Related papers: Digging Deeper: Methodologies for High-Content Phe…
In recent years, there has been a notable advancement in the integration of healthcare and technology, particularly evident in the field of medical image analysis. This paper introduces a pioneering approach in dermatology, presenting a…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
The 1mm roundworm C. elegans is a model organism used in many sub-areas of biology to investigate different types of biological processes. In order to complement the n-vivo analysis with computer-based investigations, several methods have…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
High-throughput technologies to collect field data have made observations possible at scale in several branches of life sciences. The data collected can range from the molecular level (genotypes) to physiological (phenotypic traits) and…
1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics,…
Accurate phenotypic analysis in aquaculture breeding necessitates the quantification of subtle morphological phenotypes. Existing datasets suffer from limitations such as small scale, limited species coverage, and inadequate annotation of…
Spatially-embedded complex networks, such as nervous systems, the Internet and transportation networks, generally have non-trivial topological patterns of connections combined with nearly minimal wiring costs. However the growth rules…
Predicting phenotypes with complex genetic bases based on a small, interpretable set of variant features remains a challenging task. Conventionally, data-driven approaches are utilized for this task, yet the high dimensional nature of…
Abrupt changes in behavior can often be associated with changes in underlying behavioral states. When placed off food, the foraging behavior of C. elegans can be described as a change between an initial local-search behavior characterized…
Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel…
High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions.…
We develop an artificial neural circuit for contour tracking and navigation inspired by the chemotaxis of the nematode Caenorhabditis elegans. In order to harness the computational advantages spiking neural networks promise over their…
A key goal in studies of ecology and evolution is understanding the causes of phenotypic diversity in nature. Most traits of interest, such as those relating to morphology, life-history, immunity and behaviour are quantitative, and…
We exploit the reduced space of C. elegans postures to develop a novel tracking algorithm which captures both simple shapes and also self-occluding coils, an important, yet unexplored, component of worm behavior. We apply our algorithm to…
Deep phenotyping is the detailed description of patient signs and symptoms using concepts from an ontology. The deep phenotyping of the numerous physician notes in electronic health records requires high throughput methods. Over the past…
Computational phenotyping has emerged as a practical solution to the incomplete collection of data on gender in electronic health records (EHRs). This approach relies on algorithms to infer a patient's gender using the available data in…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
Increasing interest in the acquisition of biotic and abiotic resources from within the deep sea (e.g. fisheries, oil-gas extraction, and mining) urgently imposes the development of novel monitoring technologies, beyond the traditional…