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A novel Genetic Algorithm is described that is suitable for determining the global minimum energy configurations of crystal structures and which can also be used as a polymorph search technique. This algorithm requires no prior assumptions…
Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…
Identifying genes associated with complex human diseases is one of the main challenges of human genetics and computational medicine. To answer this question, millions of genetic variants get screened to identify a few of importance. To…
Pseudoprogression (PsP) is an imitation of true tumor progression (TTP) in patients with glioblastoma multiform (GBM). Differentiating them is a challenging and time-consuming task for radiologists. Although deep neural networks can…
Genomic imprinting has been thought to play an important role in seed development in flowering plants. Seed in a flowering plant normally contains diploid embryo and triploid endosperm. Empirical studies have shown that some economically…
Recent analysis identified distinct genomic subtypes of lower-grade glioma tumors which are associated with shape features. In this study, we propose a fully automatic way to quantify tumor imaging characteristics using deep learning-based…
Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…
We present a genetic algorithm (GA) for structural search that combines the speed of structure exploration by classical potentials with the accuracy of density functional theory (DFT) calculations in an adaptive and iterative way. This…
Background: Cancers are highly heterogeneous with different subtypes. These subtypes often possess different genetic variants, present different pathological phenotypes, and most importantly, show various clinical outcomes such as varied…
We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. This framework is designed to enable detection of clusters of data in the presence of structural…
Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…
Multiple methods of finding the vertices belonging to a planted dense subgraph in a random dense $G(n, p)$ graph have been proposed, with an emphasis on planted cliques. Such methods can identify the planted subgraph in polynomial time, but…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
Differential co-expression analysis has been widely applied by scientists in understanding the biological mechanisms of diseases. However, the unknown differential patterns are often complicated; thus, models based on simplified parametric…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…
By use of complex network dynamics and graph-based machine learning, we identified critical determinants of lineage-specific plasticity across the single-cell transcriptomics of pediatric high-grade glioma (pHGGs) subtypes: IDHWT…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
The recent development of high-throughput sequencing creates a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating…
How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing…