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Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a…
Here we present ComPPI, a cellular compartment specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (http://ComPPI.LinkGroup.hu). ComPPI enables the user…
We present the Global Health Monitor, an online Web-based system for detecting and mapping infectious disease outbreaks that appear in news stories. The system analyzes English news stories from news feed providers, classifies them for…
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
In recent years, we have witnessed a dramatic data explosion in genomics, thanks to the improvement in sequencing technologies and the drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each…
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical…
Many fields of science rely on relational database management systems to analyze, publish and share data. Since RDBMS are originally designed for, and their development directions are primarily driven by, business use cases they often lack…
While several public institutions provide its data openly, the effort required to access, integrate and query this data is too high, reducing the amount of possible dataset users. The Blended Integrated Open Data (BIOD) project has as…
High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of…
Index structures are a building block of query processing and computer science in general. Since the dawn of computer technology there have been index structures. And since then, a myriad of index structures are being invented and published…
Increasingly massive volumes of multi-modal data are being accumulated in many {real world} settings, including in health care and e-commerce. This development calls for effective general-purpose data management solutions for multi-modal…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…
The INTEGRAL Science Data Centre (ISDC) processes, archives and distributes data from the INTEGRAL mission. At the ISDC incoming data from the satellite are processed and searched for transient sources and Gamma-Ray bursts. The data are…
Herbarium sheets present a unique view of the world's botanical history, evolution, and diversity. This makes them an all-important data source for botanical research. With the increased digitisation of herbaria worldwide and the advances…
Contemporary bioinformatics has seen in profound new visibility into the composition, structure, and history of the natural world around us. Arguably, the central pillar of bioinformatics is phylogenetics -- the study of hereditary…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
Biotoxins, mainly produced by venomous animals, plants and microorganisms, exhibit high physiological activity and unique effects such as lowering blood pressure and analgesia. A number of venom-derived drugs are already available on the…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…