Ernest Fraenkel

This study maps spatial metabolic activity in adult fruit flies using isotope tracing and mass-spectrometry imaging, revealing compartmentalized nutrient use across tissues.

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 shows that an IGF1-derived peptide reduces IGFBP2 in RTT astrocytes, improving synaptogenesis and mitochondrial function in neurons.

The paper introduces a spatial pharmacology platform to study how chemotherapy affects immune and metabolic states in tumors, identifying key metabolic axes and resistant macrophage populations.

The paper investigates transcriptomic changes in oligodendroglial lineage cells from PD patient-iPSCs with LRRK2-G2019S mutation, identifying altered pathways and signaling in OPCs and ODCs.

This paper introduces PhenoMol, a framework that integrates multiomic and multi-phenotypic data to identify biological pathways linked to physical fitness, outperforming traditional regression models.

This study maps metabolic changes in 12 organs of male and female mice across 5 ages, identifying sex-specific patterns and a metabolic aging clock.

This study shows that interferon gamma restores antigen presentation in medulloblastoma and enhances T cell-mediated tumor killing in a mouse model.

The paper identifies TDP-43-dependent molecular cascades in ALS/FTD by integrating multiomic data from iPSC-derived neurons and validates key genes through experimental assays.

This study integrates multi-omics data from Drosophila and human Alzheimer's disease models to identify pathways involved in neurodegeneration.

This study compares the effects of HTT knockout and CAG repeat expansion in cortical neurons, identifying shared and distinct biological pathways involved in HD.

This paper benchmarks multimodal single-cell data integration methods to improve kidney reference atlas quality by identifying adaptive states and rare cell types.

The paper integrates pathway discovery with pooled genetic perturbation to identify modifiers of Huntington's disease, revealing genes involved in neuronal development and morphology.

The paper identifies transcriptomic changes in oligodendrocytes and precursor cells linked to Parkinson's disease outcomes and shows their predictive value for cognitive and depressive symptoms.

The paper identifies a conserved role for APP in proteostasis during aging through genetic and multi-omics analyses in Drosophila and human models.

The paper analyzes ATAC-seq data from iPSC-derived motor neurons of ALS patients and controls to identify disease-specific chromatin accessibility changes and their predictive power for disease progression.

The paper presents a LINCS Microenvironment perturbation dataset cataloging transcriptional, proteomic, epigenomic, and phenotypic responses of MCF10A cells to six ligands, enabling integrative analysis of molecular and phenotypic changes.

This study uses snRNAseq to analyze HD mouse models and human brain tissue, identifying impaired oligodendrocyte maturation and a potential role for thiamine metabolism in disease pathology.

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

The paper performs an integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients to identify dysregulated pathways and validate them in vivo and in postmortem data.

The paper investigates how APOE4 affects bioenergetic pathways in specific brain regions of aged mice, finding region-specific differences that may contribute to Alzheimer's disease risk.

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

The paper introduces a computational method to identify missing signaling pathway elements from temporal phosphoproteomic data, demonstrating its effectiveness in both human EGF response and yeast osmotic stress response.

The paper develops a freezing protocol for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells, showing that slow-cooled cryopreserved samples yield comparable results to fresh cells.