Reaching the end-game for GWAS: machine learning approaches for the prioritization of complex disease loci

HL Nicholls, CR John, DS Watson, PB Munroe… - Frontiers in …, 2020 - frontiersin.org
Genome-wide association studies (GWAS) have revealed thousands of genetic loci that
underpin the complex biology of many human traits. However, the strength of GWAS–the …

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

D Szklarczyk, AL Gable, KC Nastou, D Lyon… - Nucleic acids …, 2021 - academic.oup.com
Cellular life depends on a complex web of functional associations between biomolecules.
Among these associations, protein–protein interactions are particularly important due to their …

A comprehensive survey on graph reduction: Sparsification, coarsening, and condensation

M Hashemi, S Gong, J Ni, W Fan, BA Prakash… - arXiv preprint arXiv …, 2024 - arxiv.org
Many real-world datasets can be naturally represented as graphs, spanning a wide range of
domains. However, the increasing complexity and size of graph datasets present significant …

Net: Degree-specific graph neural networks for node and graph classification

J Wu, J He, J Xu - Proceedings of the 25th ACM SIGKDD international …, 2019 - dl.acm.org
Graph data widely exist in many high-impact applications. Inspired by the success of deep
learning in grid-structured data, graph neural network models have been proposed to learn …

IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis

M Kotlyar, C Pastrello, Z Ahmed, J Chee… - Nucleic acids …, 2022 - academic.oup.com
Improved bioassays have significantly increased the rate of identifying new protein-protein
interactions (PPIs), and the number of detected human PPIs has greatly exceeded early …

SilencerDB: a comprehensive database of silencers

W Zeng, S Chen, X Cui, X Chen, Z Gao… - Nucleic acids …, 2021 - academic.oup.com
Gene regulatory elements, including promoters, enhancers, silencers, etc., control
transcriptional programs in a spatiotemporal manner. Though these elements are known to …

DeepHistone: a deep learning approach to predicting histone modifications

Q Yin, M Wu, Q Liu, H Lv, R Jiang - BMC genomics, 2019 - Springer
Motivation Quantitative detection of histone modifications has emerged in the recent years
as a major means for understanding such biological processes as chromosome packaging …

HiChIPdb: a comprehensive database of HiChIP regulatory interactions

W Zeng, Q Liu, Q Yin, R Jiang… - Nucleic acids research, 2023 - academic.oup.com
Elucidating the role of 3D architecture of DNA in gene regulation is crucial for understanding
cell differentiation, tissue homeostasis and disease development. Among various chromatin …

Revisiting genome-wide association studies from statistical modelling to machine learning

S Sun, B Dong, Q Zou - Briefings in Bioinformatics, 2021 - academic.oup.com
Over the last decade, genome-wide association studies (GWAS) have discovered thousands
of genetic variants underlying complex human diseases and agriculturally important traits …

Gut brain regulation using psychobiotics for improved neuropsychological illness

Deepika, AK Shukla, A Kumari… - Developmental …, 2023 - Wiley Online Library
Abstract “Psychobiotics” are a novel class of probiotics that are beneficial to the health and
functional efficiency of our brain and psychology. The main hold on command in ill …