Panacus: fast and exact pangenome growth and core size estimation.

Motivation: Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence.

AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.

Reconstructing ancestral gene orders from the genome data of extant species is an important problem in comparative and evolutionary genomics. In a phylogenomics setting that accounts for gene family evolution through gene duplication and gene loss, the reconstruction of ancestral gene orders involves several steps, including multiple sequence alignment, the inference of reconciled gene trees, and the inference of ancestral syntenies and gene adjacencies. For each of the steps of such a process, several methods can be used and implemented using a growing corpus of, often parameterized, tools; in practice, interfacing such tools into an ancestral gene order reconstruction pipeline is far from trivial.

Family-Free Genome Comparison.

The comparison of large-scale genome structures across distinct species offers valuable insights into the species' phylogeny, genome organization, and gene associations. In this chapter, we review the family-free genome comparison tool FFGC that, relying on built-in interfaces with a sequence comparison tool (either BLAST+ or DIAMOND) and with an ILP solver (either CPLEX or Gurobi), provides several methods for analyses that do not require prior classification of genes across the studied genomes. Taking annotated genome sequences as input, FFGC is a complete workflow for genome comparison allowing not only the computation of measures of similarity and dissimilarity but also the inference of gene families, simultaneously based on sequence similarities and large-scale genomic features.

Training an automated circulating tumor cell classifier when the true classification is uncertain.

Circulating tumor cell (CTC) and tumor-derived extracellular vesicle (tdEV) loads are prognostic factors of survival in patients with carcinoma. The current method of CTC enumeration relies on operator review and, unfortunately, has moderate interoperator agreement (Fleiss' kappa 0.60) due to difficulties in classifying CTC-like events.

Constructing founder sets under allelic and non-allelic homologous recombination.

Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism can also act between different copies of the same sequence, then called non-allelic homologous recombination (NAHR). This process can result in genomic rearrangements-including deletion, duplication, and inversion-and is underlying many genomic disorders.

A draft human pangenome reference.

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels.

Impact of Quality Improvement Bundle on Compliance with Resuscitation Guidelines during In-Hospital Cardiac Arrest in Children.

Introduction: Various quality improvement (QI) interventions have been individually assessed for the quality of cardiopulmonary resuscitation (CPR). We aimed to assess the QI bundle (hands-on training and debriefing) for the quality of CPR in our children's hospital. We hypothesized that the QI bundle improves the quality of CPR in hospitalized children.

Small parsimony for natural genomes in the DCJ-indel model.

The Small Parsimony Problem (SPP) aims at finding the gene orders at internal nodes of a given phylogenetic tree such that the overall genome rearrangement distance along the tree branches is minimized. This problem is intractable in most genome rearrangement models, especially when gene duplication and loss are considered. In this work, we describe an Integer Linear Program algorithm to solve the SPP for natural genomes, i.

The potential of family-free rearrangements towards gene orthology inference.

Recently, we proposed an efficient ILP formulation [Rubert DP, Martinez FV, Braga MDV, Natural family-free genomic distance,  :4, 2021] for exactly computing the rearrangement distance of two genomes in a setting. In such a setting, neither prior classification of genes into families, nor further restrictions on the genomes are imposed. Given two genomes, the mentioned ILP computes an optimal matching of the genes taking into account simultaneously local mutations, given by gene similarities, and large-scale genome rearrangements.

Computing the Rearrangement Distance of Natural Genomes.

The computation of genomic distances has been a very active field of computational comparative genomics over the past 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and Pevzner in 1995 and the introduction of the double cut and join distance by Yancopoulos et al. in 2005.

Athlete health and safety at large sporting events: the development of consensus-driven guidelines.

All sport events have inherent injury and illness risks for participants. Healthcare services for sport events should be planned and delivered to mitigate these risks which is the ethical responsibility of all sport event organisers. The objective of this paper was to develop consensus-driven guidelines describing the basic standards of services necessary to protect athlete health and safety during large sporting events.

Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants.

Background: Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants.

Results: Our work relies on an established workflow in the reconstruction of ancestral plants, but improves several steps of this process.

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach.

The dramatic decrease in time and cost for generating genetic sequence data has opened up vast opportunities in molecular systematics, one of which is the ability to decipher the evolutionary history of strains of a species. Under this fine systematic resolution, the standard markers are too crude to provide a phylogenetic signal. Nevertheless, among prokaryotes, genome dynamics in the form of horizontal gene transfer (HGT) between organisms and gene loss seem to provide far richer information by affecting both gene order and gene content.

Health promotion by International Olympic Sport Federations: priorities and barriers.

Objective: To identify changes in International Federations' priorities and the barriers to implementing athlete and global health initiatives. Results should influence the work of the International Federation medical committees, the IOC and the Association of Summer Olympic International Federation.

Methods: The 28 Summer and 7 Winter International Federations participating in the most recent Olympic Games (2016; 2018) were surveyed to (i) identify the importance of 27 health topics, (ii) assess their progress on implementation health-related programmes and (iii) the barriers to implementation of these programmes.

GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.

Background: Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. These are sets of genes with associated functionality that exhibit close proximity to each other in the spatial conformation of chromosomes across several related species.

Family-Free Genome Comparison.

The comparison of genome structures across distinct species offers valuable insights into the species' phylogeny, genome organization, and gene associations. In this chapter, we review the family-free genome comparison tool FFGC which provides several methods for gene order analyses that do not require prior knowledge of evolutionary relationships between the genes across the studied genomes. Moreover, the tool features a complete workflow for genome comparison, requiring nothing but annotated genome sequences as input.

Sequence-Based Synteny Analysis of Multiple Large Genomes.

Current methods for synteny analysis provide only limited support to study large genomes at the sequence level. In this chapter, we describe a pipeline based on existing tools that, applied in a suitable fashion, enables synteny analysis of large genomic datasets. We give a hands-on description of each step of the pipeline using four avian genomes for data.

Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient genomes.

is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements.

New Genome Similarity Measures based on Conserved Gene Adjacencies.

Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, for example, to elucidate the phylogenetic relationships between species. The power of different genome comparison methods varies with the underlying formal model of a genome.

The gene family-free median of three.

Background: The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We study two problems related to the breakpoint median of three genomes, which asks for the construction of a fourth genome that minimizes the sum of breakpoint distances to the input genomes.

Methods: We present a model for constructing a median of three genomes in this family-free setting, based on maximizing an objective function that generalizes the classical breakpoint distance by integrating sequence similarity in the score of a gene adjacency.

Identifying gene clusters by discovering common intervals in indeterminate strings.

Background: Comparative analyses of chromosomal gene orders are successfully used to predict gene clusters in bacterial and fungal genomes. Present models for detecting sets of co-localized genes in chromosomal sequences require prior knowledge of gene family assignments of genes in the dataset of interest. These families are often computationally predicted on the basis of sequence similarity or higher order features of gene products.