Related papers: Per-sample immunoglobulin germline inference from …
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's…
Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…
The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…
The accurate estimation of time-varying transmission rates is fundamental for understanding infectious disease dynamics and implementing effective public health interventions. To this end, we propose an improved inverse method for…
Human blood primarily comprises plasma, red blood cells, white blood cells, and platelets. It plays a vital role in transporting nutrients to different organs, where it stores essential health-related data about the human body. Blood cells…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
Hematopoiesis is the process of blood cell formation, through which progenitor stem cells differentiate into mature forms, such as white and red blood cells or mature platelets. While the precursors of the mature forms share many regulatory…
We introduce a method for approximating posterior probabilities of phylogenetic trees and reconstructing ancestral sequences under models of sequence evolution with site-dependence, where standard phylogenetic likelihood computations…
Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known…
In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…
Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…
In this paper we present a system for the detection of immunogold particles and a Transfer Learning (TL) framework for the recognition of these immunogold particles. Immunogold particles are part of a high-magnification method for the…
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about…
Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both…
Many massive data are assembled through collections of information of a large number of individuals in a population. The analysis of such data, especially in the aspect of individualized inferences and solutions, has the potential to create…
A hallmark of the adaptive immune response is the proliferation of pathogen-specific lymphocytes that leave in their wake a long lived population of cells that provide lasting immunity. A subject of ongoing investigation is when during an…
The study of immune cellular composition has been of great scientific interest in immunology because of the generation of multiple large-scale data. From the statistical point of view, such immune cellular data should be treated as…
In general, the labels used in sequence labeling consist of different types of elements. For example, IOB-format entity labels, such as B-Person and I-Person, can be decomposed into span (B and I) and type information (Person). However,…