Related papers: Hyppo-X: A Scalable Exploratory Framework for Anal…
The LIPGENE-SU.VI.MAX study, like many others, recorded high dimensional continuous phenotypic data and categorical genotypic data. LIPGENE-SU.VI.MAX focuses on the need to account for both phenotypic and genetic factors when studying the…
Mapping genotypes to phenotypes (G2P) is a fundamental goal in biology. So called PhyloG2P methods are a relatively new set of tools that leverage replicated evolution in phylogenetically independent lineages to identify genomic regions…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
Detailed phenotype information is fundamental to accurate diagnosis and risk estimation of diseases. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However,…
Measuring the complexity of high-dimensional data in physical systems becomes a critical factor in determining the information and quality of the systems. However, traditional metrics, such as Lyapunov exponent, fractal dimension, and…
Organismal phenotypes emerge from a complex set of genotypic interactions. While technological advances in sequencing provide a quantitative description of an organism's genotype, characterization of an organism's physical phenotype lags…
In recent years hypergraphs have emerged as a powerful tool to study systems with multi-body interactions which cannot be trivially reduced to pairs. While highly structured methods to generate synthetic data have proved fundamental for the…
Factor analysis is a critical component of high dimensional biological data analysis. However, modern biological data contain two key features that irrevocably corrupt existing methods. First, these data, which include longitudinal,…
A looming question that must be solved before robotic plant phenotyping capabilities can have significant impact to crop improvement programs is scalability. High Throughput Phenotyping (HTP) uses robotic technologies to analyze crops in…
The exposome recognizes that individuals are exposed simultaneously to a multitude of different environmental factors and takes a holistic approach to the discovery of etiological factors for disease. However, challenges arise when trying…
The genotype-phenotype gap is a persistent barrier to complex trait genetic dissection, worsened by the explosive growth of genomic data (1.5 billion variants identified in the UK Biobank WGS study) alongside persistently scarce and…
For the past few years, deep generative models have increasingly been used in biological research for a variety of tasks. Recently, they have proven to be valuable for uncovering subtle cell phenotypic differences that are not directly…
High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still…
Understanding which genes control which traits in an organism remains one of the central challenges in biology. Despite significant advances in data collection technology, our ability to map genes to traits is still limited. This…
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…
Phylogenetic profiles - presence-absence patterns of genes across taxa - are rich information sources for inferring the evolutionary history of genes and gene families. When aggregated across many genes, these profiles can reveal…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Technology convergence integrates distinct domains to create novel combinations, driving radical innovation that reshapes markets and industries. However, most approaches rely on pairwise networks that cannot capture multi-technology…
Post-genomic research deals with challenging problems in screening genomes of organisms for particular functions or potential for being the targets of genetic engineering for desirable biological features. 'Phenotyping' of wild type and…