Michael DeBerardine

PIANO: Probabilistic Inference Autoencoder Networks for multi-Omics enables robust generative modeling of gene expression and scales single-cell integration to 100 million cells

PIANO integrates single-cell data across species and modalities, models gene expression, and scales to 100 million cells for drug perturbation analysis.

Altered postnatal chromatin development in the nucleus accumbens primes lifelong stress sensitivity

This study shows that increased H3K4me1 in the nucleus accumbens during early life primes lifelong stress sensitivity by altering chromatin structure and neuronal function.

Cross-species consensus atlas of the primate basal ganglia

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

Spatial patterning of transcriptional and regulatory programs in the primate subcortex

The paper presents a spatially resolved transcriptomic and gene regulatory atlas of primate subcortical regions, revealing spatially tuned transcriptional and regulatory programs across cell types.

Fast Optimization of Robust Transcriptomics Embeddings using Probabilistic Inference Autoencoder Networks for multi-Omics

The paper introduces PIANO, a variational autoencoder for multi-omics integration, showing improved performance on single-species and multi-atlas datasets.

Conservation, alteration, and redistribution of mammalian striatal interneurons

The paper analyzes the conservation and evolution of striatal interneurons across mammals, finding that TAC3 interneurons are conserved and that neuronal types evolve through redistribution and refinement.

A lineage-specific nascent RNA assay unveils principles of gene regulation in tissue biology

The paper introduces PReCIS-seq, a nascent RNA assay, to study lineage-specific Pol II activity in mouse skin, revealing mechanisms of gene regulation in adult homeostasis.

Identification of human RNA Polymerase II interactors at early stages of transcription.

The paper identifies human RNA Polymerase II interactors at early transcription stages using biochemical purification and mass spectrometry, revealing new factors involved in PIC assembly and promoter-proximal pausing.