Molly Hammell

This paper evaluates combining expression-based surrogate variables and genotype-based principal components in differential expression analysis, finding the combined approach improves replicability and biological recall in ALS datasets.

The paper investigates TE transcription in Parkinson's disease brains, finding region- and cell-type-specific TE activation linked to an interferon response in microglia and neurons.

TEsingle provides locus-specific transposable element expression analysis in single-cell data, revealing cell-type-specific TE expression in Parkinson's Disease.

This study identifies TDP-43-dependent cryptic gene-TE fusions (crypTEs) in neurons and ALS/FTD tissues, showing their association with altered gene expression and potential pathogenic effects.

This study shows that L1 retrotransposons influence human pluripotency exit and early brain development through their expression and derived transcripts.

This study shows that TDP-43 pathology in mice triggers LINE-1 retrotransposon replication in motor cortex neurons and glia, leading to cell-intrinsic and non-cell autonomous programmed cell death.

This study introduces DANcer, a deep learning classifier that identifies robust ALS molecular subtypes across bulk and single-cell datasets, showing they correlate with clinical features and cellular mechanisms.

The paper identifies TDP-43 dysregulation of polyadenylation site selection as a key feature of RNA misprocessing in ALS/FTD and related disorders, linking it to increased tau phosphorylation.

This study shows L1 retrotransposons contribute to human brain transcriptome complexity and functional diversification through cell-type specific transcripts and regulatory RNAs.

This study shows that TDP-43 pathology in Drosophila glial cells causes systemic toxicity, which can be reduced by knocking down SF2/SRSF1.

The paper uses snRNA-seq to analyze TBI brain tissue, finding oligodendroglia activate endogenous retroviruses, linking them to neuroinflammation.

The paper compares TDP-43's transcriptional and splicing effects in muscle and neuronal cells, showing tissue-specific roles in disease.

The paper uses unsupervised machine learning to identify three molecular subtypes in ALS cortex samples, associated with oxidative stress, retrotransposon activation, and glial activation.

TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma by analyzing multiple small RNA classes in an integrated workflow.

SAKE identifies markers of resistance to BRAF inhibitors in melanoma cells by analyzing scRNA-Seq data from multiple platforms.

This paper shows that TDP-43 expression in Drosophila causes retrotransposon activation, leading to neurodegeneration through DNA damage and programmed cell death.