Ann‐Marie Mallon

The paper analyzes 3,313 genetically engineered mouse lines to identify gene essentiality as the main factor affecting Cas9-based genome editing success.

The paper develops a convolutional neural network to automate MRI defacing quality control, reducing manual checks and improving efficiency.

The paper identifies novel Mendelian genes by analyzing mouse embryo lethality and linking them to human disease phenotypes and genetic variants.

The paper investigates the functional relationships of genes within TADs, finding that genes in CTCF-bound TADs are not more co-expressed or functionally similar than expected by proximity, but functionally important genes are more likely to occupy TADs alone.

The paper phenotypes Dp1Tyb mice, a Down syndrome model, and identifies multiple DS-like traits including cognitive and physical abnormalities.

This study shows that DNA repair mechanisms in mice reduce the rate of nonsense mutations by prioritizing substitutions that are more deleterious to fitness.

The paper introduces DeepCytometer, a deep learning pipeline for segmenting whole slides of mouse white adipose tissue, and uses it to analyze phenotypes in Klf14 mouse models.

The paper reports the generation of over 5,000 new mouse mutant strains for targeted genes, significantly expanding the available genetic resources for biomedical research.

LAMA automates 3D image analysis for mouse embryo phenotyping, integrating with an anatomical atlas to annotate dysmorphologies.

OpenStats improves speed and scalability for high-throughput phenotypic data analysis, showing significant performance gains in the International Mouse Phenotyping Consortium.

The paper integrates gene essentiality data from human and mouse screens to classify genes into FUSIL categories, identifying developmental lethal genes associated with rare diseases.

The paper introduces a method called soft windowing to improve analysis of high-throughput phenotyping data by reducing false positives and increasing significant results.

The paper estimates intraspecific constraint for mouse genes and shows strong correlation with human orthologues, linking constraint to pleiotropy and Mendelian disease.