Daniel M. Ramos

Integration of cell-specific gene expression and chromatin accessibility facilitates localization of neurodegenerative risk in microglia

The paper integrates cell-specific gene expression and chromatin accessibility to identify neurodegenerative disease risk loci specific to microglia.

Prevention of Transgene Silencing During Human PluripotentStem Cell Differentiation

The paper identifies strategies to prevent transgene silencing during human pluripotent stem cell differentiation and introduces a robust vector construct.

Novel reporter of the PINK1-Parkin mitophagy pathway identifies its damage sensor in the import gate

A HaloTagged MFN2 reporter enabled CRISPRi screens showing diverse mitochondrial damage activates PINK1-Parkin via membrane potential loss, with TOM retaining PINK1 when TIM23 is blocked.

Maintenance of neuronal TDP-43 expression requires axonal lysosome transport

The paper identifies BORC as a modifier of TDP-43 protein levels in neurons, showing lysosome transport is required for TDP-43 turnover.

Temporal dynamics of proteome and phosphorproteome during neuronal differentiation in the reference KOLF2.1J iPSC line

The paper profiles proteome and phosphoproteome dynamics during neuronal differentiation of the KOLF2.1J iPSC line, revealing distinct molecular signatures and kinase activity changes.

Proteomic Analysis of Endemic Viral Infections in Neuronsoffers Insights into Neurodegenerative Diseases

The paper investigates how endemic viral infections alter the neuronal proteome and links these changes to neurodegenerative disease pathways.

African ancestry neurodegeneration risk variant disrupts an intronic branchpoint in GBA1

The paper identifies a non-coding risk variant in GBA1 associated with Parkinson's disease in African ancestry populations, showing it disrupts splicing and reduces glucocerebrosidase activity.

Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD

The paper shows that loss of TDP-43 function leads to the expression of de novo proteins from mis-spliced mRNA transcripts in ALS/FTD.

Enhancer-driven regulatory network of forebrain human development provides insights into autism

The paper constructs an enhancer-driven gene regulatory network from human forebrain organoids with ASD and neurotypical controls, identifying key regulators of excitatory neuron specification in macrocephalic ASD.

Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors

This paper develops compact CRISPRi sgRNA libraries and optimal effectors to improve knockdown consistency and efficiency in mammalian cells.

A reference induced pluripotent stem cell line for large-scale collaborative studies

The paper identifies and characterizes a reference iPSC line, KOLF2.1J, for standardized use in collaborative studies across multiple differentiation protocols and assays.

Application of Aligned-UMAP to longitudinal biomedical studies

This paper applies Aligned-UMAP to longitudinal biomedical datasets to reveal time-dependent patterns and provides best practices for its use.

A fully automated FAIMS-DIA proteomic pipeline for high-throughput characterization of iPSC-derived neurons

The paper presents a fully automated FAIMS-DIA proteomic pipeline for iPSC-derived neurons, showing high protein identification and reproducibility, validated against single-cell RNA-Seq data.