13 papers · ranked by Valyu relevance
Timothy A. Pitman, Xiaomeng Huang, Gabor T. Marth, Yi Qiao
In precision medicine, genomic data needs to be processed as fast as possible to arrive at treatment decisions in a timely fashion. We developed mmbam, a library to allow sequence analysis informatics software to access raw sequencing data stored in BAM files extremely fast. Taking advantage of memory mapped file…
G.R. van der Ploeg, J.A. Westerhuis, A. Heintz-Buschart, A.K. Smilde
Recently, studies that investigate microbial temporal dynamics have become more frequent. In a longitudinal microbiome study design, microbial abundance data are collected across multiple time points from the same subjects. In this context, exploratory analysis of longitudinal microbiome data using Principal Component…
Nicola F. Müller, Remco R. Bouckaert
With ever more complex models used to study evolutionary patterns, approaches that facilitate efficient inference under such models are needed. Parallel tempering has long been used to speed up phylogenetic analyses and to make use of multi-core CPUs. Parallel tempering essentially runs multiple MCMC chains in…
Stuart Byma, Akash Dhasade, Adrian Altenhoff, Christophe Dessimoz + 1 more
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find similar pairs in a set of n elements such as protein sequences. Precise…
Shile Qi, Jing Sui, Jiayu Chen, Jingyu Liu + 20 more
There is growing evidence that rather than using a single brain imaging modality to study its association with physiological or symptomatic features, the field is paying more attention to fusion of multimodal information. However, most current multimodal fusion approaches that incorporate functional magnetic resonance…
D. M. Jensen, E. Zendehrouh, J. Liu, V. D. Calhoun + 1 more
Parallel independent component analysis (pICA) is a data-driven method that identifies the maximally independent components of multiple imaging modalities while simultaneously investigating the strength of their correlations. Researchers using pICA are given the option to use the suggested model order calculated by the…
Andreas Härer, Diana J. Rennison
Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e.…
Constantin Scholl, Kassian Kobert, Tomáš Flouri, Alexandros Stamatakis
Motivated by load balance issues in parallel calculations of the phylogenetic likelihood function, we recently introduced an approximation algorithm for efficiently distributing partitioned alignment data to a given number of CPUs. The goal is to balance the accumulated number of sites per CPU, and, at the same time…
Hüsser Alejandra, Caron-Desrochers Laura, Tremblay Julie, Vannasing Phetsamone + 2 more
Functional near infrared spectroscopy (fNIRS) is a neuroimaging technique that uses light at two different wavelengths in the near infrared spectrum to estimate cerebral hemodynamic response, based on concentration changes in both oxygenated and deoxygenated hemoglobin. A multi-dimensional decomposition technique…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Markus Ekvall, Michael Höhle, Lukas Käll
Permutation tests offer a straight forward framework to assess the significance of differences in sample statistics. A significant advantage of permutation tests are the relatively few assumptions about the distribution of the test statistic are needed, as they rely on the assumption of exchangeability of the group…
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread…
Sage Hahn, Max M. Owens, DeKang Yuan, Anthony C Juliano + 3 more
The use of pre-defined parcellations on surface-based representations of the brain as a method for data reduction is common across neuroimaging studies. In particular, prediction-based studies typically employ parcellation-driven summaries of brain measures as input to predictive algorithms, but the choice of…