66 items found

Tags: Computer Science Applications

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  • publication

    Drug voyager: a computational platform for exploring unintended drug action

    Abstract Background The dominant paradigm in understanding drug action focuses on the intended therapeutic effects and frequent...
  • publication

    DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predict...

    Background Dystrophinopathy is one of the most common human monogenic diseases which results in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Mutations...
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    metaX: a flexible and comprehensive software for processing metabolomics data

    Background Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated...
  • publication

    The spatial distribution of knowledge production in Europe. Evidence from KET...

    In this paper, we develop an analysis of the spatial distribution of knowledge production related to Key Emerging Technologies (KETs) and Societal Grand Challenges (SGCs) in...
  • publication

    NEAT: a framework for building fully automated NGS pipelines and analyses

    Background: The analysis of next generation sequencing (NGS) has become a standard task for many laboratories in the life sciences. Though there exists several tools to support...
  • publication

    Ambiguity of non-systematic chemical identifiers within and between small-mol...

    Background A wide range of chemical compound databases are currently available for pharmaceutical research. To retrieve compound information, including structures, researchers...
  • publication

    Bioalerts: a python library for the derivation of structural alerts from bioa...

    Background Assessing compound toxicity at early stages of the drug discovery process is a crucial task to dismiss drug candidates likely to fail in clinical trials. Screening...
  • publication

    Algorithm and software to automatically identify latency and amplitude featur...

    Background Local field potentials (LFPs) evoked by sensory stimulation are particularly useful in electrophysiological research. For instance, spike timing and current...
  • publication

    gtrellis: an R/Bioconductor package for making genome-level Trellis graphics

    Background Trellis graphics are a visualization method that splits data by one or more categorical variables and displays subsets of the data in a grid of panels. Trellis...
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    Assessment of k-mer spectrum applicability for metagenomic dissimilarity anal...

    Background A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates...
  • publication

    Context-specific functional module based drug efficacy prediction

    Background It is necessary to evaluate the efficacy of individual drugs on patients to realize personalized medicine. Testing drugs on patients in clinical trial is the only way...
  • publication

    MultiDataSet: an R package for encapsulating multiple data sets with applicat...

    BACKGROUND: Reduction in the cost of genomic assays has generated large amounts of biomedical-related data. As a result, current studies perform multiple experiments in the same...
  • publication

    Risk-conscious correction of batch effects: maximising information extraction...

    Background Batch effects are a persistent and pervasive form of measurement noise which undermine the scientific utility of high-throughput genomic datasets. At their most...
  • publication

    Roar: detecting alternative polyadenylation with standard mRNA sequencing lib...

    Background Post-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications...
  • publication

    ClinQC: a tool for quality control and cleaning of Sanger and NGS data in cli...

    Background Traditional Sanger sequencing has been used as a gold standard method for genetic testing in clinic to perform single gene test, which has been a cumbersome and...
  • publication

    From raw data to data-analysis for magnetic resonance spectroscopy – the miss...

    Background Magnetic resonance spectroscopy provides metabolic information about living tissues in a non-invasive way. However, there are only few multi-centre clinical studies,...
  • publication

    Innovation indices: the need for positioning them where they properly belong

    A specific quality of the discussion about innovation indices (scoreboards) is that more often than not the subject is dealt with from a purely technical point of view. Such a...
  • publication

    Tilting the Lasso by Knowledge-Based Post-Processing

    Background It is useful to incorporate biological knowledge on the role of genetic determinants in predicting an outcome. It is, however, not always feasible to fully elicit...
  • publication

    msBiodat analysis tool, big data analysis for high-throughput experiments

    Background Mass spectrometry (MS) are a group of a high-throughput techniques used to increase knowledge about biomolecules. They produce a large amount of data which is...
  • publication

    "A scalability study of phylogenetic network inference methods using empirica...

    Background Branching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be...