Delaney K. Sullivan

The impact of package selection and versioning on single-cell RNA-seq analysis

This study compares Seurat and Scanpy, finding significant differences in their scRNA-seq analysis outputs, comparable to low sequencing depth or cell coverage.

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation

The paper characterizes transcriptomes across 8 tissues in 8 mouse strains to identify expression variation linked to genetic differences and phenotypic traits.

Long-read sequencing transcriptome quantification with lr-kallisto

The paper develops lr-kallisto, a tool for accurate long-read transcriptome quantification using ONT data, showing improved results with exome capture.

Reference-based variant detection with varseek

varseek improves variant detection in challenging cases like insertions, deletions, and low-coverage data using a reference-based approach.

Pseudoassembly of k-mers

The paper introduces a pseudoassembly method using colored de Bruijn graphs to identify cell-type specific de novo variants from single-cell RNA-seq in a mouse melanoma model.

Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression

The paper detects viral sequences in single-cell data to identify novel viruses affecting host gene expression in rhesus macaques.

KDM5B expression is suppressed by MYC in a negative feedback loop to promote cell survival.

The paper identifies a negative feedback loop where MYC suppresses KDM5B, leading to increased cell survival and tumor progression.

kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq

The paper describes using kallisto, bustools, and kb-python to quantify RNA-seq data from bulk, single-cell, and single-nucleus samples.

Flexible parsing, interpretation, and editing of technical sequences with splitcode

splitcode is a tool for parsing, interpreting, and editing sequencing reads with synthetic constructs, supporting various sequencing assays.

3D genome organization around nuclear speckles drives mRNA splicing efficiency

The paper shows that gene proximity to nuclear speckles increases spliceosome binding and co-transcriptional splicing efficiency, highlighting the role of 3D genome organization in mRNA splicing.

Universal preprocessing of single-cell genomics data

The paper describes a universal preprocessing workflow for single-cell genomics data using the cellatlas package.

Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers

This paper introduces a method to improve RNA-seq quantification by expanding the transcriptome reference to include both nascent and mature mRNA and using distinguishing flanking k-mers to enhance mapping accuracy.