Olivier Tremblay-Savard's research while affiliated with University of Manitoba and other places
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Publications (20)
Background
During the 30-day period prior to initiating dialysis, there is a 10-fold rise in emergency department visits and hospitalizations related to kidney failure.
Objective
The Virtual Ward Incorporating Electronic Wearables (VIEWER) trial implemented a home telemonitoring system to track changes in patients’ vitals and assess their adherenc...
Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the class of orchard networks, which is composed of networks that can be reduced to a single leaf using cherry red...
Classical compartmental models of infectious disease assume that spread occurs through a homogeneous population. This produces poor fits to real data, because individuals vary in their number of epidemiologically-relevant contacts, and hence in their ability to transmit disease. In particular, network theory suggests that super-spreading events ten...
Background
Glomerulonephritis (GN) represents a common cause of chronic kidney disease, and treatment to slow or prevent progression of GN is associated with significant morbidity. Large patient registries have improved the understanding of risk stratification, treatment selection, and definitions of treatment response in GN, but can be resource-in...
The expression of quantitative traits of a line of a crop depends on its genetics, the environment where it is sown and the interaction between the genetic information and the environment known as GxE. Thus to maximize food production, new varieties are developed by selecting superior lines of seeds suitable for a specific environment. Genomic sele...
Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the class of orchard networks, which is composed of networks that can be reduced to a single leaf using cherry red...
Relaxing the homogeneous mixing assumption in a population is often necessary to improve fits of epidemic models to observed infection counts. Establishing a link between observed infections and the underlying network of contacts is paramount to understanding how the network structure affects the speed of spread of a pathogen. In this paper we argu...
Clustering is a central task in many data analysis applications. However, there is no universally accepted metric to decide the occurrence of clusters. Ultimately, we have to resort to a consensus between experts. The problem is amplified with high-dimensional datasets where classical distances become uninformative and the ability of humans to full...
In phylogenetic networks, picking a cherry consists of removing a leaf that shares a parent with another leaf, or removing a reticulate edge whose endpoints are parents of leaves. Cherry-picking operations were recently shown to have several structural and algorithmic applications in the study of networks, for instance in determining their reconstr...
We present BOPAL 2.0, an improved version of the BOPAL algorithm for the evolutionary history inference of tRNA and rRNA genes in bacterial genomes. Our approach can infer complete evolutionary scenarios and ancestral gene orders on a phylogeny and considers a wide range of events such as duplications, deletions, substitutions, inversions and trans...
In phylogenetic networks, picking a cherry consists of removing a leaf that shares a parent with another leaf, or removing a reticulate edge whose endpoints are parents of leaves. Cherry-picking operations were recently shown to have several structural and algorithmic applications in the study of networks, for instance in determining their reconstr...
Background:
In bacterial genomes, rRNA and tRNA genes are often organized into operons, i.e. segments of closely located genes that share a single promoter and are transcribed as a single unit. Analyzing how these genes and operons evolve can help us understand what are the most common evolutionary events affecting them and give us a better pictur...
Background
Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity...
Crowdsourcing with human-computing games is now a well-established approach to help solving difficult computational problems (e.g. Foldit, Phylo). The current strategies used to distribute problems among participants are currently limited to (i) delivering the full problem to every single user and ask them to explore the complete search space (e.g....
We present OrthoAlign, an algorithm for the gene order alignment problem (alignment of orthologs), accounting for most genome-wide evolutionary events such as duplications, losses, rearrangements and substitutions. We use OrthoAlign in a phylogenetic framework, to infer the evolution of transfer RNA repertoires of 50 fully sequenced bacteria in the...
Understanding the history of a gene family that evolves through duplication, speciation, and loss is a fundamental problem in comparative genomics. Features such as function, position, and structural similarity between genes are intimately connected to this history; relationships between genes such as orthology (genes related through a speciation e...
Citations
... A rehabilita�on game or an exercise game, for example, can provide an engaging and mo�va�ng way for individuals to improve their physical abili�es (Rego, Moreira, & Reis, 2010). In addi�on, games that promote collabora�ve problem-solving, such as ci�zen science tools like Foldit (Cur�s, 2015) or genome sor�ng games (De Leon Pereira & Tremblay-Savard, 2023), can provide individuals with the opportunity to contribute to important scien�fic research while at the same �me enjoying a pleasurable gaming experience. There are many types of serious games, which can be described by their genre, applica�on domain, gameplay and scope, as well as by their modali�es, interac�on styles, and environments. ...
... [61]) and continued participation in it(cf. [12,22,47]). Where disengagement is addressed, it is often done so with a negative connotation through the lens of player attrition (e.g., [3,32,36]), and from a restrictive perspective such as external terminating of play [68]. ...
... Similarly, Cantador and Marczewski [20] examine rewards (primarily badges) in an e-learning environment. Matin et al. [37] examine the effect of a timer, top score, and leader board on performance and motivation in human computing games. ...
... In genomics, petabytes of complete sequenced genomes for many organisms (e.g., eukaryotes and prokaryotes) are available currently in public repositories. This avalanche of genomic datasets has led to new challenges for researchers, and has demanded for improved computational approaches for bioinformatics tasks like gene analytics [59,86], gene classification [26], gene prediction [60,70], motifs discovery [3,41,87,95], omic analytics [80], palindrome identification in gene sequence [85], sequence alignment [22,43], and sequence assembly [31]. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272488726790165-1441977783558_Q64/Carson-Leung.jpg)
... Due to limited human memory capability, users always tend to create passwords with a certain pattern including names, dates, keyboard layouts, etc., or associate the generating passwords with corresponding online service characteristics and features. Glory et al. (2019) have also reported that manual password creation can be inspired by common sources or personal related words, or others' passwords. They argued that when users are forced to create high entropy passwords, sometimes users tend to use random password generators to create strong passwords. ...
... However, we accept requests to create new ones. Badges are efficient tools to improve user retention in learning games and a key component to keep gamers engaged [25,26]. For an educator, it also is a convenient tool to define the objectives and track the progresses of the students. ...
... The accumulation and comparison of complete canonical tRNA gene set data (i.e. tRNA genes in the first category) paves the way for conclusions regarding the evolution of tRNA gene sets across the tree of life [5,[18][19][20][21][22][23][24][25][26]. In addition, such information may have important medical implications [27][28][29][30][31]. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/11431281089285928-1665503619373_Q64/Nadia-El-Mabrouk.jpg)
... In [83], maximal Túran (complete multipartite) graphs are computed. These form a special class of co-graphs and accommodate so-called inparalogs [24,84], i.e., duplicate gene that originated after the most recent speciation event in each lineage. Complementarily, it is of interest to partition a gene set such that out-paralogs (i.e., pairs of genes arising from duplications that pre-date all speciation events) are placed in different clusters. ...
Reference: The Theory of Gene Family Histories
