Aaron Streets

This paper introduces a Shannon entropy-based method to filter high-quality nuclei in scATAC-seq data, improving signal-to-noise ratio and downstream analysis reliability.

The paper identifies distinct adipocyte subsets in human white adipose tissue with different metabolic profiles and links TSHZ3 to their regulation and metabolic disease associations.

This paper introduces MethylSeqNet, a model that improves sequence-based gene regulation predictions by conditioning on CpG methylation, showing benefits for cell-type-specific regulation and allele-specific phenomena.

The paper shows preselection CD4+CD8+ thymocytes undergo gene expression changes linked to reduced TCR responsiveness and impaired CD4 fate gene upregulation, connecting these changes to T cell lineage commitment.

This study examines how different fixation methods affect SRS microscopy signals in HeLa cells, finding that Paraformaldehyde causes less disruption than other fixatives.

This paper introduces a method to verify LLM-extracted text by aligning it with ordered subword tokenization, showing improved accuracy over word-level tokenization.

The paper introduces dimelo-toolkit, a Python package for analyzing multimodal long-read epigenetic data, demonstrating its use with a novel DiMeLo-seq protocol to study chromatin state in GM12878 cells.

Scvi-hub provides a platform for sharing and analyzing single-cell omics datasets using pre-trained models, enabling efficient tasks like visualization and annotation with reduced computational demands.

DiMeLo-cito improves DiMeLo-seq by eliminating wash steps, enabling mitotic protein-DNA interaction analysis in diploid human cells and revealing CTCF bookmarking.

The paper uses SRS microscopy to show caloric restriction extends C. elegans lifespan by inhibiting vitellogenesis, a process linked to protein buildup in the pseudocoelom.

The paper introduces DiMeLo-seq, a method for mapping protein-DNA interactions using long-read sequencing, and provides a protocol and analysis tool.

This paper introduces veloVI, a deep generative model for RNA velocity analysis, showing improved data fit, consistency, and uncertainty quantification compared to existing methods.

popV improves cell-type annotation by providing uncertainty scores and reducing manual inspection through ensemble voting.

DiMeLo-seq maps protein-DNA interactions genome-wide with single-molecule resolution by methylating DNA near binding sites and using long-read sequencing.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

scvi-tools provides a Python package for probabilistic analysis of single-cell omics data, offering standardized interfaces and extensible tools for various analysis tasks.

This study uses CITE-seq to analyze thymocyte development and identifies TCR signaling waves and the TCR/calcineurin/NFAT/GATA3 axis as drivers of CD4/CD8 lineage commitment.

This study shows that low self-reactive thymocytes have shorter TCR signals, delayed positive selection, and retain preselection gene expression signatures, suggesting ion channels modulate TCR sensitivity during development.

The paper identifies a new source of cold-induced brown adipocytes, specifically vascular smooth muscle-derived progenitors expressing TRPV1.

The paper introduces totalVI, a probabilistic framework for joint analysis of RNA and protein data from single cells, demonstrating its utility in integration, dimensionality reduction, clustering, and differential expression testing.

The paper introduces totalVI, a probabilistic framework for analyzing CITE-seq data by jointly modeling RNA and protein measurements, addressing technical noise and enabling batch correction.

This paper develops an ultrasensitive nanosensor for dopamine and norepinephrine using ssDNA-SWNT conjugates and elucidates the photophysical mechanisms behind its fluorescence modulation.