Studying and modelling dynamic biological processes using time-series gene expression data

Z Bar-Joseph, A Gitter, I Simon - Nature Reviews Genetics, 2012 - nature.com
Biological processes are often dynamic, thus researchers must monitor their activity at
multiple time points. The most abundant source of information regarding such dynamic …

[HTML][HTML] Dynamics in transcriptomics: advancements in RNA-seq time course and downstream analysis

D Spies, C Ciaudo - Computational and structural biotechnology journal, 2015 - Elsevier
Abstract Analysis of gene expression has contributed to a plethora of biological and medical
research studies. Microarrays have been intensively used for the profiling of gene …

AngClust: angle feature-based clustering for short time series gene expression profiles

A Li, S Xiong, J Li, S Mallik, Y Liu, R Fei… - IEEE/ACM …, 2022 - ieeexplore.ieee.org
When clustering gene expression, it is expected that correlation coefficients of genes in the
same clusters are high, and that gene ontology (GO) enrichment analysis of most clusters …

Natural cubic spline regression modeling followed by dynamic network reconstruction for the identification of radiation-sensitivity gene association networks from time …

A Michna, H Braselmann, M Selmansberger, A Dietz… - PloS one, 2016 - journals.plos.org
Gene expression time-course experiments allow to study the dynamics of transcriptomic
changes in cells exposed to different stimuli. However, most approaches for the …

Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays

JR Williams, R Yang, JL Clifford, D Watson… - Bmc Bioinformatics, 2019 - Springer
Background Life science research is moving quickly towards large-scale experimental
designs that are comprised of multiple tissues, time points, and samples. Omic time-series …

Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress

K Jo, HB Kwon, S Kim - Methods, 2014 - Elsevier
Measuring expression levels of genes at the whole genome level can be useful for many
purposes, especially for revealing biological pathways underlying specific phenotype …

The transcriptomic revolution and radiation biology

SA Amundson - International journal of radiation biology, 2022 - Taylor & Francis
Purpose This article will briefly review the origins and evolution of functional genomics, first
describing the experimental technology, and then some of the approaches applied to data …

Comparative analysis of pathology and behavioural phenotypes in mouse models of Huntington's disease

SP Brooks, L Jones, SB Dunnett - Brain research bulletin, 2012 - Elsevier
The longitudinal characterisation of Huntington's disease (HD) mouse lines is essential for
the understanding of the differential developmental time course, nature and severity of …

A survey of computational tools for downstream analysis of proteomic and other omic datasets

A Karimpour-Fard, LE Epperson, LE Hunter - Human genomics, 2015 - Springer
Proteomics is an expanding area of research into biological systems with significance for
biomedical and therapeutic applications ranging from understanding the molecular basis of …

[HTML][HTML] Transcriptomic analysis reveals up-regulated histone genes may play a key role in zebrafish embryo-larvae response to Bisphenol A (BPA) exposure

H Yu, W Song, X Chen, Q Zhao, X Du - Ecotoxicology and Environmental …, 2023 - Elsevier
Bisphenol A (BPA) can induce complex regulatory mechanisms in many aquatic organisms,
and it is difficult to find a suitable analytical method to efficiently enrich key genes …