Rob Patro

spearfish improves long-read mapping efficiency by leveraging transcriptome redundancy, achieving faster speeds and lower memory usage than existing tools.

This paper introduces simpleaf, a tool for efficient sub-gene-level quantification of probe-based single-cell data, showing improved speed and memory use compared to existing tools.

scRM is a single-cell foundation model trained on raw scRNA-seq reads, showing that raw data pretraining is feasible and cost-effective compared to count-based models.

Gravlax archives single-cell RNA-seq data in a compact format that preserves molecular evidence, enabling reanalysis under new annotations and discovery of unannotated features.

Bramble improves transcript quantification by projecting spliced genomic alignments into transcriptomic coordinates, enhancing accuracy across simulated datasets.

seqproc is a tool that efficiently compiles sequence-geometry descriptions into execution graphs, outperforming existing tools in speed and memory usage for single-cell RNA-sequencing protocols.

This paper explores the use of LLM-based coding agents in scientific computing, presenting case studies in the life sciences and discussing their potential and challenges.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The paper introduces an optimized sparse and skew hashing data structure for efficient k-mer representation, showing improved query speed and space efficiency compared to existing methods.

This study introduces a kinetic model that integrates scRNA-seq and imaging data to simulate gene transcription dynamics and identifies conserved quantities and improved models for transcription factor mechanisms.

QCatch provides a standardized QC reporting framework for single-cell sequencing data, generating interactive HTML reports and annotated H5AD files for downstream analysis.

kache-hash improves k-mer hash table performance for genomic analysis by leveraging minimizers and cache efficiency, achieving faster builds and queries across multiple datasets.

Kaminari improves approximate k-mer query performance by using k-mer minimizers and integer compression, outperforming Bloom filters in memory and speed with minimal false positive impact.

The paper introduces mim, a lightweight index to accelerate parallel parsing of gzipped FASTQ files with minimal overhead and storage.

The paper introduces mehenDi, a tree-based differential testing method for RNA-Seq that accounts for inferential uncertainty, improving detection of differentially expressed transcripts and inner nodes.

Oarfish improves long read transcriptome quantification by incorporating a novel coverage score into its probabilistic model, leading to more accurate quantification estimates.

Alevin-fry-atac provides a fast, memory-efficient method for single-cell ATAC-seq data processing with high accuracy compared to existing tools.

Cuttlefish 3 is a parallel external-memory algorithm for constructing colored compacted de Bruijn graphs, achieving significant speedup over existing tools.

The paper introduces lossless compression methods for colored de Bruijn graphs, reducing memory usage while maintaining query efficiency.

The paper introduces a replicable benchmark for long-read transcript quantification tools and evaluates their performance on synthetic datasets.

DifferentialRegulation identifies differentially regulated genes by analyzing unspliced mRNA abundance across experimental conditions using a Bayesian hierarchical model.

Forseti predicts the splicing status of scRNA-seq reads by combining binding affinity and fragment length models, improving accuracy in downstream analyses.

This paper introduces new randstrobe construction methods, identifies biases in previous approaches, and improves accuracy in short-read mapping.

scCensus evaluates off-target scRNA-seq reads and shows they contain valuable information about chromatin structure, antisense transcription, and cell clustering.

Fulgor is a compact k-mer index for efficient sequence matching and color queries, outperforming existing methods in space and speed.

The paper introduces a new data structure, Mac-dBG, that improves space efficiency for colored de Bruijn graphs by compressing color representations, while maintaining query efficiency.

simpleaf simplifies single-cell data processing using alevin-fry tools, adding new functionality while maintaining flexibility and performance.

TreeTerminus groups transcripts into a tree structure to balance uncertainty and resolution for RNA-seq analysis, improving performance over transcripts and other methods.

The paper evaluates a new method for classifying splicing status in single-cell and single-nucleus RNA-seq data, finds it conservative but ambiguous, and introduces new tools to improve classification.

The paper introduces a method to reduce the space required for reference indexing by using spectrum preserving tilings and sampling schemes, achieving significant space savings with minimal query slowdown.