An Updated Overview of Existing Cancer Databases and Identified Needs

BK Austin, A Firooz, H Valafar, AV Blenda - Biology, 2023 - mdpi.com
Simple Summary This review examines the current state of cancer databases and identifies
key needs in the field. The analysis of 71 databases reveals a lack of dedicated lipidomic …

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

D Chicco, F Cumbo, C Angione - PLOS Computational Biology, 2023 - journals.plos.org
Data are the most important elements of bioinformatics: Computational analysis of
bioinformatics data, in fact, can help researchers infer new knowledge about biology …

[HTML][HTML] Data quality-aware genomic data integration

A Bernasconi - Computer Methods and Programs in Biomedicine …, 2021 - Elsevier
Genomic data are growing at unprecedented pace, along with new protocols, update
polices, formats and guidelines, terminologies and ontologies, which are made available …

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

NJ LeRoy, O Khoroshevskyi, A O'Brien, R Stępień… - …, 2024 - academic.oup.com
Background As biological data increase, we need additional infrastructure to share them
and promote interoperability. While major effort has been put into sharing data, relatively …

[HTML][HTML] PoliViews: A comprehensive and modular approach to the conceptual modeling of genomic data

A Bernasconi, A García, S Ceri, O Pastor - Data & Knowledge Engineering, 2023 - Elsevier
The human genome complexity is captured by many signals, representing for instance DNA
variations, the expression of gene activity, or DNA's structural rearrangements; a rich set of …

A comprehensive approach for the conceptual modeling of genomic data

A Bernasconi, A García S, S Ceri, O Pastor - International Conference on …, 2022 - Springer
The human genome is traditionally represented as a DNA sequence of three billion base
pairs. However, its intricacies are captured by many more complex signals, representing …

Genomic data integration and user-defined sample-set extraction for population variant analysis

T Alfonsi, A Bernasconi, A Canakoglu, M Masseroli - BMC bioinformatics, 2022 - Springer
Background Population variant analysis is of great importance for gathering insights into the
links between human genotype and phenotype. The 1000 Genomes Project established a …

Processing genome-wide association studies within a repository of heterogeneous genomic datasets

A Bernasconi, A Canakoglu, F Comolli - BMC genomic data, 2023 - Springer
Abstract Background Genome Wide Association Studies (GWAS) are based on the
observation of genome-wide sets of genetic variants–typically single-nucleotide …

Big Data Analytics for Precision Health and Prevention

E Capobianco, J Deng - Frontiers in big Data, 2022 - frontiersin.org
In the oncological context, big data analyses are quite complex due to heterogeneous data
structures and varieties (Agarwala et al., 2018). The defining characteristic of precision …

BEDMS: A metadata standardizer for genomic region attributes

S Tambe, O Khoroshevskyi, SH Park, NJ LeRoy… - bioRxiv, 2024 - biorxiv.org
High-throughput sequencing technologies have generated vast omics data annotating
genomic regions. A challenge arises in integrating this data because the associated …