Big data and deep learning for RNA biology

H Hwang, H Jeon, N Yeo, D Baek - Experimental & Molecular Medicine, 2024 - nature.com
The exponential growth of big data in RNA biology (RB) has led to the development of deep
learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL …

Opportunities and challenges in sharing and reusing genomic interval data

B Xue, O Khoroshevskyi, RA Gomez… - Frontiers in …, 2023 - frontiersin.org
Major advances in genome sequencing technology have driven a dramatic increase in the
production of epigenome data (ENCODE Consortium, 2012; Sheffield and Furey, 2012; …

CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning

G Serna García, R Al Khalaf, F Invernici, S Ceri… - …, 2023 - academic.oup.com
Abstract Background Literature about SARS-CoV-2 widely discusses the effects of variations
that have spread in the past 3 years. Such information is dispersed in the texts of several …

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 …

Challenges to sharing sample metadata in computational genomics

NC Sheffield, NJ LeRoy, O Khoroshevskyi - Frontiers in Genetics, 2023 - frontiersin.org
The genomic data deluge has led to challenges with sharing and integrating genomic data.
While substantial effort has been devoted to making genomics data easier to share, one …

Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata

H Yuan, P Hicks, M Ahmadian… - Briefings in …, 2025 - academic.oup.com
Reusing massive collections of publicly available biomedical data can significantly impact
knowledge discovery. However, these public samples and studies are typically described …

Investigation of machine learning algorithms for taxonomic classification of marine metagenomes

H Park, SJ Lim, J Cosme, K O'Connell… - Microbiology …, 2023 - Am Soc Microbiol
Microbial communities play key roles in ocean ecosystems through regulation of
biogeochemical processes such as carbon and nutrient cycling, food web dynamics, and gut …

Identification of genomic alteration and prognosis using pathomics-based artificial intelligence in oral leukoplakia and head and neck squamous cell carcinoma: a …

XJ Cai, CR Peng, YY Cui, L Li, MW Huang… - … Journal of Surgery, 2025 - journals.lww.com
Background: Loss of chromosome 9p is an important biomarker in the malignant
transformation of oral leukoplakia (OLK) to head and neck squamous cell carcinoma …

Model, Integrate, Search... Repeat

A Bernasconi - LECTURE NOTES IN BUSINESS INFORMATION …, 2023 - Springer
This book is a revised version of the Ph. D. dissertation written and successfully defended by
the author to receive her Ph. D. from the School of Information Technology, Politecnico di …

Conceptual Modeling for Bioinformatics

A Bernasconi, A García S - Encyclopedia of Bioinformatics and …, 2024 - re.public.polimi.it
Conceptual Modeling is a standard practice in Database and Information Systems research
community. It has also been applied to Bioinformatics-related problems, representing …