Renz, Alina Widerspick, Lina Dräger, Andreas
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...
Kerin, Matthew Marchini, Jonathan
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...
Bekkar, Amel Nasrallah, Anita Guex, Nicolas Fajas, Lluis Xenarios, Ioannis Lopez-Mejia, Isabel C
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...
Wen, Canhong Yang, Yuhui Xiao, Quan Huang, Meiyan Pan, Wenliang
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 ...
Chen, Shaoqi Xue, Dongyu Chuai, Guohui Yang, Qiang Liu, Qi
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...
Borgsmüller, Nico Bonet, Jose Marass, Francesco Gonzalez-Perez, Abel Lopez-Bigas, Nuria Beerenwinkel, Niko
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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...
Reardon, Hue V Che, Anney Luke, Brian T Ravichandran, Sarangan Collins, Jack R Mudunuri, Uma S
Published in
Bioinformatics (Oxford, England)
The Annotation, Visualization and Impact Analysis (AVIA) is a web application combining multiple features to annotate and visualize genomic variant data. Users can investigate functional significance of their genetic alterations across samples, genes, and pathways. Version 3.0 of AVIA offers filtering options through interactive charts and by linki...
Wang, Yan Correa Marrero, Miguel Medema, Marnix H van Dijk, Aalt D J
Published in
Bioinformatics (Oxford, England)
Polyketide synthases (PKSs) are enzymes that generate diverse molecules of great pharmaceutical importance, including a range of clinically used antimicrobials and antitumor agents. Many polyketides are synthesized by cis-AT modular PKSs, which are organized in assembly lines, in which multiple enzymes line up in a specific order. This order is def...
Ekvall, Markus Höhle, Michael Käll, Lukas
Published in
Bioinformatics (Oxford, England)
Permutation tests offer a straightforward framework to assess the significance of differences in sample statistics. A significant advantage of permutation tests are the relatively few assumptions about the distribution of the test statistic are needed, as they rely on the assumption of exchangeability of the group labels. They have great value, as ...
Shi, Yi Guo, Zehua Su, Xianbin Meng, Luming Zhang, Mingxuan Sun, Jing Wu, Chao Zheng, Minhua Shang, Xueyin Zou, Xin
...
Published in
Bioinformatics (Oxford, England)
The mutations of cancers can encode the seeds of their own destruction, in the form of T-cell recognizable immunogenic peptides, also known as neoantigens. It is computationally challenging, however, to accurately prioritize the potential neoantigen candidates according to their ability of activating the T-cell immunoresponse, especially when the s...