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Processing genome-wide association studies within a repository of heterogeneous genomic datasets
BackgroundGenome Wide Association Studies (GWAS) are based on the observation of genome-wide sets of genetic variants – typically single-nucleotide...
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Genomic data integration and user-defined sample-set extraction for population variant analysis
BackgroundPopulation variant analysis is of great importance for gathering insights into the links between human genotype and phenotype. The 1000...
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Elucidating the causal relationship of mechanical power and lung injury: a dynamic approach to ventilator management
BackgroundMechanical power (MP) serves as a crucial predictive indicator for ventilator-induced lung injury and plays a pivotal role in tailoring the...
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PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets
BackgroundWith the growth of available sequenced datasets, analysis of heterogeneous processed data can answer increasingly relevant biological and...
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Automated Integration of Genomic Metadata with Sequence-to-Sequence Models
While exponential growth in public genomic data can afford great insights into biological processes underlying diseases, a lack of structured...
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Empowering Virus Sequence Research Through Conceptual Modeling
The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral...
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Designing and Evaluating Deep Learning Models for Cancer Detection on Gene Expression Data
Transcription profiling enables researchers to understand the activity of the genes in various experimental conditions; in human genomics, abnormal...
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The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational...
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Evaluating Deep Semi-supervised Learning for Whole-Transcriptome Breast Cancer Subtyping
We investigate the important clinical problem of predicting prognosis-related breast cancer molecular subtypes using whole-transcriptome information...
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Exploiting Conceptual Modeling for Searching Genomic Metadata: A Quantitative and Qualitative Empirical Study
Providing a common data model for the metadata of several heterogeneous genomic data sources is hard, as they do not share any standard or agreed...
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From a Conceptual Model to a Knowledge Graph for Genomic Datasets
Data access at genomic repositories is problematic, as data is described by heterogeneous and hardly comparable metadata. We previously introduced a...
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Machine Learning and Principles and Practice of Knowledge Discovery in Databases International Workshops of ECML PKDD 2022, Grenoble, France, September 19–23, 2022, Proceedings, Part I
This volume constitutes the papers of several workshops which were held in conjunction with the International Workshops of ECML PKDD 2022 on Machine...
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Machine Learning and Principles and Practice of Knowledge Discovery in Databases International Workshops of ECML PKDD 2022, Grenoble, France, September 19–23, 2022, Proceedings, Part II
This volume constitutes the papers of several workshops which were held in conjunction with the International Workshops of ECML PKDD 2022 on Machine...
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Exploiting Ladder Networks for Gene Expression Classification
The application of deep learning to biology is of increasing relevance, but it is difficult; one of the main difficulties is the lack of massive...
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Experiences in the Development of a Data Management System for Genomics
GMQL is a high-level query language for genomics, which operates on datasets described through GDM, a unifying data model for processed data formats....
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Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language
Novel technologies and growing interest have resulted in a large increase in the amount of data available for genomics and transcriptomics studies,...
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Overview of GeCo: A Project for Exploring and Integrating Signals from the Genome
Next Generation Sequencing is a 10-year old technology for reading the DNA, capable of producing massive amounts of genomic data - in turn, reshaping...
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Biomolecular Annotation Integration and Querying to Help Unveiling New Biomedical Knowledge
Targeting biological questions requires comprehensive evaluation of multiple types of annotations describing current biological knowledge; they are...