Published in Bioinformatics (Oxford, England)
Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or by using a vector graphic software. pyGenomeTracks (PGT) is a modular plotting tool that easily combines multiple tracks. It enables a reproducible an...
Published in Bioinformatics (Oxford, England)
Integrative multi-feature fusion analysis on biomedical data has gained much attention recently. In breast cancer, existing studies have demonstrated that combining genomic mRNA data and DNA methylation data can better stratify can-cer patients with distinct prognosis than using single signature. However, those ex-isting methods are simply combinin...
Published in Bioinformatics (Oxford, England)
Epigenetic modifications reflect key aspects of transcriptional regulation, and many epigenomic data sets have been generated under different biological contexts to provide insights into regulatory processes. However, the technical noise in epigenomic data sets and the many dimensions (features) examined make it challenging to effectively extract b...
Published in Bioinformatics (Oxford, England)
Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitatio...
Published in Bioinformatics (Oxford, England)
The novel coronavirus (SARS-CoV-2) currently spreads worldwide, causing the disease COVID-19. The number of infections increases daily, without any approved antiviral therapy. The recently released viral nucleotide sequence enables the identification of therapeutic targets, e.g. by analyzing integrated human-virus metabolic models. Investigations o...
Published in Bioinformatics (Oxford, England)
Gene-environment (GxE) interactions are one of the least studied aspects of the genetic architecture of human traits and diseases. The environment of an individual is inherently high dimensional, evolves through time and can be expensive and time consuming to measure. The UK Biobank study, with all 500,000 participants having undergone an extensive...
Published in Bioinformatics (Oxford, England)
Protein phosphorylation--catalyzed by protein kinases-is the most common post-translational modification. It increases the functional diversity of the proteome and influences various aspects of normal physiology and can be altered in disease states. High throughput profiling of kinases is becoming an essential experimental approach to investigate t...
Published in Bioinformatics (Oxford, England)
Imaging genetics is mainly used to reveal the pathogenesis of neuropsychiatric risk genes and understand the relationship between human brain structure, functional and individual differences. Increasingly, the brain-wide imaging phenotypes in voxels are available to test the association with genetic markers. A challenge with analyzing such data is ...
Published in Bioinformatics (Oxford, England)
Quantitative structure-activity relationship (QSAR) analysis is commonly used in drug discovery. Collaborations among pharmaceutical institutions can lead to a better performance in QSAR prediction, however, intellectual property and related financial interests remain substantially hindering inter-institutional collaborations in QSAR modeling for d...
Published in Bioinformatics (Oxford, England)
The high resolution of single-cell DNA sequencing (scDNA-seq) offers great potential to resolve intratumor heterogeneity (ITH) by distinguishing clonal populations based on their mutation profiles. However, the increasing size of scDNA-seq datasets and technical limitations, such as high error rates and a large proportion of missing values, complic...
