- Home
- Publications
- Publication Search
- Publication Details
Title
Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data
Authors
Keywords
-
Journal
Genes
Volume 12, Issue 3, Pages 352
Publisher
MDPI AG
Online
2021-02-28
DOI
10.3390/genes12030352
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Lag penalized weighted correlation for time series clustering
- (2020) Thevaa Chandereng et al. BMC BIOINFORMATICS
- TimeMeter assesses temporal gene expression similarity and identifies differentially progressing genes
- (2020) Peng Jiang et al. NUCLEIC ACIDS RESEARCH
- rmRNAseq: Differential Expression Analysis for Repeated-measures RNA-seq Data
- (2020) Yet Nguyen et al. BIOINFORMATICS
- State-transition analysis of time-sequential gene expression identifies critical points that predict development of acute myeloid leukemia
- (2020) Russell C Rockne et al. CANCER RESEARCH
- dream: Powerful differential expression analysis for repeated measures designs
- (2020) Gabriel E Hoffman et al. BIOINFORMATICS
- Gene regulatory network inference from sparsely sampled noisy data
- (2020) Atte Aalto et al. Nature Communications
- Interpretation of deep learning in genomics and epigenomics
- (2020) Amlan Talukder et al. BRIEFINGS IN BIOINFORMATICS
- A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data
- (2020) Hung Nguyen et al. BRIEFINGS IN BIOINFORMATICS
- Temporal dynamics in meta longitudinal RNA-Seq data
- (2019) Sunghee Oh et al. Scientific Reports
- Current best practices in single‐cell RNA‐seq analysis: a tutorial
- (2019) Malte D Luecken et al. Molecular Systems Biology
- Large Scale Maximum Average Power Multiple Inference on Time‐Course Count Data with Application to RNA‐Seq Analysis
- (2019) Meng Cao et al. BIOMETRICS
- Function Network analysis of time-course liver transcriptome data to reveal novel circadian transcriptional regulators in mammals
- (2019) Maria Simak et al. Journal of the Chinese Medical Association
- Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data
- (2019) Jiajun Zhang et al. PLoS Computational Biology
- Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
- (2018) Laleh Haghverdi et al. NATURE BIOTECHNOLOGY
- Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease
- (2018) Raffaella Nativio et al. NATURE NEUROSCIENCE
- OUP accepted manuscript
- (2018) NUCLEIC ACIDS RESEARCH
- dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data
- (2018) Vân Anh Huynh-Thu et al. Scientific Reports
- iDREM: Interactive visualization of dynamic regulatory networks
- (2018) Jun Ding et al. PLoS Computational Biology
- Clustering gene expression time series data using an infinite Gaussian process mixture model
- (2018) Ian C. McDowell et al. PLoS Computational Biology
- Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent giant cell arteritis
- (2018) Elisabeth De Smit et al. BMC Medical Genomics
- The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression
- (2018) Mark D. Long et al. ONCOGENE
- Recurrent Neural Network for Predicting Transcription Factor Binding Sites
- (2018) Zhen Shen et al. Scientific Reports
- The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
- (2018) Minghui Wang et al. Scientific Data
- Genetic Neural Networks: An artificial neural network architecture for capturing gene expression relationships
- (2018) Ameen Eetemadi et al. BIOINFORMATICS
- GPrank: an R package for detecting dynamic elements from genome-wide time series
- (2018) Hande Topa et al. BMC BIOINFORMATICS
- Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments
- (2018) Rhonda Bacher et al. BMC BIOINFORMATICS
- LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data
- (2018) Jordan M. Singer et al. JOURNAL OF BIOLOGICAL RHYTHMS
- Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains
- (2018) Hans-Ulrich Klein et al. NATURE NEUROSCIENCE
- Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae
- (2017) Maria Simak et al. PLoS One
- Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains
- (2017) Gabriel E. Hoffman et al. Nature Communications
- A high-resolution mRNA expression time course of embryonic development in zebrafish
- (2017) Richard J White et al. eLife
- ImpulseDE: detection of differentially expressed genes in time series data using impulse models
- (2016) Jil Sander et al. BIOINFORMATICS
- Differential rhythmicity: detecting altered rhythmicity in biological data
- (2016) Paul F. Thaben et al. BIOINFORMATICS
- MetaCycle: an integrated R package to evaluate periodicity in large scale data
- (2016) Gang Wu et al. BIOINFORMATICS
- Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets
- (2016) Yalchin Oytam et al. BMC BIOINFORMATICS
- Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model
- (2016) Xiaoxiao Sun et al. BMC BIOINFORMATICS
- EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data
- (2016) Jianying Li et al. BMC GENOMICS
- A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer
- (2016) Daniel Dominguez et al. CELL RESEARCH
- Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data
- (2016) Agata Michna et al. PLoS One
- A transcription factor hierarchy defines an environmental stress response network
- (2016) L. Song et al. SCIENCE
- Bayesian state space models for dynamic genetic network construction across multiple tissues
- (2016) Yulan Liang et al. Statistical Applications in Genetics and Molecular Biology
- Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease
- (2016) Jerome Bouquet et al. mBio
- Continuous time Bayesian networks identify Prdm1 as a negative regulator of TH17 cell differentiation in humans
- (2016) Enzo Acerbi et al. Scientific Reports
- Bayesian state space models for dynamic genetic network construction across multiple tissues
- (2016) Yulan Liang et al. Statistical Applications in Genetics and Molecular Biology
- On the Evaluation of Module Preservation
- (2016) Greg Gibson Cell Systems
- A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets
- (2016) Scott C. Ritchie et al. Cell Systems
- EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
- (2015) Ning Leng et al. BIOINFORMATICS
- DINGO: differential network analysis in genomics
- (2015) Min Jin Ha et al. BIOINFORMATICS
- Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses
- (2015) Vegard Nygaard et al. BIOSTATISTICS
- Multiobjective triclustering of time-series transcriptome data reveals key genes of biological processes
- (2015) Anirban Bhar et al. BMC BIOINFORMATICS
- FunPat: function-based pattern analysis on RNA-seq time series data
- (2015) Tiziana Sanavia et al. BMC GENOMICS
- High-Resolution Chromatin Dynamics during a Yeast Stress Response
- (2015) Assaf Weiner et al. MOLECULAR CELL
- Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
- (2015) Florian Buettner et al. NATURE BIOTECHNOLOGY
- Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses
- (2015) Ruijie Liu et al. NUCLEIC ACIDS RESEARCH
- A Linear Mixed Model Spline Framework for Analysing Time Course ‘Omics’ Data
- (2015) Jasmin Straube et al. PLoS One
- Dynamic profiling of the protein life cycle in response to pathogens
- (2015) M. Jovanovic et al. SCIENCE
- Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks
- (2015) Shijia Zhu et al. Scientific Reports
- Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data
- (2015) Alan L. Hutchison et al. PLoS Computational Biology
- Time-Course Gene Set Analysis for Longitudinal Gene Expression Data
- (2015) Boris P. Hejblum et al. PLoS Computational Biology
- Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction
- (2014) Markus Heinonen et al. BIOINFORMATICS
- Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
- (2014) M. J. Nueda et al. BIOINFORMATICS
- Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
- (2014) Tarmo Äijö et al. BIOINFORMATICS
- High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies
- (2014) Michal Rabani et al. CELL
- Evaluation of Five Methods for Genome-Wide Circadian Gene Identification
- (2014) Gang Wu et al. JOURNAL OF BIOLOGICAL RHYTHMS
- Detecting Rhythms in Time Series with RAIN
- (2014) Paul F. Thaben et al. JOURNAL OF BIOLOGICAL RHYTHMS
- Normalization of RNA-seq data using factor analysis of control genes or samples
- (2014) Davide Risso et al. NATURE BIOTECHNOLOGY
- svaseq: removing batch effects and other unwanted noise from sequencing data
- (2014) Jeffrey T. Leek NUCLEIC ACIDS RESEARCH
- Analysis of clock-regulated genes inNeurosporareveals widespread posttranscriptional control of metabolic potential
- (2014) Jennifer M. Hurley et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Comparison of the transcriptional landscapes between human and mouse tissues
- (2014) Shin Lin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Chromatin state dynamics during blood formation
- (2014) D. Lara-Astiaso et al. SCIENCE
- voom: precision weights unlock linear model analysis tools for RNA-seq read counts
- (2014) Charity W Law et al. GENOME BIOLOGY
- The analytical landscape of static and temporal dynamics in transcriptome data
- (2014) Sunghee Oh et al. Frontiers in Genetics
- EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments
- (2013) Ning Leng et al. BIOINFORMATICS
- A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis
- (2013) Sarah E. Reese et al. BIOINFORMATICS
- Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data
- (2013) Anastasia Deckard et al. BIOINFORMATICS
- Dynamic regulatory network controlling TH17 cell differentiation
- (2013) Nir Yosef et al. NATURE
- Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
- (2013) Simon Anders et al. Nature Protocols
- RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism
- (2013) James D. Mills et al. NEUROSCIENCE LETTERS
- Removing technical variability in RNA-seq data using conditional quantile normalization
- (2012) K. D. Hansen et al. BIOSTATISTICS
- GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion
- (2011) N. X. Vinh et al. BIOINFORMATICS
- ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments
- (2011) M. j. Nueda et al. BIOSTATISTICS
- Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing
- (2011) Marten Jäger et al. BMC GENOMICS
- Impulse Control: Temporal Dynamics in Gene Transcription
- (2011) Nir Yosef et al. CELL
- Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
- (2011) A. Pauli et al. GENOME RESEARCH
- Alternative splicing of mRNA in the molecular pathology of neurodegenerative diseases
- (2011) James Dominic Mills et al. NEUROBIOLOGY OF AGING
- Circadian Control of Global Gene Expression Patterns
- (2010) Colleen J. Doherty et al. Annual Review of Genetics
- Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation
- (2010) R. Yang et al. BIOINFORMATICS
- Asymptotic Conditional Singular Value Decomposition for High-Dimensional Genomic Data
- (2010) Jeffrey T. Leek BIOMETRICS
- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
- (2010) James H Bullard et al. BMC BIOINFORMATICS
- TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach
- (2010) Pietro Zoppoli et al. BMC BIOINFORMATICS
- JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets
- (2010) Michael E. Hughes et al. JOURNAL OF BIOLOGICAL RHYTHMS
- A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
- (2010) Oliver Stegle et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Tackling the widespread and critical impact of batch effects in high-throughput data
- (2010) Jeffrey T. Leek et al. NATURE REVIEWS GENETICS
- Optimal Tests Shrinking Both Means and Variances Applicable to Microarray Data Analysis
- (2010) J.T. Gene Hwang et al. Statistical Applications in Genetics and Molecular Biology
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- A Genome-wide RNAi Screen for Modifiers of the Circadian Clock in Human Cells
- (2009) Eric E. Zhang et al. CELL
- Inference of Gene Regulatory Networks Using Time-Series Data: A Survey
- (2009) Chao Sima et al. CURRENT GENOMICS
- Timing of Gene Expression Responses to Environmental Changes
- (2009) Gal Chechik et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Harmonics of Circadian Gene Transcription in Mammals
- (2009) Michael E. Hughes et al. PLoS Genetics
- Bayesian biclustering of gene expression data
- (2008) Jiajun Gu et al. BMC GENOMICS
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now