Parallel and Scalable Bioinformatics

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Fairness of decision-making algorithms is an increasingly important issue. In this paper, we focus on spectral clustering with group fairness constraints, where every demographic group is represented in each cluster proportionally as in the general populat ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

Engineering and characterizing proteins can be time-consuming and cumbersome, motivating the development of generalist CRISPR-Cas enzymes1–4 to enable diverse genome editing applications. However, such enzymes have caveats such as an increased risk of off- ...

Optical biosensors offer significant advantages for minimally invasive in vivo and in vitro diagnostics. Optical sensors that are based on the fluorescence of semiconducting single-walled carbon nanotubes (SWCNTs) especially benefit from a near-infrared (n ...

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Introduction: EGFR mutations are key oncogenic drivers in lung adenocarcinoma (LUAD), predominantly affecting Asian, nonsmoking, and female populations. Although common mutations, such as exon 19 deletions and L858R, respond well to tyrosine kinase inhibit ...

Recent advances in machine learning have dramatically increased model size and computational requirements, increasingly straining computing system capabilities. This tension is particularly acute for resource-constrained edge scenarios, for which careful h ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

In less than a century, electronic computers have become essential to everyday life and have transformed scientific research. Their use in solving scientific problems has integrated theoretical and experimental approaches, often blurring the lines between ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...

Dataset corresponding to the following manuscript: Slagter, A., Setyadji, J.A., Vogt, E.L. et al. Nanoindentation Hardness and Modulus of Al2O3–SiO2–CaO and MnO–SiO2–FeO Inclusions in Iron. Metall Mater Trans A (2024). https://doi.org/10.1007/s11661-024-0 ...

We propose a comparative study of three different methods aimed at optimizing existing groundwater monitoring networks. Monitoring piezometric heads in subsurface porous formations is crucial at regional scales to properly characterize the relevant subsurf ...

This paper presents a novel hybrid framework for generating and updating a synthetic population. We call it hybrid because it combines model-based and data-driven approaches. Existing generators produce a snapshot of synthetic data that becomes outdated ov ...

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

This data set contains the data collected during the FNS project Green Piezo (Grant no. 179064) in association with the recent publication entitled “3D printing of customizable transient bioelectronics and sensors”. This work aims to study and demonstrate ...

In light of the challenges posed by climate change and the goals of the Paris Agreement, electricity generation is shifting to a more renewable and decentralized pattern, while the operation of systems like buildings is increasingly electrified. This calls ...

This document contains all the data and the details of the analysis used in the manuscript titled " Control of Ge island coalescence for the formation of nanowires on silicon." https://doi.org/10.1039/D3NH00573A ...

Parallel and Scalable Bioinformatics

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Accelerating Spectral Clustering under Fairness Constraints

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning

Designing DNA-based nanotubes as near-infrared sensors for detecting cancer biomarkers

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Decoding the Clinical and Molecular Signatures of EGFR Common, Compound, and Uncommon Mutations in NSCLC: A Brief Report

Keep All in Memory with Maxwell: a Near-SRAM Computing Architecture for Edge AI Applications

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Simulating Interacting Quantum Systems with Near-Term Quantum Computers

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures

Nanoindentation hardness and modulus of Al2O3-SiO2-CaO and MnO-SiO2-FeO inclusions in iron

Data-driven statistical optimization of a groundwater monitoring network

Hybrid Simulator for Capturing Dynamics of Synthetic Populations

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Dataset for '3D printing of customizable transient bioelectronics and sensors'

Quantifying the Unknown: Data-Driven Approaches and Applications in Energy Systems

Data set for control of Ge island coalescence for the formation of nanowires on silicon