Related papers: eQTL Studies: from Bulk Tissues to Single Cells
The QQ plot is a commonly used technique for informally deciding whether a univariate random sample of size n comes from a specified distribution F. The QQ plot graphs the sample quantiles against the theoretical quantiles of F and then a…
Statistical inference on the cancer-site specificities of collective ultra-rare whole genome somatic mutations is an open problem. Traditional statistical methods cannot handle whole-genome mutation data due to their…
Unlike the standard Quantum Computational Logic (QCL), where the carrier of information (target) is conventionally assumed to be only the last qubit over a sequence of many qubits, here we propose an extended version of the QCL (we call…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
Multi-task learning (MTL) is useful for domains in which data originates from multiple sources that are individually under-sampled. MTL methods are able to learn classification models that have higher performance as compared to learning a…
Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investigation of the spatial variation of gene expressions and their…
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…
We analyze large, multi-dimensional, sparse counting data sets, finding unsupervised groups to provide unique insights into genetic data. We create gene and biological pathway groups based on patients' variants to find common risk factors…
Proliferating cell populations at steady state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by…
We present a novel approach to selective model quantization that transcends the limitations of architecture-specific and size-dependent compression methods for Large Language Models (LLMs) using Entropy-Weighted Quantization (EWQ). By…
Diagnostic testing provides a unique setting for studying and developing tools in classification theory. In such contexts, the concept of prevalence, i.e. the number of individuals with a given condition, is fundamental, both as an inherent…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
During epithelial-mesenchymal transition (EMT), epithelial cells change their morphology, disperse, and gain mesenchymal-like characteristics. Usually, cells are categorized into discrete cell types or states based on gene expression and…
Although cone-beam CT (CBCT) has been used to guide irradiation for pre-clinical radiotherapy(RT) research, it is limited to localize soft tissue target especially in a low imaging contrast environment. Knowledge of target shape is a…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
The past decade has seen a rapid growth in omics technologies. Genome-wide association studies (GWAS) have uncovered susceptibility variants for a variety of complex traits. However, the functional significance of most discovered variants…
Predicting the effects of chemical and genetic perturbations on quantitative cell states is a central challenge in computational biology, molecular medicine and drug discovery. Recent work has leveraged large-scale single-cell data and…
The quantum fluctuations of a physical property can be observed in the measurement statistics of any measurement that is at least partially sensitive to that physical property. Quantum theory indicates that the effective distribution of…
Trait differences between species may be attributable to natural selection. However, quantifying the strength of evidence for selection acting on a particular trait is a difficult task. Here we develop a population-genetic test for…
Cellular contractility, migration, and extracellular matrix (ECM) mechanics are critical for a wide range of biological processes including embryonic development, wound healing, tissue morphogenesis, and regeneration. Even though the…