Related papers: PhaBOX: A web server for identifying and character…
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler that addresses the challenge of…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
Background: The secure management of sensitive clinical data, particularly human genomics data, has become a critical requirement in modern biomedical research. Although the necessary software and algorithms are readily available, their use…
This paper introduces the \proglang{R} package \pkg{meta4diag} for implementing Bayesian bivariate meta-analyses of diagnostic test studies. Our package \pkg{meta4diag} is a purpose-built front end of the \proglang{R} package \pkg{INLA}.…
Structural biology has made significant progress in determining membrane proteins, leading to a remarkable increase in the number of available structures in dedicated databases. The inherent complexity of membrane protein structures,…
Space-borne gravitational wave detectors will expand the scope of gravitational wave astronomy to the milli-Hertz band in the near future. The development of data analysis software infrastructure at the current stage is crucial. In this…
Cloud computing provides resources over the Internet and allows a plethora of applications to be deployed to provide services for different industries. The major bottleneck being faced currently in these cloud frameworks is their limited…
Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support…
Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
Motivation: The rapid growth in genome-wide association studies (GWAS) in plants and animals has brought about the need for a central resource that facilitates i) performing GWAS, ii) accessing data and results of other GWAS, and iii)…
Background/aims: While randomized controlled trials are the gold standard for measuring causal effects, robust conclusions about causal relationships can be obtained using data from observational studies if proper statistical techniques are…
Self-organizing complex systems typically are comprised of a large number of frequently similar components or events. Through their process, a pattern at the global-level of a system emerges solely from numerous interactions among the…
Parasitic infections remain a pressing global health challenge, particularly in low-resource settings where diagnosis still depends on labor-intensive manual inspection of blood smears and the availability of expert domain knowledge. While…
Be it for a malicious or legitimate purpose, packing, a transformation that consists in applying various operations like compression or encryption to a binary file, i.e. for making reverse engineering harder or obfuscating code, is widely…
When developing a (web) interface for a deductive database, functionality required by the client is provided by means of HTTP handlers that wrap the logical data access predicates. These handlers are responsible for converting between…
Steering a complex system towards a desired outcome is a challenging task. The lack of clarity on the system's exact architecture and the often scarce scientific data upon which to base the operationalisation of the dynamic rules that…
Phosphorylation site prediction based on kinase-substrate interaction plays a vital role in understanding cellular signaling pathways and disease mechanisms. Computational methods for this task can be categorized into kinase-family-focused…
Hyperbox-based machine learning algorithms are an important and popular branch of machine learning in the construction of classifiers using fuzzy sets and logic theory and neural network architectures. This type of learning is characterised…
In recent years microbiome studies have become increasingly prevalent and large-scale. Through high-throughput sequencing technologies and well-established analytical pipelines, relative abundance data of operational taxonomic units and…