Related papers: Comprehensive Detection of Genes Causing a Phenoty…
Phenotypic heterogeneity is a most fascinating property of a population of cells, which shows the differences among individuals even with the same genetic background and extracellular environmental conditions. However, the lack of…
The discovery of motifs underlying gene expression is a challenging one. Some of these motifs are known transcription factors, but sequence inspection often provides valuable clues, even discovery of novel motifs with uncharacterized…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
Converging evidence suggests that common complex diseases with the same or similar clinical manifestations could have different underlying genetic etiologies. While current research interests have shifted toward uncovering rare variants and…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
Type 1 diabetes (T1D) is a highly metabolically heterogeneous disease that cannot be adequately characterized by conventional biomarkers such as glycated hemoglobin (HbA1c). This study proposes an explainable deep learning framework that…
Phenomics is an emerging branch of modern biology that uses high throughput phenotyping tools to capture multiple environmental and phenotypic traits, often at massive spatial and temporal scales. The resulting high dimensional data…
Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria,…
Identification of causal genes and pathways is a critical step for understanding the genetic underpinnings of rare diseases. We propose novel approaches to gene prioritization and pathway identification using DNA language model, graph…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Motivation: Despite advances in the computational analysis of high-throughput molecular profiling assays (e.g. transcriptomics), a dichotomy exists between methods that are simple and interpretable, and ones that are complex but with lower…
Assessing the statistical power to detect susceptibility variants plays a critical role in GWA studies both from the prospective and retrospective points of view. Power is empirically estimated by simulating phenotypes under a disease model…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…
Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…
Clinical end-point traits are often characterized by quantitative or qualitative precursors and it has been argued that it may be statistically a more powerful strategy to analyze these precursor traits to decipher the genetic architecture…
We study mathematically a method for discovering which gene is related to a cell phenotype of interest. The method is based on RNA interference -- a molecular process for gene deactivation -- and on coupling the phenotype with fluorescence…