Diet Quality Is Associated with Cardiometabolic Outcomes in Survivors of Childhood Leukemia.

There is little information about how diet influences the health of childhood acute lymphoblastic leukemia (cALL) survivors. This study explores the associations between diet quality indices, cardiometabolic health indicators and inflammatory biomarkers among cALL survivors. Participants were part of the PETALE study ( = 241, median age: 21.

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.

Background: New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies.

Efficient algorithms for Longest Common Subsequence of two bucket orders to speed up pairwise genetic map comparison.

Genetic maps order genetic markers along chromosomes. They are, for instance, extensively used in marker-assisted selection to accelerate breeding programs. Even for the same species, people often have to deal with several alternative maps obtained using different ordering methods or different datasets, e.

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

Background: Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions.

Results: We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats.

Comparative Methods for Reconstructing Ancient Genome Organization.

Comparative genomics considers the detection of similarities and differences between extant genomes, and, based on more or less formalized hypotheses regarding the involved evolutionary processes, inferring ancestral states explaining the similarities and an evolutionary history explaining the differences. In this chapter, we focus on the reconstruction of the organization of ancient genomes into chromosomes. We review different methodological approaches and software, applied to a wide range of datasets from different kingdoms of life and at different evolutionary depths.