Small data methods in omics: the power of one

KG Johnston, SF Grieco, Q Nie, FJ Theis, X Xu - Nature Methods, 2024‏ - nature.com
Over the last decade, biology has begun utilizing 'big data'approaches, resulting in large,
comprehensive atlases in modalities ranging from transcriptomics to neural connectomics …

siVAE: interpretable deep generative models for single-cell transcriptomes

Y Choi, R Li, G Quon - Genome Biology, 2023‏ - Springer
Neural networks such as variational autoencoders (VAE) perform dimensionality reduction
for the visualization and analysis of genomic data, but are limited in their interpretability: it is …

Exploring gene regulation and biological processes in insects: Insights from omics data using gene regulatory network models

CF Ting, S Harun, KM Daud, S Sulaiman… - Progress in Biophysics …, 2024‏ - Elsevier
Gene regulatory network (GRN) comprises complicated yet intertwined gene-regulator
relationships. Understanding the GRN dynamics will unravel the complexity behind the …

Explaining identity-aware graph classifiers through the language of motifs

A Perotti, P Bajardi, F Bonchi… - 2023 International joint …, 2023‏ - ieeexplore.ieee.org
Most methods for explaining black-box classifiers (eg, on tabular data, images, or time
series) rely on measuring the impact that removing/perturbing features has on the model …

Interpretable AI for inference of causal molecular relationships from omics data

P Dibaeinia, A Ojha, S Sinha - Science Advances, 2025‏ - science.org
The discovery of molecular relationships from high-dimensional data is a major open
problem in bioinformatics. Machine learning and feature attribution models have shown …

Comparative transcriptome profiling reveals the basis of differential sheath blight disease response in tolerant and susceptible rice genotypes

P Samal, KA Molla, A Bal, S Ray, H Swain, A Khandual… - Protoplasma, 2022‏ - Springer
Rice sheath blight (ShB) disease, caused by the fungal pathogen Rhizoctonia solani AG1-
IA, is one of the devastating diseases and causes severe yield losses all over the world. No …

[HTML][HTML] DiffBrainNet: Differential analyses add new insights into the response to glucocorticoids at the level of genes, networks and brain regions

N Gerstner, AC Krontira, C Cruceanu, S Roeh… - Neurobiology of …, 2022‏ - Elsevier
Genome-wide gene expression analyses are invaluable tools for studying biological and
disease processes, allowing a hypothesis-free comparison of expression profiles …

Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework

BMH Heuts, S Arza-Apalategi, S Frölich… - Scientific Reports, 2022‏ - nature.com
Advanced computational methods exploit gene expression and epigenetic datasets to
predict gene regulatory networks controlled by transcription factors (TFs). These methods …

Research on gastric cancer's drug-resistant gene regulatory network model

Z Li, T Zhang, H Lei, L Wei, Y Liu, Y Shi, S Li… - Current …, 2020‏ - benthamdirect.com
Objective: Based on bioinformatics, differentially expressed gene data of drug-resistance in
gastric cancer were analyzed, screened and mined through modeling and network modeling …

A pseudo-value regression approach for differential network analysis of co-expression data

S Ahn, T Grimes, S Datta - BMC bioinformatics, 2023‏ - Springer
Background The differential network (DN) analysis identifies changes in measures of
association among genes under two or more experimental conditions. In this article, we …