Related papers: Distinguishing Cell Phenotype Using Cell Epigenoty…

Cell image classification methods are currently being used in numerous applications in cell biology and medicine. Applications include understanding the effects of genes and drugs in screening experiments, understanding the role and…

The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we…

Identifying concentrations of components from an observed mixture is a fundamental problem in signal processing. It has diverse applications in fields ranging from hyperspectral imaging to denoising biomedical sensors. This paper focuses on…

Computational Phenotype Discovery research has taken various pragmatic approaches to disentangling phenotypes from the episodic observations in Electronic Health Records. In this work, we use transformation into continuous, longitudinal…

The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…

Predicting phenotype from genotype is a central challenge in genetics. Traditional approaches in quantitative genetics typically analyze this problem using methods based on linear regression. These methods generally assume that the genetic…

Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique…

Monitoring the distribution of microfossils in stratigraphic successions is an essential tool for biostratigraphic, evolutionary and paleoecologic/paleoceanographic studies. To estimate the relative abundance (%) of a given species, it is…

Cellular decision making allows cells to assume functionally different phenotypes in response to microenvironmental cues, without genetic change. It is an open question, how individual cell decisions influence the dynamics at the tissue…

To learn about a physical system of interest, experimental results must be able to discriminate among models. We introduce a geometrical measure to quantify the distance between models for pseudoscalar-meson photoproduction in amplitude…

The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects.…

The behaviour of an organism often reflects a strategy for coping with its environment. Such behaviour in higher organisms can often be reduced to a few stereotyped modes of movement due to physiological limitations, but finding such modes…

Before we attempt to learn a function between two (sets of) observables of a physical process, we must first decide what the inputs and what the outputs of the desired function are going to be. Here we demonstrate two distinct, data-driven…

Cellular populations are typically heterogenous collections of cells at different points in their respective cell cycles, each with a cell cycle time that varies from individual to individual. As a result, true single-cell behavior,…

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…

Homophily -- the tendency of individuals to interact with similar others -- shapes how networks form and function. Yet existing approaches typically collapse homophily to a single scale, either one parameter for the whole network or one per…

How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to…

Understanding the forces governing human behavior and social dynamics is a challenging problem. Individuals' decisions and actions are affected by interlaced factors, such as physical location, homophily, and social ties. In this paper, we…

Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to…

Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…