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Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop
(2018)DNA ResearchFinger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, ...Journal Article -
graphkernels: R and Python packages for graph comparison
(2018)BioinformaticsMeasuring the similarity of graphs is a fundamental step in the analysis of graphstructured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based ...Journal Article -
The SysteMHC Atlas project
(2018)Nucleic Acids ResearchMass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the ...Journal Article -
The AraGWAS Catalog: A curated and standardized Arabidopsis thaliana GWAS catalog
(2018)Nucleid Acids ResearchThe abundance of high-quality genotype and phenotype data for the model organism Arabidopsis thaliana enables scientists to study the genetic architecture of many complex traits at an unprecedented level of detail using genome-wide association studies (GWAS). GWAS have been a great success in A. thaliana and many SNP-trait associations have been published. With the AraGWAS Catalog (https://aragwas.1001genomes.org) we provide a publicly ...Journal Article -
Ultrafast Rotation of Magnetically Levitated Macroscopic Steel Spheres
(2018)Science AdvancesOur world is increasingly powered by electricity, which is largely converted to or from mechanical energy using electric motors. Several applications have driven the miniaturization of these machines, resulting in high rotational speeds. Although speeds of several hundred thousand revolutions per minute have been used industrially, we report the realization of an electrical motor reaching 40 million rpm to explore the underlying physical ...Journal Article -
Supersaturated calcium carbonate solutions are classical
(2018)Science AdvancesMechanisms of CaCO3 nucleation from solutions that depend on multistage pathways and the existence of species far more complex than simple ions or ion pairs have recently been proposed. Herein, we provide a tightly coupled theoretical and experimental study on the pathways that precede the initial stages of CaCO3 nucleation. Starting from molecular simulations, we succeed in correctly predicting bulk thermodynamic quantities and experimental ...Journal Article -
Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity
(2018)Molecular Biology and EvolutionPathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as “per-parasite pathogenicity”. Using viral load and CD4+ T-cell measures from 2014 HIV-1 subtype B-infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence—measured as the rate ...Journal Article -
Birds use of vegetated and non-vegetated high-density buildings—a case study of Milan
(2018)Journal of Urban EcologyOur study provides a first look at the relationship between large-scale buildings incorporating vegetation (Dense and Green) and bird species richness in Milan, and is one of the studies conducted so far to assess this relationship globally. We carried out our survey in and around three Dense and Green and six high-density buildings with no vegetation (Normal Dense). Dense and Green buildings had a higher mean bird species richness (5) ...Journal Article -
Trade in the telecoupling framework: evidence from the metals industry
(2018)Ecology and SocietyAs a conceptual framework for understanding contemporary sustainability challenges, telecoupling emphasizes the importance of socioeconomic and environmental interactions over long distances. These long-distance interactions can occur through multiple human activities. We focus on international trade, a major channel of telecoupling flows, and in particular on the international trade of metals. We use the data of physical products and ...Journal Article -
De Novo Design of Bioactive Small Molecules by Artificial Intelligence
(2018)Molecular InformaticsJournal Article