Related papers: Utilizing de Bruijn graph of metagenome assembly f…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
In this work, we propose to study the utility of different meta-graphs, as well as how to simultaneously leverage multiple meta-graphs for HIN embedding in an unsupervised manner. Motivated by prolific research on homogeneous networks,…
Heterogeneous graphs generally refers to graphs with different types of nodes and edges. A common approach for extracting useful information from heterogeneous graphs is to use meta-graphs, which can be seen as a special kind of directed…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
Network embedding in heterogeneous information networks (HINs) is a challenging task, due to complications of different node types and rich relationships between nodes. As a result, conventional network embedding techniques cannot work on…
Many researchers have used tag information to improve the performance of recommendation techniques in recommender systems. Examining the tags of users will help to get their interests and leads to more accuracy in the recommendations. Since…
Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated the microbiome study. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome…
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently,…
Decrypting intelligence from the human brain construct is vital in the detection of particular neurological disorders. Recently, functional brain connectomes have been used successfully to predict behavioral scores. However,…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…
Detection of overlapping communities in real-world networks is a generally challenging task. Upon recognizing that a network is in fact the union of its egonets, a novel network representation using multi-way data structures is advocated in…
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers…
More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Representation learning on text-attributed graphs (TAGs) is vital for real-world applications, as they combine semantic textual and contextual structural information. Research in this field generally consist of two main perspectives:…
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…