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Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how…
The recent rise of cryo-EM and X-ray high-throughput techniques is providing a wealth of new structures trapped in different conformations. Understanding how proteins transition between different conformers, and how they relate to each…
Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
The vast amount of sequencing data presently available allow the scientific community to explore a range of genetic variables that may drive and progress cancer. A myriad of predictive tools has been proposed, allowing researchers and…
Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions. However, mathematical models are still most often created de novo, based on reading the literature and…
Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. For this reason, these data are…
Computation biology helps to understand all processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a…
A prototype for a web application was designed and implemented as a guide to be used by clinicians when designing the best drug therapy for a specific cancer patient, given biological data derived from the patients tumor tissue biopsy. A…
Computational analyses of, e.g., genomic, proteomic, or metabolomic data, commonly result in one or more sets of candidate genes, proteins, or enzymes. These sets are often the outcome of clustering algorithms. Subsequently, it has to be…
The integration of multi-modal data, such as pathological images and genomic data, is essential for understanding cancer heterogeneity and complexity for personalized treatments, as well as for enhancing survival predictions. Despite the…
Introduction: To leverage functionality and clinical relevance into understanding systems biology, one needs to understand the pathway of the genetic effects on risk factors/disease through intermediate molecular levels, such as…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
The Globaltest is a powerful test for the global null hypothesis that there is no association between a group of features and a response of interest, which is popular in pathway testing in metabolomics. Evaluating multiple pathways,…
Predictive modeling based on genomic data has gained popularity in biomedical research and clinical practice by allowing researchers and clinicians to identify biomarkers and tailor treatment decisions more efficiently. Analysis…
Addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
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…