Related papers: VTCdb: A transcriptomics & co-expression database …
The estimation of Bayesian networks given high-dimensional data, in particular gene expression data, has been the focus of much recent research. Whilst there are several methods available for the estimation of such networks, these typically…
We developed an online database, ExprTargetDB, of human miRNA targets predicted by an approach that integrates gene expression profiling into a broader framework involving important features of miRNA target site predictions.
Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…
This study presents a novel method for improving rice disease classification using 8 different convolutional neural network (CNN) algorithms, which will further the field of precision agriculture. Tkinter-based application that offers…
Motivation: Genome-wide association studies (GWAS) have identified many loci implicated in disease susceptibility. Integration of GWAS summary statistics (p values) and functional genomic datasets should help to elucidate mechanisms.…
Predicting transcriptional responses to genetic perturbations is a central problem in functional genomics. In practice, perturbation responses are rarely gene-independent but instead manifest as coordinated, program-level transcriptional…
In this work we propose a model for gene expression based on the theory of random dynamical systems (RDS) and show that it has a "modularity property" in the following sense: given any collection of genes that are linked in a…
For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to…
The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our…
A vine copula model is a flexible high-dimensional dependence model which uses only bivariate building blocks. However, the number of possible configurations of a vine copula grows exponentially as the number of variables increases, making…
Background:Gene regulations often change over time rather than being constant. But many of gene regulatory networks extracted from databases are static. The tumor suppressor gene $P53$ is involved in the pathogenesis of many tumors, and its…
Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…
Spatial variable genes (SVGs) reveal critical information about tissue architecture, cellular interactions, and disease microenvironments. As spatial transcriptomics (ST) technologies proliferate, accurately identifying SVGs across diverse…
In this paper, we propose a novel behavior model for wideband PAs using a real-valued time-delay convolutional neural network (RVTDCNN). The input data of the model are sorted and arranged as the graph composed of the in-phase and…
Social media processing is a fundamental task in natural language processing with numerous applications. As Vietnamese social media and information science have grown rapidly, the necessity of information-based mining on Vietnamese social…
Cluster closure, defined as the progressive filling of gaps between the berries in a grape bunch, is a key trait in vineyard management, impacting disease risk. However, traditional visual scoring methods are labor-intensive, subjective,…
Therapeutic antibodies require not only high-affinity target engagement, but also favorable manufacturability, stability, and safety profiles for clinical effectiveness. These properties are collectively called `developability'. To enable a…
Evolving software is challenging, even more when it exists in many different variants. Such software evolves not only in time, but also in space--another dimension of complexity. While evolution in space is supported by a variety of…
We propose a class of dynamic vine copula models. This is an extension of static vine copulas and a generalization of dynamic C-vine and D-vine copulas studied by Almeida et al (2016) and Goel and Mehra (2019). Within this class, we allow…
Patent documents in the patent database (PatDB) are crucial for research, development, and innovation as they contain valuable technical information. However, PatDB presents a multifaceted challenge compared to publicly available…