A simple approach to ranking differentially expressed gene expression time courses through Gaussian process regression

AA Kalaitzis, ND Lawrence - BMC bioinformatics, 2011 - Springer
Background The analysis of gene expression from time series underpins many biological
studies. Two basic forms of analysis recur for data of this type: removing inactive (quiet) …

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series

O Stegle, KJ Denby, EJ Cooke, DL Wild… - Journal of …, 2010 - liebertpub.com
Understanding the regulatory mechanisms that are responsible for an organism's response
to environmental change is an important issue in molecular biology. A first and important …

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data

PDW Kirk, MPH Stumpf - Bioinformatics, 2009 - academic.oup.com
Motivation: Although widely accepted that high-throughput biological data are typically
highly noisy, the effects that this uncertainty has upon the conclusions we draw from these …

Gaussian process test for high-throughput sequencing time series: application to experimental evolution

H Topa, Á Jónás, R Kofler, C Kosiol, A Honkela - Bioinformatics, 2015 - academic.oup.com
Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to
monitor genomes in great detail. New experiments not only use HTS to measure genomic …

Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction

M Heinonen, O Guipaud, F Milliat, V Buard… - …, 2015 - academic.oup.com
Motivation: Identifying the set of genes differentially expressed along time is an important
task in two-sample time course experiments. Furthermore, estimating at which time periods …

Inferring the perturbation time from biological time course data

J Yang, CA Penfold, MR Grant, M Rattray - Bioinformatics, 2016 - academic.oup.com
Motivation: Time course data are often used to study the changes to a biological process
after perturbation. Statistical methods have been developed to determine whether such a …

Complex network analysis and robustness evaluation of spatial variation of monthly rainfall

H Tongal, B Sivakumar - Stochastic Environmental Research and Risk …, 2024 - Springer
Recently, complex network-based approaches are shown to be efficient for spatial analysis
of rainfall variation. One of the most critical limitations of correlation-based networks is using …

Estimating replicate time shifts using Gaussian process regression

Q Liu, KK Lin, B Andersen, P Smyth, A Ihler - Bioinformatics, 2010 - academic.oup.com
Motivation: Time-course gene expression datasets provide important insights into dynamic
aspects of biological processes, such as circadian rhythms, cell cycle and organ …

A method to identify differential expression profiles of time-course gene data with Fourier transformation

J Kim, RT Ogden, H Kim - BMC bioinformatics, 2013 - Springer
Background Time course gene expression experiments are an increasingly popular method
for exploring biological processes. Temporal gene expression profiles provide an important …

Multiple Gaussian process models for direct time series forecasting

T Hachino, V Kadirkamanathan - IEEJ transactions on electrical …, 2011 - Wiley Online Library
This paper focuses on the problem of time series forecasting using the Gaussian process
models. The Gaussian process model is a nonparametric model and the output of the model …