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Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of…
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for…
Statistical phylogenetic inference methods use tree rearrangement operations to perform either hill-climbing local search or Markov chain Monte Carlo across tree topologies. The canonical class of such moves are the subtree-prune-regraft…
Animal re-identification (ReID) has become an indispensable tool in ecological research, playing a critical role in tracking population dynamics, analyzing behavioral patterns, and assessing ecological impacts, all of which are vital for…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
Probabilistic modeling over the combinatorially large space of tree topologies remains a central challenge in phylogenetic inference. Previous approaches often necessitate pre-sampled tree topologies, limiting their modeling capability to a…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
Gait recognition is a rapidly advancing vision technique for person identification from a distance. Prior studies predominantly employed relatively shallow networks to extract subtle gait features, achieving impressive successes in…
Genotype imputation enables dense variant coverage for genome-wide association and risk-prediction studies, yet conventional reference-panel methods remain limited by ancestry bias and reduced rare-variant accuracy. We present Genotype…
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between…
Recently, an elegant approach in phylogenetics was introduced by Billera-Holmes-Vogtmann that allows a systematic comparison of different evolutionary histories using the metric geometry of tree spaces. In many problem settings one…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
Proximity sensing detects an object's presence without contact. However, research has rarely explored proximity sensing in granular materials (GM) due to GM's lack of visual and complex properties. In this paper, we propose a…
Effective search methods are crucial for improving the performance of deep generative models at test time. In this paper, we introduce a novel test-time search method, Neural Genetic Search (NGS), which incorporates the evolutionary…
The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…
Fine-Grained Change Detection and Regression Analysis are essential in many applications of ArtificialIntelligence. In practice, this task is often challenging owing to the lack of reliable ground truth information andcomplexity arising…
Variations in mitochondrial genes are usually considered to infer phylogenies. However some of these genes are lesser constraint than other ones, and thus may blur the phylogenetic signals shared by the majority of the mitochondrial DNA…
Many different species are adversely affected by poaching. In response to this escalating crisis, efforts to stop poaching using hidden cameras, drones and DNA tracking have been implemented with varying degrees of success. Limited…