citeshttps://doi.org/10.1093/bib/bbx036openalex-snapshot
Dynamic modeling and network approaches for omics time course data: overview of computational approaches and applications
inferred← citeshttps://doi.org/10.1093/bioinformatics/btl056openalex-snapshot
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
inferred← citeshttps://doi.org/10.1093/bioinformatics/btl633openalex-snapshot
Enrichment or depletion of a GO category within a class of genes: which test?
inferred← citeshttps://doi.org/10.1093/bioinformatics/btl667openalex-snapshot
A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors
inferred← citeshttps://doi.org/10.1093/bioinformatics/btl676openalex-snapshot
Inferring pairwise regulatory relationships from multiple time series datasets
inferred← citeshttps://doi.org/10.1093/bioinformatics/btm514openalex-snapshot
Ensemble learning of genetic networks from time-series expression data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btm568openalex-snapshot
Clustering of change patterns using Fourier coefficients
inferred← citeshttps://doi.org/10.1093/bioinformatics/btm605openalex-snapshot
TimeClust: a clustering tool for gene expression time series
inferred← citeshttps://doi.org/10.1093/bioinformatics/btn153openalex-snapshot
Inferring differentiation pathways from gene expression
inferred← citeshttps://doi.org/10.1093/bioinformatics/btn375openalex-snapshot
An unsupervised conditional random fields approach for clustering gene expression time series
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp206openalex-snapshot
Clustered alignments of gene-expression time series data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp222openalex-snapshot
Constrained mixture estimation for analysis and robust classification of clinical time series
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq422openalex-snapshot
Multiple gene expression profile alignment for microarray time-series data clustering
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr037openalex-snapshot
Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr057openalex-snapshot
tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr250openalex-snapshot
An integrative clustering and modeling algorithm for dynamical gene expression data
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts322openalex-snapshot
Bayesian model-based clustering of temporal gene expression using autoregressive panel data approach
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts476openalex-snapshot
Identifying multi-layer gene regulatory modules from multi-dimensional genomic data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv108openalex-snapshot
Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv193openalex-snapshot
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx116openalex-snapshot
ctsGE—clustering subgroups of expression data
inferred← citeshttps://doi.org/10.1093/biostatistics/kxn017openalex-snapshot
Gene profiling for determining pluripotent genes in a time course microarray experiment
inferred← citeshttps://doi.org/10.1093/hr/uhac133openalex-snapshot
VviAGL11 self-regulates and targets hormone- and secondary metabolism-related genes during seed development
inferred← citeshttps://doi.org/10.1093/jxb/eru119openalex-snapshot
Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences
inferred← citeshttps://doi.org/10.1093/molbev/msab288openalex-snapshot
New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos
inferred← citeshttps://doi.org/10.1093/molbev/msz216openalex-snapshot
Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen
inferred← citeshttps://doi.org/10.1093/nar/gkab629openalex-snapshot
TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles
inferred← citeshttps://doi.org/10.1093/nar/gkm284openalex-snapshot
Extracting binary signals from microarray time-course data
inferred← citeshttps://doi.org/10.1093/nar/gkn434openalex-snapshot
A probabilistic generative model for GO enrichment analysis
inferred← citeshttps://doi.org/10.1099/mic.0.021790-0openalex-snapshot
Metabolite and transcriptome analysis of Campylobacter jejuni in vitro growth reveals a stationary-phase physiological switch
inferred← citeshttps://doi.org/10.1099/vir.0.82187-0openalex-snapshot
Distinct gene subsets are induced at different time points after human respiratory syncytial virus infection of A549 cells
inferred← citeshttps://doi.org/10.1101/2020.11.18.388504openalex-snapshot
High-dimensional association detection in large scale genomic data
inferred← citeshttps://doi.org/10.1101/2022.07.23.501235openalex-snapshot
Multi-omics integrated analysis reveals a specific phenotype of CD8+ T cell may contribute to immunothromosis via Th17 response in severe and critical COVID-19
inferred← citeshttps://doi.org/10.1101/349894openalex-snapshot
Transcriptomic atlas of mushroom development highlights an independent origin of complex multicellularity
inferred← citeshttps://doi.org/10.1101/514356openalex-snapshot
Transcriptomic basis and evolution of ant nurse-larval social regulatory interactions
inferred← citeshttps://doi.org/10.1101/582106openalex-snapshot
On triangular inequalities of correlation-based distances for gene expression profiles
inferred← citeshttps://doi.org/10.1101/633693openalex-snapshot
Stress-driven transposable element de-repression dynamics in a fungal pathogen
inferred← citeshttps://doi.org/10.1101/gad.338202.120openalex-snapshot
Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells
inferred← citeshttps://doi.org/10.1104/pp.16.01100openalex-snapshot
A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis
showing the first 200 of 494
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