Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series

Yuan, Yuan
Chen, Yi-Ping Phoebe
Ni, Shengyu
Xu, Augix Guohua
Tang, Lin
Vingron, Martin
Somel, Mehmet
Khaitovich, Philipp
Background: Comparing biological time series data across different conditions, or different specimens, is a common but still challenging task. Algorithms aligning two time series represent a valuable tool for such comparisons. While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements.


Discovering functional interaction patterns in protein-protein interaction networks
Turanalp, Mehmet E.; Can, Tolga (Springer Science and Business Media LLC, 2008-06-11)
Background: In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution...
MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs
Sacan, Ahmet; Ferhatosmanoglu, Nilgun; Ferhatosmanoglu, Hakan (Springer Science and Business Media LLC, 2009-9-22)
Background: Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing. Description: An efficient and scalable search method for finding nea...
Finding differentially expressed genes for pattern generation
Abul, O; Alhajj, R; Polat, Faruk; Barker, K (Oxford University Press (OUP), 2005-02-15)
Motivation: It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation.
ImaGene: a convolutional neural network to quantify natural selection from genomic data
Torada, Luis; Lorenzon, Lucrezia; Beddis, Alice; Isildak, Ulas; Pattini, Linda; Mathieson, Sara; Fumagalli, Matteo (Springer Science and Business Media LLC, 2019-11-22)
Background: The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms...
JOA: Joint Overlap Analysis of multiple genomic interval sets
Otlu, Burcak; Can, Tolga (Springer Science and Business Media LLC, 2019-03-08)
BackgroundNext-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose restrictions such as not allowing nested intervals or requiring intervals to be sorted when finding overlaps in two or more interval sets.ResultsWe proposed segment tree (ST) and indexed segment tree forest (ISTF) based solutions for intersection of multiple genomic interval sets in parallel...
Citation Formats
Y. Yuan et al., “Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series,” BMC BIOINFORMATICS, pp. 0–0, 2011, Accessed: 00, 2020. [Online]. Available: