Related papers: PhaBOX: A web server for identifying and character…
Quantifying the phagocytosis of dynamic, unstained cells is essential for evaluating neurodegenerative diseases. However, measuring rapid cell interactions and distinguishing cells from background make this task very challenging when…
Leveraging medical record information in the era of big data and machine learning comes with the caveat that data must be cleaned and de-identified. Facilitating data sharing and harmonization for multi-center collaborations are…
Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…
Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing…
Microbiome interventions provide valuable data about microbial ecosystem structure and dynamics. Despite their ubiquity in microbiome research, few rigorous data analysis approaches are available. In this study, we extend transfer…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
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…
Background: Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning…
There has been rapid growth in biomedical literature, yet capturing the heterogeneity of the bibliographic information of these articles remains relatively understudied. Although graph mining research via heterogeneous graph neural networks…
Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through…
Although web applications evolved to mature solutions providing sophisticated user experience, they also became complex for the same reason. Complexity primarily affects the server-side generation of dynamic pages as they are aggregated…
In multi-modal biomedical research, integrating high-dimensional genomic data with clinical baselines is essential for precision medicine. However, standard deep neural network approaches often entangle these modalities, obscuring the…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
There are around 5.3 billion Internet users, amounting to 65.7% of the global population, and web technology is the backbone of the services delivered via the Internet. To ensure web applications are free from security-related bugs, web…
The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share…
One important problem in microbiome analysis is to identify the bacterial taxa that are associated with a response, where the microbiome data are summarized as the composition of the bacterial taxa at different taxonomic levels. This paper…
The solutions of a system of polynomials in several variables are often needed, e.g.: in the design of mechanical systems, and in phase-space analyses of nonlinear biological dynamics. Reliable, accurate, and comprehensive numerical…
A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of…
A bipartite graph extensively models relationships between real-world entities of two different types, such as user-product data in e-commerce. Such graph data are inherently becoming more and more streaming, entailing continuous insertions…