Searching for possible biochemical networks that perform a certain function is a challenge in systems biology. For simple functions and small networks, this can be achieved through an exhaustive search of the network topology space. However, it is di...
Allele specific expression (ASE) concerns divergent expression quantity of alternative alleles and is measured by RNA sequencing. Multiple studies show that ASE plays a role in hereditary diseases by modulating penetrance or phenotype severity. Howev...
Non-Markovian models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parame...
The Translational Machine (TM) is a machine learning (ML)-based analytic pipeline that translates genotypic/variant call data into biologically contextualized features that richly characterize complex variant architectures and permit greater interpre...
Circulation. Genomic and precision medicine
Apr 23, 2021
BACKGROUND: Genetic testing can determine family screening strategies and has prognostic and diagnostic value in hypertrophic cardiomyopathy (HCM). However, it can also pose a significant psychosocial burden. Conventional scoring systems offer modest...
International journal of molecular sciences
Apr 16, 2021
In this paper, we introduce a novel algorithm that aims to estimate chromosomes' structure from their Hi-C contact data, called Curriculum Based Chromosome Reconstruction (CBCR). Specifically, our method performs this three dimensional reconstruction...
Ribozyme switches are a class of RNA-encoded genetic switch that support conditional regulation of gene expression across diverse organisms. An improved elucidation of the relationships between sequence, structure, and activity can improve our capaci...
We describe the design and implementation of a system for executing search-and-replace text processing tasks automatically, based only on examples of the desired behavior. The examples consist of pairs describing the original string and the desired m...
With the advancement of technology, analysis of large-scale data of gene expression is feasible and has become very popular in the era of machine learning. This paper develops an improved ridge approach for the genome regression modeling. When multic...
IEEE/ACM transactions on computational biology and bioinformatics
Apr 6, 2021
Increasing evidences revealed that microRNAs (miRNAs) play critical roles in important biological processes. The identification of disease-related miRNAs is critical to understand the molecular mechanisms of human diseases. Most existing computationa...
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