Alan G. Herbert

OmiXAI: An Ensemble XAI Pipeline for Interpretable Deep Learning in Omics Data

OmiXAI is an ensemble XAI pipeline for deep learning in omics data that reduces feature sets and benchmarks XAI methods on Z-DNA prediction.

The YTHDC1 glutamate-rich domain docks to the ADAR1 Zα Domain, linking the N6-methyladenosine modification of pre-mRNAs to dsRNA editing

The paper uses AI-driven protein design to discover that ADAR1 interacts with YTHDC1, linking m6A modification to dsRNA editing and suggesting a mechanism for RNA editing regulation.

Zα and Zβ domains of ADAR1 and ZBP1 bind to G-quadruplexes with low micromolar affinity

The paper shows that Zβ domains of ADAR1 and ZBP1 bind to G-quadruplex RNA and DNA with low micromolar affinity, providing experimental evidence for their interaction.

OmicsFUSION: A Pretrained Hyena-Based Framework for Encoding, Reconstruction, and Representation of the Omics and DNA Data

The paper introduces a framework that integrates DNA sequences with omics data using a pretrained model, enabling reconstruction and unified representation of genomic and functional information.

Z-Flipons conserved between human and mouse are associated with increased transcription initiation rates

The paper identifies conserved Z-flipons between human and mouse that are linked to increased transcription initiation rates in CpG-promoters.

Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping

The paper uses G4-DNABERT to map G-quadruplexes to enhancer and promoter regions, supporting their role in chromatin looping and gene regulation.

Z-Flipon Variants reveal the many roles of Z-DNA and Z-RNA in health and disease

The paper identifies Z-flipon variants' roles in health and disease by analyzing Z-DNA and Z-RNA effects across multiple genomic features and disease associations.

Graph Neural Networks for Z-DNA prediction in Genomes

This study applies graph neural networks to predict Z-DNA in genomes, showing improved performance over previous methods using sequence and omics data.

A role for Flipons and miRNAs in Promoter Specification during Development?

The paper explores the role of flipons and miRNAs in promoter specification during development, suggesting a connection between RNA and DNA mechanisms in establishing cell identity.