11 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…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
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…
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…
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As demand rises for scalable and sustainable energy storage, fast and low-cost diagnostics capable of identifying cell-to-cell variations are urgently needed, particularly for factory-produced sorting and second-life assessment. Electrochemical impedance spectroscopy (EIS) is widely used but remains slow, expensive and…
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Background: Pharmaceutical batch scheduling in multi-reactor configurations presents complex optimization challenges under operational uncertainty, yet limited research addresses how parallel processing capacity affects heuristic performance and predictive modeling. Objectives: This study investigated scheduling…
Andrew Simmonett, Bernard Brooks, Thomas Darden
Evaluation of noncovalent electrostatic interactions is the dominant bottleneck in classical molecular dynamics simulations, and evaluation of Coulombic matrix elements similarly limits quantum mechanical self consistent field calculations. These difficulties are a result of the Coulomb operator’s slow decay, which…
Caroline Arnoux, Luis-Adrian Perez-Covarrubias, Alexandre Khaldi, Quentin Carlier + 4 more
Although additive manufacturing using multi-photon direct laser writing is nowadays considered as a major tool in the fabrication of future nano/micro-objects and optical components, it is currently limited by the low throughput of the writing process. To circumvent this issue, massive parallelization of the write…
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Raman spectroscopy is an increasingly powerful and fast-growing analytical technique across diverse disciplines, from materials science and chemistry to biology and medicine, thanks to advances in Raman instrumentation and greatly supported by the flourishing of chemometrics and artificial intelligence (AI). However…