Carl Nettelblad

Imaging aerosolized viruses with an X-ray free-electron laser using single-particle rotational invariants

Tim B. Berberich, Johan Bielecki, Jonas A. Sellberg, Benedikt J. Daurer et autres

X-ray free-electron lasers (XFELs) enable diffraction-before-destruction measurements of individual nanosized bioparticles, making it possible to study the structure and dynamics of non-crystalline targets under near-biologically relevant conditions. In this work, we employ rotational invariants for model-guided and ab initio three-dimensional (3D) structure …

Imaging aerosolized viruses with an X-ray free-electron laser using single-particle rotational invariants

Tim B. Berberich, Johan Bielecki, Jonas A. Sellberg, Benedikt J. Daurer et autres

X-ray free-electron lasers (XFELs) enable diffraction-before-destruction measurements of individual nanosized bioparticles, making it possible to study the structure and dynamics of non-crystalline targets under near-biologically relevant conditions. In this work, we employ rotational invariants for model-guided and ab initio three-dimensional (3D) structure …

Learning Genomic Structure from $k$-mers

Filip Thor, Carl Nettelblad

Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data using contrastive learning, in …

Dimensionality reduction of genetic data using contrastive learning

Filip Thor, Carl Nettelblad

We introduce a framework for using contrastive learning for dimensionality reduction on genetic datasets to create principal component analysis (PCA)-like population visualizations. Contrastive learning is a self-supervised deep learning method that uses similarities between samples to train the neural network to discriminate …

se (code pays fourni par la source)

Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost

Camille Clouard, Carl Nettelblad

Conducting genomic selection (GS) in plant breeding programs can substantially speed up the development of new varieties. GS provides more reliable insights when it is based on dense marker data, in which the rare variants can be particularly informative. Despite the availability …

se (code pays fourni par la source)

Dimensionality Reduction of Genetic Data using Contrastive Learning

Filip Thor, Carl Nettelblad

Abstract We introduce a framework for using contrastive learning for dimensionality reduction on genetic datasets to create PCA-like population visualizations. Contrastive learning is a self-supervised deep learning method that uses similarities between samples to train the neural network to discriminate between samples. …

se (code pays fourni par la source)

Data-Driven Locality-Aware Batch Scheduling

Maxime Gonthier, Elisabeth Larsson, Loris Marchal, Carl Nettelblad et autres

Clusters employ workload schedulers such as the Slurm Workload Manager to allocate computing jobs onto nodes. These schedulers usually aim at a good tradeoff between increasing resource utilization and user satisfaction (decreasing job waiting time). However, these schedulers are typically unaware of …

fr, us, se (code pays fourni par la source)

Project Hephaistos – II. Dyson sphere candidates from Gaia DR3, 2MASS, and WISE

Matías Suazo, Erik Zackrisson, Priyatam K Mahto, Fabian Lundell et autres

ABSTRACT The search for extraterrestrial intelligence is currently being pursued using multiple techniques and in different wavelength bands. Dyson spheres, megastructures that could be constructed by advanced civilizations to harness the radiation energy of their host stars, represent a potential technosignature, that …

se, in, us, gb (code pays fourni par la source)

Observation of a single protein by ultrafast X-ray diffraction

Tomas Ekeberg, Dameli Assalauova, Johan Bielecki, Rebecca Boll et autres

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal …

se, de, gb, no, it, us, cz, au (code pays fourni par la source)

Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation

Camille Clouard, Carl Nettelblad

KEY MESSAGE: Pooling and imputation are computational methods that can be combined for achieving cost-effective and accurate high-density genotyping of both common and rare variants, as demonstrated in a MAGIC wheat population. The plant breeding industry has shown growing interest in using …

se (code pays fourni par la source)

Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost

Camille Clouard, Carl Nettelblad

Abstract Conducting genomic selection in plant breeding programs can substantially speed up the development of new varieties. Genomic selection provides more reliable insights when it is based on dense marker data, in which the rare variants can be particularly informative while they …

se (code pays fourni par la source)

Half-cost array-based genotyping of SNPs in bread wheat from pooled experiments and imputation

Camille Clouard, Carl Nettelblad

se (code pays fourni par la source)